https://dmu.ghpc.au.dk/lmt/wiki/api.php?action=feedcontributions&feedformat=atom&user=BoernerLinear Mixed Models Toolbox - User contributions [en]2026-05-15T02:46:03ZUser contributionsMediaWiki 1.37.1https://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1447Examples2022-04-20T02:22:32Z<p>Boerner: /* Defining a ssSNPBLUP variance */</p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}} and {{cc|<model>}} are automatic-compulsory. Since {{cc|solve}} is the default job and we are using the default solver in default parameterization no further information about the job or solver is required.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
== Example code chunks ==<br />
<br />
The following code chunks are only subset of a full parameter file. It is assumed that all other parts of the instruction file are functional and all necessary input data available.<br />
<br />
=== Providing several pedigrees ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a pedigree containing genetic groups ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
phantomparents: 2<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a probabilistic pedigree ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
switch: probabilistic<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing several genotype files ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Constructing several GRMs ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Running a model with two ssGBLUP factors ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
...<br />
</a><br />
<pedigrees><br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
pedigree: a<br />
</a><br />
<b><br />
...<br />
pedigree: a<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
<vars><br />
...<br />
vars: g1,g2<br />
<g1><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: x<br />
</H><br />
</gamma><br />
</g1><br />
<g2><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: y<br />
</H><br />
</gamma><br />
</g2><br />
</vars><br />
...<br />
<models><br />
<eqn><br />
y1=mu*b1+id*u11(v(g1(1))+id*u21(v(g2(1))<br />
y2=mu*b2+id*u12(v(g1(2))+id*u22(v(g2(2))<br />
</eqn><br />
</models><br />
</root><br />
</syntaxhighlight><br />
<br />
=== Defining a ssSNPBLUP variance ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
...<br />
</a><br />
<pedigrees><br />
<genotypes><br />
genotypes: a<br />
<a><br />
...<br />
pedigree: a<br />
</a><br />
<vars><br />
...<br />
vars: g<br />
<g><br />
type: snpblup1<br />
genotype: a<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
file: covG.csv<br />
</sigma><br />
<marker_sb1><br />
<sigma><br />
file: covG.csv<br />
</sigma><br />
</marker_sb1><br />
</g><br />
</vars><br />
...<br />
<models><br />
<eqn><br />
y1=mu*b1+individual*u1(v(g(1))+dam*m1(v(g(2))<br />
y2=mu*b2+individual*u2(v(g(3))+dam*m2(v(g(4))<br />
</eqn><br />
</models><br />
</root><br />
</syntaxhighlight><br />
<br />
=== Defining a random-regression test-day model ===<br />
<br />
=== Override the default job parameters ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: default<br />
<default><br />
conv: -9.21 <! log(10e-5)><br />
</default><br />
</jobs><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Use job "solve" instead of "default" ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: x<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: x<br />
<x><br />
</x><br />
</solvers><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Use a direct solver in stead of the default solver ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: x<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: x<br />
<x><br />
<direct><br />
</direct><br />
</x><br />
</solvers><br />
...<br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1446Examples2022-04-20T02:21:52Z<p>Boerner: /* Example code chunks */</p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}} and {{cc|<model>}} are automatic-compulsory. Since {{cc|solve}} is the default job and we are using the default solver in default parameterization no further information about the job or solver is required.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
== Example code chunks ==<br />
<br />
The following code chunks are only subset of a full parameter file. It is assumed that all other parts of the instruction file are functional and all necessary input data available.<br />
<br />
=== Providing several pedigrees ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a pedigree containing genetic groups ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
phantomparents: 2<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a probabilistic pedigree ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
switch: probabilistic<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing several genotype files ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Constructing several GRMs ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Running a model with two ssGBLUP factors ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
...<br />
</a><br />
<pedigrees><br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
pedigree: a<br />
</a><br />
<b><br />
...<br />
pedigree: a<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
<vars><br />
...<br />
vars: g1,g2<br />
<g1><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: x<br />
</H><br />
</gamma><br />
</g1><br />
<g2><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: y<br />
</H><br />
</gamma><br />
</g2><br />
</vars><br />
...<br />
<models><br />
<eqn><br />
y1=mu*b1+id*u11(v(g1(1))+id*u21(v(g2(1))<br />
y2=mu*b2+id*u12(v(g1(2))+id*u22(v(g2(2))<br />
</eqn><br />
</models><br />
</root><br />
</syntaxhighlight><br />
<br />
=== Defining a ssSNPBLUP variance ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
...<br />
</a><br />
<pedigrees><br />
<genotypes><br />
genotypes: a<br />
<a><br />
...<br />
pedigree: a<br />
</a><br />
<vars><br />
...<br />
vars: g<br />
<g><br />
type: snpblup1<br />
genotype: ga<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
file: covG.csv<br />
</sigma><br />
<marker_sb1><br />
<sigma><br />
file: covG.csv<br />
</sigma><br />
</marker_sb1><br />
</g><br />
</vars><br />
...<br />
<models><br />
<eqn><br />
y1=mu*b1+individual*u1(v(g(1))+dam*m1(v(g(2))<br />
y2=mu*b2+individual*u2(v(g(3))+dam*m2(v(g(4))<br />
</eqn><br />
</models><br />
</root><br />
</syntaxhighlight><br />
<br />
=== Defining a random-regression test-day model ===<br />
<br />
=== Override the default job parameters ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: default<br />
<default><br />
conv: -9.21 <! log(10e-5)><br />
</default><br />
</jobs><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Use job "solve" instead of "default" ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: x<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: x<br />
<x><br />
</x><br />
</solvers><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Use a direct solver in stead of the default solver ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: x<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: x<br />
<x><br />
<direct><br />
</direct><br />
</x><br />
</solvers><br />
...<br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1445Examples2022-04-20T02:11:55Z<p>Boerner: /* Example code chunks */</p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}} and {{cc|<model>}} are automatic-compulsory. Since {{cc|solve}} is the default job and we are using the default solver in default parameterization no further information about the job or solver is required.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
== Example code chunks ==<br />
<br />
The following code chunks are only subset of a full parameter file. It is assumed that all other parts of the instruction file are functional and all necessary input data available.<br />
<br />
=== Providing several pedigrees ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a pedigree containing genetic groups ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
phantomparents: 2<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a probabilistic pedigree ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
switch: probabilistic<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing several genotype files ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Constructing several GRMs ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Running a model with two ssGBLUP factors ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
...<br />
</a><br />
<pedigrees><br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
pedigree: a<br />
</a><br />
<b><br />
...<br />
pedigree: a<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
<vars><br />
...<br />
vars: g1,g2<br />
<g1><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: x<br />
</H><br />
</gamma><br />
</g1><br />
<g2><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: y<br />
</H><br />
</gamma><br />
</g2><br />
</vars><br />
...<br />
<models><br />
<eqn><br />
y1=mu*b1+id*u11(v(g1(1))+id*u21(v(g2(1))<br />
y2=mu*b2+id*u12(v(g1(2))+id*u22(v(g2(2))<br />
</eqn><br />
</models><br />
</root><br />
</syntaxhighlight><br />
<br />
=== Override the default job parameters ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: default<br />
<default><br />
conv: -9.21 <! log(10e-5)><br />
</default><br />
</jobs><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Use job "solve" instead of "default" ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: x<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: x<br />
<x><br />
</x><br />
</solvers><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Use a direct solver in stead of the default solver ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: x<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: x<br />
<x><br />
<direct><br />
</direct><br />
</x><br />
</solvers><br />
...<br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1444Examples2022-04-20T02:04:40Z<p>Boerner: /* Running a model with two ssGBLUP factors */</p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}} and {{cc|<model>}} are automatic-compulsory. Since {{cc|solve}} is the default job and we are using the default solver in default parameterization no further information about the job or solver is required.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
== Example code chunks ==<br />
<br />
The following code chunks are only subset of a full parameter file. It is assumed that all other parts of the instruction file are functional and all necessary input data available.<br />
<br />
=== Providing several pedigrees ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a pedigree containing genetic groups ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
phantomparents: 2<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a probabilistic pedigree ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
switch: probabilistic<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing several genotype files ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Constructing several GRMs ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Running a model with two ssGBLUP factors ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
...<br />
</a><br />
<pedigrees><br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
pedigree: a<br />
</a><br />
<b><br />
...<br />
pedigree: a<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
<vars><br />
...<br />
vars: g1,g2<br />
<g1><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: x<br />
</H><br />
</gamma><br />
</g1><br />
<g2><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: y<br />
</H><br />
</gamma><br />
</g2><br />
</vars><br />
...<br />
<models><br />
<eqn><br />
y1=mu*b1+id*u11(v(g1(1))+id*u21(v(g2(1))<br />
y2=mu*b2+id*u12(v(g1(2))+id*u22(v(g2(2))<br />
</eqn><br />
</models><br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1443Examples2022-04-20T02:01:08Z<p>Boerner: </p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}} and {{cc|<model>}} are automatic-compulsory. Since {{cc|solve}} is the default job and we are using the default solver in default parameterization no further information about the job or solver is required.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
== Example code chunks ==<br />
<br />
The following code chunks are only subset of a full parameter file. It is assumed that all other parts of the instruction file are functional and all necessary input data available.<br />
<br />
=== Providing several pedigrees ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a pedigree containing genetic groups ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
phantomparents: 2<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing a probabilistic pedigree ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
switch: probabilistic<br />
...<br />
</a><br />
</pedigrees><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Providing several genotype files ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Constructing several GRMs ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
...<br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
</a><br />
<b><br />
...<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
...<br />
</root><br />
</syntaxhighlight><br />
<br />
=== Running a model with two ssGBLUP factors ===<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<pedigrees><br />
pedigrees: a<br />
<a><br />
...<br />
</a><br />
<pedigrees><br />
<genotypes><br />
genotypes: a,b<br />
<a><br />
...<br />
pedigree: a<br />
</a><br />
<b><br />
...<br />
pedigree: a<br />
</b><br />
</genotypes><br />
<grms><br />
grms: x,y<br />
<x><br />
genotype: a<br />
...<br />
</x><br />
<y><br />
genotype: b<br />
...<br />
</y><br />
</grms><br />
<vars><br />
...<br />
vars: g1,g2<br />
<g1><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: x<br />
</H><br />
</gamma><br />
</g1><br />
<g2><br />
...<br />
<gamma><br />
<H><br />
...<br />
grm: y<br />
</H><br />
</gamma><br />
</g2><br />
</vars><br />
...<br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1442Examples2022-04-20T01:41:12Z<p>Boerner: /* Solving linear mixed model equations */</p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}} and {{cc|<model>}} are automatic-compulsory. Since {{cc|solve}} is the default job and we are using the default solver in default parameterization no further information about the job or solver is required.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1441Examples2022-04-20T01:40:04Z<p>Boerner: /* Estimating a mean in a uni-variate model */</p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}} and {{cc|<model>}} are automatic-compulsory. Since {{cc|solve}} is the default job and we are using the default solver in default parameterization no further information about the job or solver is required.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: my_solver<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: my_solver<br />
<my_solver><br />
</my_solver><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: my_solver<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: my_solver<br />
<my_solver><br />
</my_solver><br />
</solvers><br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1440Examples2022-04-20T01:38:49Z<p>Boerner: /* Estimating a mean in a uni-variate model */</p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}} and {{cc|<model>}} are automatic-compulsory. Since {{cc|solve}} is the default job and we are using the default solver in default parameterization no further information about the job or solver is required.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by. However, for the sake of contrast, all words starting with {{cc|my_}} are user defined. For example the tag {{cc|solvers}} contains key string {{cc|solvers: my_solver}} which nominates a [[Parameterfile1#Parsing logic|nominated-compulsory]] tag {{cc|<my_solver>}} to be invoked by {{lmt}}. Since tag {{cc|<my_solver>}} contains no further tags or key strings the used solver will be the default solver running on default parameters. Subsequently the name "my_solver" is used in job solve to provide the job with a solver to fulfil the task.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: my_solver<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: my_solver<br />
<my_solver><br />
</my_solver><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: my_solver<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: my_solver<br />
<my_solver><br />
</my_solver><br />
</solvers><br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1439Parameter file elements2022-04-20T01:30:15Z<p>Boerner: /* default> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[#<pcgiod>|<pcgiod>]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1438Parameter file elements2022-04-20T01:29:23Z<p>Boerner: /* */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[#<pcgiod>|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1437Parameter file elements2022-04-20T01:28:44Z<p>Boerner: /* default> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[#<pcgiod>|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
==='''<pcgiod>'''===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1436Parameter file elements2022-04-20T01:28:05Z<p>Boerner: /* pcgiod */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[#pcgiod|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
==='''<pcgiod>'''===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1435Parameter file elements2022-04-20T01:27:20Z<p>Boerner: /* default> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[#pcgiod|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
==='''pcgiod'''===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1434Parameter file elements2022-04-20T01:26:45Z<p>Boerner: /* default> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[pcgiod|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
==='''pcgiod'''===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1433Parameter file elements2022-04-20T01:26:35Z<p>Boerner: /* pcgiod> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[<pcgiod>|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
==='''pcgiod'''===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1432Parameter file elements2022-04-20T01:24:35Z<p>Boerner: /* default> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[<pcgiod>|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1431Parameter file elements2022-04-20T01:20:48Z<p>Boerner: /* default> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[#pcgiod|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1430Parameter file elements2022-04-20T01:20:07Z<p>Boerner: /* default> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''default'''<br />
}}<br />
<br />
content: see [[pcgiod|model strings]] for a list of all possible key strings<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1429Parameter file elements2022-04-20T01:16:32Z<p>Boerner: /* jobs> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<default>'''<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''default'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<default><br />
conv: -18.42<br />
</default><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1428Parameter file elements2022-04-20T01:10:54Z<p>Boerner: /* jobs> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele2|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization)<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Template:Tableele2&diff=1427Template:Tableele22022-04-20T01:09:39Z<p>Boerner: Created page with "{| class="wikitable" |scope="col" style="min-width: 300px;"|example |host element |element type |purpose |default |- {{{1}}} |}"</p>
<hr />
<div>{| class="wikitable"<br />
|scope="col" style="min-width: 300px;"|example<br />
|host element<br />
|element type<br />
|purpose<br />
|default<br />
|-<br />
{{{1}}}<br />
|}</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1426Parameter file elements2022-04-20T01:04:38Z<p>Boerner: /* poly> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0 <br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1425Parameter file elements2022-04-20T01:02:19Z<p>Boerner: /* jobs> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0<br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1424Parameter file elements2022-04-20T00:58:00Z<p>Boerner: /* poly> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0<br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Parameter_file_elements&diff=1423Parameter file elements2022-04-20T00:57:17Z<p>Boerner: /* eqn> */</p>
<hr />
<div>Below is a list of all possible parameter file xml elements. For each element an example is provided as well as information about the element's host element, the element's type and the element's content. '''Note that all words(element names, key string words, key string variables) in bold are hard-coded, all in italic are user-defined (this does not apply to the example box)'''. The spelling of hard-coded words must be abide by, the spelling of user-defined words is user-defined.<br />
<br />
=<'''model'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
..<br />
</eqn><br />
<poly attribute="strings"><br />
..<br />
</poly><br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations and the polynomials.<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<eqn attributes="strings">'''<br />
*optional element '''<poly attributes="strings">'''<br />
==<'''eqn'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<eqn attribute="strings"><br />
y1=x*b1+z*u1(v(g(1))<br />
y2=x*b2+z*u2(v(g(2))<br />
y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))<br />
</eqn><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the equations.<br />
}}<br />
<br />
content:<br />
<br />
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
==<'''poly'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<model><br />
<poly attribute="strings"><br />
x^0<br />
x^2<br />
3*x^2+sqrt(sin(x))<br />
</poly><br />
..<br />
</model><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''model'''<br />
{{!}}optional<br />
{{!}}hosts user defined polynomials and references to hard-coded polynomials. Note that there can only be one polynomial per line. Model strings will reference polynomials by their line number.<br />
}}<br />
<br />
content<br />
<br />
*[[Linear_mixed_model_terminology#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag.<br />
<br />
=<'''pedigrees'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: a,b<br />
...<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific pedigree}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigrees'''<br />
{{!}}'''pedigrees''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''pedigree names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements}}<br />
*nominated-compulsory elements<br />
==<''pedigree name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<pedigrees><br />
pedigrees: myped<br />
..<br />
<myped><br />
file: myped.csv<br />
switch: selfing<br />
phantomparents: 2<br />
qfile: myq.coocsv<br />
</myped><br />
..<br />
</pedigrees><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''pedigrees'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific pedigree identified by ''pedigree name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''myped.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}list content determines the name of the file containing the pedigree<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''selfing'''<br />
{{!}}optional<br />
{{!}}csv-word-list<br />
{{!}}'''selfing,probabilistic'''<br />
{{!}}none<br />
{{!}}list content determines pedigree properties.<br />
*'''selfing''': both parents can have the same id<br />
*'''probabilistic''': each individual can have more than 1 pair of parents<br />
{{!}}-<br />
{{!}}'''phantomparents'''<br />
{{!}}'''phantomparents''': 2<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents<br />
{{!}}-<br />
{{!}}'''qfile'''<br />
{{!}}'''qfile''': myq.coocsv<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}provides name of file to which the genetic regression matrix should be written. Supported file name suffixes are ".bin" for binary block file, ".blkcsv" for csv blockfile and ".coocsv" for csv coordinate format.<br />
}}<br />
<br />
=<'''genotypes'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: a,b<br />
...<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about different sets of genotypes<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''genotypes'''<br />
{{!}}'''genotypes''': ''a,b''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''genotype names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''genotype name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<genotypes><br />
genotypes: mygn<br />
..<br />
<mygn><br />
file: genotypes.txt<br />
pedigree: myped<br />
cross: crossref.csv<br />
</mygn><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''genotypes'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''genotype.txt''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the genotypes<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file<br />
{{!}}-<br />
{{!}}'''pqfile'''<br />
{{!}}'''pqfile''': ''mypq.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the allele frequencies. Note that the file content is used as a substitute for the column means of the marker matrix. It must therefore contain 2p.<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''ignorefixed'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''ignorefixed,ignoremissing'''<br />
{{!}}none<br />
{{!}}<br />
*ignorefixed: fixed markers are ignored '''but may lead to program crash or spurious results latter on'''<br />
*ignoremissing: marker coded as missing(3) are set to 0.<br />
}}<br />
<br />
=<'''grms'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: a,b<br />
...<br />
</grms><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}automatic-optional<br />
{{!}}hosts one to several elements each containing information about a specific grm<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''grms'''<br />
{{!}}'''grms''': ''x,y''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''grm names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
==<''grm name''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<grms><br />
grms: mygrm<br />
..<br />
<mygrm><br />
genotype: mygn<br />
method: YA<br />
</mygrm><br />
..<br />
</genotypes><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''grms'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about a specific grm identified by ''grm name''<br />
}}<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygrm.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the grm. mutually exclusive with keyword '''genotype'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used for building the grm. mutually exclusive with keyword '''file'''.<br />
{{!}}-<br />
{{!}}'''cross'''<br />
{{!}}'''cross''': ''mycross.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the pedigree ids related to the genotypes. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file. if this information has already been supplied to the genotypes it cannot be supplied here.<br />
{{!}}-<br />
{{!}}'''method'''<br />
{{!}}'''method''':'''YA'''<br />
{{!}}optional<br />
{{!}}alternative words<br />
{{!}}'''VR<nowiki>|</nowiki>YA'''<br />
{{!}}'''VR'''<br />
{{!}}content determines the method to be used for building a grm from genotypes<br />
*'''VR''': VanRaden Method 1 is used<br />
*'''YA''': VanRaden Method 2(method Yang) is used<br />
{{!}}-<br />
{{!}}'''outfile'''<br />
{{!}}'''outfile''': ''mygrm.bin''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file where the grm should be written to. will only take effect if the grm was build from genotypes. if the genotypes had a pedigree assigned a cross-reference file will be written out as well which contains the original pedigree ids of the genotyped individuals in the order of the rows/columns of the grm. the file name of the cross-reference file is that of the grm with the prefix '''cross_'''.<br />
}}<br />
<br />
=<'''vars'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
vars: g,p<br />
...<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific variance.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''vars'''<br />
{{!}}'''vars''': ''g,p''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''variance names''<br />
{{!}}none<br />
{{!}}list content determines names of nominated-compulsory elements<br />
}}<br />
*nominated-compulsory elements<br />
*compulsory element '''<res>'''<br />
=='''Kronecker products'''==<br />
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default.<br />
==='''<res>'''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
<res><br />
<sigma><br />
..<br />
</sigma><br />
</res><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}compulsory<br />
{{!}}hosts information about the residual variance structure.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element [[#<sigma>|'''<sigma>''']]<br />
*optional element [[#<gamma>|'''<gamma>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
}}<br />
<br />
===='''<sigma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''file'''<br />
{{!}}'''file''': ''mymatrix.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''block'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''block'''<br />
{{!}}none<br />
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]]<br />
{{!}}-<br />
{{!}}'''scale'''<br />
{{!}}'''scale''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>0.0<br />
{{!}}none<br />
{{!}}multiplies $$\Sigma$$ once by the provided value after reading.<br />
{{!}}-<br />
{{!}}'''priordf'''<br />
{{!}}'''priordf''': ''10''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number>=0.0<br />
{{!}}0.0<br />
{{!}}prior degree of freedom when doing Gibbs sampling<br />
}}<br />
<br />
*optional element '''<matrix attributes="array">'''<br />
=====<'''matrix attributes="array"'''>=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<sigma><br />
<matrix attributes="array"><br />
5.0,0.5<br />
0.5,1.8<br />
</matrix><br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''sigma'''<br />
{{!}}optional<br />
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''.<br />
}}<br />
<br />
===='''<gamma>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
..<br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}optional<br />
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.<br />
}}<br />
<br />
content:<br />
<br />
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''<br />
<br />
====='''<A>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<A><br />
pedigree: myped<br />
</A><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree previously invoked to be used to construct A.<br />
{{!}}-<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''gg'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''gg'''<br />
{{!}}none<br />
{{!}}<br />
*gg: the pedigree contains genetic groups which will be fitted as random <br />
}}<br />
<br />
====='''<H>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<H><br />
type: tblup<br />
pedigree: myped<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
</H><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed as combined single step relationship matrix H using pedigree ''pedigree name'' and genomic information. the genomic information can be supplied<br />
*via a grm element for single step H-BLUP models<br />
*via a genotype element for single step T-BLUP models<br />
Note that for '''type:tblup''' it is not necessary to have an automatic-optional [[#<grms>|<grms>]] element in the parameter file. Doing so will cause the construction and RAM-storage of $$G$$ although it is not need for building H, thus maybe leading to substantial increase in processing time and RAM demand.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''pedigree'''<br />
{{!}}'''pedigree''': ''myped''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the name of a pedigree element to be used to construct H.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''tblup'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''tblup<nowiki>|</nowiki>gblup'''<br />
{{!}}'''gblup'''<br />
{{!}}content determines the way the inverse of H is constructed.<br />
{{!}}-<br />
{{!}}'''grm'''<br />
{{!}}'''grm''': ''mygrm''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''pedigree name''<br />
{{!}}none<br />
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
{{!}}-<br />
{{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. The policy is<br />
*if '''aweight'''>0.0, nothing will be added to the diagonals<br />
*if '''aweight''' is not supplied or is zero:<br />
** if '''grmdadd''' is not supplied 0.001 will be added to the diagonals<br />
** otherwise '''grmdadd''' will be used<br />
}}<br />
<br />
====='''<G>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<G><br />
grm: mygrm<br />
</G><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''grmdadd'''<br />
{{!}}'''grmdadd''': ''0.05''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}real number >=0.0<br />
{{!}}none<br />
{{!}} value added to the diagonal of $$G$$ to ensure invertibility.<br />
}}<br />
<br />
====='''<E>'''=====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
<gamma><br />
<E><br />
file: mygamma.csv<br />
</E><br />
</gamma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''gamma'''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file.<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''file'''<br />
{{!}}'''file''': ''mygamma.csv''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}content determines the file which contains $$\Gamma^{-1}$$.<br />
{{!}}-<br />
{{!}}'''type'''<br />
{{!}}'''type''': '''dense'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''dense<nowiki>|</nowiki>sparse_csr_ut'''<br />
{{!}}'''sparse_csr_ut'''<br />
{{!}}content determines the file storage of $$\Gamma^{-1}$$<br />
*dense: full squared symmetric matrix<br />
*sparse_csr_ut: squared symmetric sparse upper triangular matrix in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format<br />
}}<br />
<br />
=='''snpblup1'''==<br />
<br />
===''<variance name>''===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
genotype: mygn<br />
aweight: 0.05<br />
switch: adjustg2a<br />
<sigma><br />
..<br />
</sigma><br />
<gamma><br />
..<br />
</gamma><br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''vars'''<br />
{{!}}nominated-compulsory<br />
{{!}}hosts information about variance structure identified by ''variance name''.<br />
}}<br />
<br />
content:<br />
*compulsory element '''<sigma>'''<br />
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']]<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''type'''<br />
{{!}}'''type''': ''kronecker''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''kronecker,snpblup_1''<br />
{{!}}kronecker<br />
{{!}}determines whether the variance structure deviates from a Kronecker product.<br />
{{!}}-<br />
{{!}}'''genotype'''<br />
{{!}}'''genotype''': ''mygn''<br />
{{!}}conditional-compulsory<br />
{{!}}word<br />
{{!}}''genotype name''<br />
{{!}}none<br />
{{!}}content determines the genotype element to be used to construct H. compulsory for '''type: tblup'''.<br />
{{!}}-<br />
{{!}}'''aweight'''<br />
{{!}}'''aweight: 0.05'''<br />
{{!}}optional<br />
{{!}}single numeric value<br />
{{!}}0.0<=aweight<=1.0<br />
{{!}}0.0<br />
{{!}}blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''adjustg2a'''<br />
{{!}}optional<br />
{{!}}csv word-list<br />
{{!}}'''adjustg2a,gg,diag'''<br />
{{!}}none<br />
{{!}}<br />
*adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method<br />
*gg: the pedigree contains genetic groups which will be fitted as random<br />
*diag: calculate H diagonal elements and write to file (only supported for gblup).<br />
}}<br />
<br />
===='''<sigma>'''====<br />
<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''variance name''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure.<br />
}}<br />
<br />
content:<br />
<br />
see [[#<sigma>|'''<sigma''']]<br />
<br />
<br />
===='''<marker_sb1>'''====<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].<br />
}}<br />
<br />
content:<br />
<br />
*compulsory element '''<sigma>'''<br />
*optional element '''<gamma>'''<br />
<br />
====='''<sigma>'''=====<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<vars><br />
..<br />
vars: myvar<br />
<myvar><br />
type: snpblup1<br />
..<br />
<marker_sb1><br />
<sigma><br />
..<br />
</sigma><br />
..<br />
</marker_sb1><br />
..<br />
</myvar><br />
..<br />
</vars><br />
</root><br />
</syntaxhighlight><br />
{{!}}''marker''<br />
{{!}}compulsory<br />
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]] for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight).<br />
}}<br />
<br />
see [[#<sigma>|'''<sigma>''']]<br />
<br />
=<'''jobs'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: solve,yh<br />
...<br />
</jobs><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}compulsory<br />
{{!}}hosts one to several elements each containing information about a specific job<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''jobs'''<br />
{{!}}'''jobs''': '''solve,yhat'''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}'''solve,sample,pevsample,mcemreml,yhat'''<br />
{{!}}none<br />
{{!}}job sequence is determined by the list sequence. list content determines nominated-compulsory elements<br />
}}<br />
<br />
*nominated-compulsory elements<br />
**'''<solve>'''<br />
**'''<sample>'''<br />
**'''<pevsample>'''<br />
**'''<pevsolve>'''<br />
**'''<mcemreml>'''<br />
**'''<yhat>'''<br />
<br />
==<'''solve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
..<br />
<solve><br />
solver: mysolver<br />
</solve><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''solve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
}}<br />
<br />
==<'''sample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: sample,..<br />
<sample><br />
sampler: mysampler<br />
</sample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''sample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''pevsample'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsample,..<br />
<pevsample><br />
sampler: mysampler<br />
</pevsample><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsample'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev<br />
}}<br />
<br />
==<'''pevsolve'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: pevsolve,..<br />
<pevsolve><br />
solver: mysolver<br />
</pevsolver><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''pevsolve'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
1={{!}}'''solver'''<br />
{{!}}'''solver''': ''mysolver''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''solver name''<br />
{{!}}none<br />
{{!}}''solver name'' must be the name of a previously defined solver<br />
{{!}}-<br />
{{!}}'''factor'''<br />
{{!}}'''factor''': ''gen''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''factor name''<br />
{{!}}none<br />
{{!}}''factor name'' must be the name of a random factor<br />
{{!}}-<br />
{{!}}'''levels'''<br />
{{!}}'''levels''': ''5,10,20''<br />
{{!}}optional<br />
{{!}}csv integer list<br />
{{!}}''factor level ids''<br />
{{!}}none<br />
{{!}}original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levelfile'''.<br />
{{!}}-<br />
{{!}}'''levelfile'''<br />
{{!}}'''levelfile''': ''myfile.csv''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}''file name''<br />
{{!}}none<br />
{{!}}file containing original factor level ids(.e.g. pedigree ids etc). If not supplied the prediction error co-variance blocks of all factor levels associated to the nominated factor will be calculated. Mutually exclusive with '''levels'''.<br />
{{!}}-<br />
{{!}}'''nrhs'''<br />
{{!}}'''nrhs''': ''50''<br />
{{!}}optional<br />
{{!}}integer<br />
{{!}}''number of right-hand sides''<br />
{{!}}1000<br />
{{!}}number of right-hand-sides to be solved for simultaneously. Has only effect if the direct solver is used. The default may exceed the available RAM.<br />
}}<br />
<br />
==<'''mcemreml'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: mcemreml,..<br />
<mcemreml><br />
emrounds: 500<br />
sampler: mysampler<br />
</mcemreml><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''mcemreml'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''emrounds'''<br />
{{!}}'''emrounds''': ''500''<br />
{{!}}compulsory<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}none<br />
{{!}}provides the number of mcemreml-rounds to run<br />
{{!}}-<br />
{{!}}'''sampler'''<br />
{{!}}'''sampler''': ''mysampler''<br />
{{!}}compulsory<br />
{{!}}word<br />
{{!}}''sampler name''<br />
{{!}}none<br />
{{!}}''sampler name'' must be the name of a previously defined sampler<br />
}}<br />
<br />
==<'''yhat'''>==<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<jobs><br />
jobs: yhat,..<br />
<yhat><br />
</yhat><br />
..<br />
</jobs><br />
..<br />
</root><br />
</syntaxhighlight><br />
{{!}}'''jobs'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts information about job '''yhat'''<br />
}}<br />
Currently '''yhat''' has no key strings or nested elements defined.<br />
<br />
=<'''samplers'''>=<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,b,..<br />
...<br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific sampler<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samplers'''<br />
{{!}}'''samplers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''sampler names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''sampler name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
..<br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''samplers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of sampler ''sampler name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements<br />
**'''<singlepass>'''<br />
**'''<blocked>'''<br />
**'''<pev>'''<br />
<br />
===<'''singlepass'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<singlepass><br />
samples: 10000<br />
burnin: 1000<br />
</singlepass><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''singlepass'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''blocked'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<blocked><br />
samples: 10000<br />
burnin: 1000<br />
</blocked><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''blocked'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
}}<br />
<br />
===<'''pev'''>===<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<samplers><br />
samplers: a,..<br />
<a><br />
<pev><br />
samples: 10000<br />
burnin: 1000<br />
chains: 10<br />
</pev><br />
</a><br />
</samplers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''sampler name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a sampler of type '''pev'''<br />
}}<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''samples'''<br />
{{!}}'''samples''': ''100000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the total number of samples to draw<br />
{{!}}-<br />
{{!}}'''burnin'''<br />
{{!}}'''burnin''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}0<br />
{{!}}provides the number of samples to be discarded as burnin<br />
{{!}}-<br />
{{!}}'''chains'''<br />
{{!}}'''chains''': ''10''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}1<br />
{{!}}provides the number of parallel chains to run<br />
{{!}}-<br />
{{!}}'''switch'''<br />
{{!}}'''switch''': '''trace'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''trace'''<br />
{{!}}none<br />
{{!}}changes sampler from sampling prediction error variances to sampling traces required for emreml<br />
}}<br />
<br />
=<'''solvers'''>=<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,b,..<br />
...<br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''root'''<br />
{{!}}optional<br />
{{!}}hosts one to several elements each containing information about a specific solver<br />
}}<br />
<br />
content:<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''solvers'''<br />
{{!}}'''solvers''': ''a''<br />
{{!}}compulsory<br />
{{!}}csv word-list<br />
{{!}}''solver names''<br />
{{!}}none<br />
{{!}}list content determines nominated-compulsory elements<br />
}}<br />
*conditional-compulsory elements<br />
<br />
==<''solver name''>==<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
..<br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}'''solvers'''<br />
{{!}}conditional-compulsory<br />
{{!}}hosts one of several mutually exclusive elements defining the type of solver ''solver name''<br />
}}<br />
<br />
content:<br />
*compulsory mutually exclusive elements with default element<br />
**'''<pcgiod>''', default<br />
**'''<direct>'''<br />
<br />
===<'''pcgiod'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<pcgiod><br />
rounds: 1000<br />
conv: -20.0<br />
</pcgiod><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''pcgiod'''<br />
}}<br />
<br />
content:<br />
<br />
*key strings<br />
{{tablekeys2|<br />
{{!}}'''rounds'''<br />
{{!}}'''rounds''': ''1000''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}positive integer<br />
{{!}}10000<br />
{{!}}provides the maximum number of rounds to run<br />
{{!}}-<br />
{{!}}'''conv'''<br />
{{!}}'''conv''': ''-15.0''<br />
{{!}}optional<br />
{{!}}numeric value<br />
{{!}}any real number<br />
{{!}} -18.42<br />
{{!}}provides the convergence threshold<br />
{{!}}-<br />
{{!}}'''convtype'''<br />
{{!}}'''convtype''': '''cd'''<br />
{{!}}optional<br />
{{!}}word<br />
{{!}}'''cr<nowiki>|</nowiki>cd'''<br />
{{!}} '''cr'''<br />
{{!}}provides the convergence parameter type<br />
}}<br />
<br />
===<'''direct'''>===<br />
<br />
{{tableele1|<br />
{{!}}<syntaxhighlight lang="xml" line><br />
<root><br />
..<br />
<solvers><br />
solvers: a,..<br />
<a><br />
<direct><br />
</direct><br />
</a><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
{{!}}''solver name''<br />
{{!}}compulsory<br />
{{!}}defines parameters of a solver of type '''direct'''<br />
}}<br />
<br />
content: no content defined</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Supported_features&diff=1422Supported features2022-03-04T11:17:38Z<p>Boerner: /* Supported features related to genomic data */</p>
<hr />
<div>=== Supported operations ===<br />
<br />
Currently {{lmt}} support the following operations on linear mixed models:<br />
<br />
*Solving for BLUP and BLUE solutions conditional on supplied variances for random and fixed factor, respectively;<br />
*Gibbs sampling of variance components in single pass and blocked mode;<br />
*MC-EM-REML estimation of variance components<br />
*Sampling (block)diagonal elements of the inverse of the mixed model coefficient matrix<br />
*Solving for (block)diagonal elements of the inverse of the mixed model coefficient matrix<br />
<br />
=== Supported factors and variables ===<br />
{{lmt}} supports<br />
*fixed<br />
*random factors<br />
*classification variables<br />
*continuous co-variables, which can be nested. For continuous co-variables {{lmt}} support user-defined polynomials and hard coded [https://en.wikipedia.org/wiki/Legendre_polynomials Legendre polynomials] up to order 6.<br />
*genetic group co-variables<br />
<br />
All classification and co-variables can be associated to a fixed or random factor.<br />
<br />
=== Supported variance structures ===<br />
For random factor {{lmt}} supports variance structures of<br />
*structure [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Sigma$$ is an dense symmetric positive definite matrix, and<br />
*$$\Theta_L(\Gamma\otimes I_{\Sigma})\Theta_L^{'}$$, where $$\Theta$$ is symmetric positive definite [https://en.wikipedia.org/wiki/Block_matrix#Block_diagonal_matrices block-diagonal matrix] of $$n$$ symmetric positive definite martices $$\Sigma_i, i=1,..,n$$, $$\Theta_L$$ is the lower [https://en.wikipedia.org/wiki/Cholesky_decomposition Cholesky factor] of $$\Theta$$ and $$I_{\Sigma}$$ is an identity matrix of dimension $$\Sigma_i$$.<br />
<br />
When solving linear mixed models $$\Sigma$$ and $$\Gamma$$ are user determined constants, whereas when estimating variances $$\Gamma$$ is a user determined constant and $$\Sigma$$ is a function of the data.<br />
<br />
Supported type for $$\Gamma$$ are<br />
*an [https://en.wikipedia.org/wiki/Identity_matrix identity matrix]<br />
*an arbitrary positive definite [https://en.wikipedia.org/wiki/Diagonal_matrix diagonal matrix]<br />
*a pedigree-based numerator relationship matrix $$A$$ which may contain meta-founders<br />
*a pedigree- and genotype-based relationship matrix $$H$$ which may contain meta-founders<br />
*genetic groups absorbed into $$A$$ or $$H$$<br />
*a user-defined(u.d.) symmetric, positive definite matrix of which inverse is supplied<br />
**as a sparse upper-triangular matrix stored in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr format]<br />
**as a dense matrix<br />
*a co-variance matrix of a selected auto-regressive process<br />
<br />
Further {{lmt}} supports special variance structures which are not covered by the above description<br />
*SNP-BLUP variance for the model of Liu and Goddard 2014 with the option to model marker co-variances as above.<br />
<br />
=== Supported linear mixed model solvers ===<br />
{{lmt}} supports<br />
<br />
*a direct solver requiring to explicitly build the linear mixed model equations left-hand-side coefficient matrix($$C$$)<br />
*an iteration-on-data pre-conditioned gradient solver which '''does not''' require $$C$$<br />
<br />
=== Supported features related to genomic data ===<br />
*direct use of genomic marker data<br />
*building of genomic relationship matrices($$G$$) from supplied genomic data<br />
*uploading of a u.d. $$G$$<br />
*adjustment of $$G$$ to $$A_{gg}$$ in ssGBLUP and ssSNPBLUP<br />
*solving ssGBLUP models<br />
*Variance component estimation for ssGBLUP models<br />
*solving ssGTBLUP models<br />
*solving ssSNPBLUP models<br />
*calculation of true H matrix diagonal elements for ssGBLUP models<br />
*all Single-Step models can be run from "bottom-up", that is the user supplies the genotypes and all necessary ingredients(e.g. $$G$$) are built on the fly.<br />
<br />
=== Supported pedigree types===<br />
*ordinary pedigrees<br />
*probabilistic pedigrees with an unlimited number of parent pairs per individual<br />
*genetic group pedigrees<br />
*meta-founder pedigrees<br />
*ignoring of inbreeding<br />
*iterative derivation of inbreeding coefficients<br />
<br />
=== Supported features related to meta-founders and genetic groups ===<br />
*meta-founders can be modeled for all $$\Gamma$$ which contain $$A$$(.e.g. $$A$$, $$H$$ for ssGBLUP, ssGTBLUP and ssSNPBLUP)<br />
*genetic groups can be modeled as an extra factor or can be absorbed into all $$\Gamma$$ which contain $$A$$</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Supported_features&diff=1421Supported features2022-03-04T11:16:35Z<p>Boerner: </p>
<hr />
<div>=== Supported operations ===<br />
<br />
Currently {{lmt}} support the following operations on linear mixed models:<br />
<br />
*Solving for BLUP and BLUE solutions conditional on supplied variances for random and fixed factor, respectively;<br />
*Gibbs sampling of variance components in single pass and blocked mode;<br />
*MC-EM-REML estimation of variance components<br />
*Sampling (block)diagonal elements of the inverse of the mixed model coefficient matrix<br />
*Solving for (block)diagonal elements of the inverse of the mixed model coefficient matrix<br />
<br />
=== Supported factors and variables ===<br />
{{lmt}} supports<br />
*fixed<br />
*random factors<br />
*classification variables<br />
*continuous co-variables, which can be nested. For continuous co-variables {{lmt}} support user-defined polynomials and hard coded [https://en.wikipedia.org/wiki/Legendre_polynomials Legendre polynomials] up to order 6.<br />
*genetic group co-variables<br />
<br />
All classification and co-variables can be associated to a fixed or random factor.<br />
<br />
=== Supported variance structures ===<br />
For random factor {{lmt}} supports variance structures of<br />
*structure [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Sigma$$ is an dense symmetric positive definite matrix, and<br />
*$$\Theta_L(\Gamma\otimes I_{\Sigma})\Theta_L^{'}$$, where $$\Theta$$ is symmetric positive definite [https://en.wikipedia.org/wiki/Block_matrix#Block_diagonal_matrices block-diagonal matrix] of $$n$$ symmetric positive definite martices $$\Sigma_i, i=1,..,n$$, $$\Theta_L$$ is the lower [https://en.wikipedia.org/wiki/Cholesky_decomposition Cholesky factor] of $$\Theta$$ and $$I_{\Sigma}$$ is an identity matrix of dimension $$\Sigma_i$$.<br />
<br />
When solving linear mixed models $$\Sigma$$ and $$\Gamma$$ are user determined constants, whereas when estimating variances $$\Gamma$$ is a user determined constant and $$\Sigma$$ is a function of the data.<br />
<br />
Supported type for $$\Gamma$$ are<br />
*an [https://en.wikipedia.org/wiki/Identity_matrix identity matrix]<br />
*an arbitrary positive definite [https://en.wikipedia.org/wiki/Diagonal_matrix diagonal matrix]<br />
*a pedigree-based numerator relationship matrix $$A$$ which may contain meta-founders<br />
*a pedigree- and genotype-based relationship matrix $$H$$ which may contain meta-founders<br />
*genetic groups absorbed into $$A$$ or $$H$$<br />
*a user-defined(u.d.) symmetric, positive definite matrix of which inverse is supplied<br />
**as a sparse upper-triangular matrix stored in [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr format]<br />
**as a dense matrix<br />
*a co-variance matrix of a selected auto-regressive process<br />
<br />
Further {{lmt}} supports special variance structures which are not covered by the above description<br />
*SNP-BLUP variance for the model of Liu and Goddard 2014 with the option to model marker co-variances as above.<br />
<br />
=== Supported linear mixed model solvers ===<br />
{{lmt}} supports<br />
<br />
*a direct solver requiring to explicitly build the linear mixed model equations left-hand-side coefficient matrix($$C$$)<br />
*an iteration-on-data pre-conditioned gradient solver which '''does not''' require $$C$$<br />
<br />
=== Supported features related to genomic data ===<br />
*direct use of genomic marker data<br />
*building of genomic relationship matrices($$G$$) from supplied genomic data<br />
*uploading of a u.d. $$G$$<br />
*adjustment of $$G$$ to $$A_{gg}$$ in SS-G-BLUP and SS-SNP-BLUP<br />
*solving Single-Step-G-BLUP models<br />
*Variance component estimation for Single-Step-G-BLUP models<br />
*solving Single-Step-T-BLUP models<br />
*solving Single-Step-SNP-BLUP models<br />
*calculation of true H matrix diagonal elements<br />
*all Single-Step models can be run from "bottom-up", that is the user supplies the genotypes and all necessary ingredients(e.g. $$G$$) are built on the fly.<br />
<br />
=== Supported pedigree types===<br />
*ordinary pedigrees<br />
*probabilistic pedigrees with an unlimited number of parent pairs per individual<br />
*genetic group pedigrees<br />
*meta-founder pedigrees<br />
*ignoring of inbreeding<br />
*iterative derivation of inbreeding coefficients<br />
<br />
=== Supported features related to meta-founders and genetic groups ===<br />
*meta-founders can be modeled for all $$\Gamma$$ which contain $$A$$(.e.g. $$A$$, $$H$$ for ssGBLUP, ssGTBLUP and ssSNPBLUP)<br />
*genetic groups can be modeled as an extra factor or can be absorbed into all $$\Gamma$$ which contain $$A$$</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Jump_Start&diff=1418Jump Start2022-03-04T06:44:04Z<p>Boerner: Boerner moved page Jump Start to Examples</p>
<hr />
<div>#REDIRECT [[Examples]]</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Examples&diff=1417Examples2022-03-04T06:44:03Z<p>Boerner: Boerner moved page Jump Start to Examples</p>
<hr />
<div>The examples provided in this section are meant to provide a practical examples about the {{lmt}} facilities and the parameter file syntax. It is assumed that the reader is familiar with [[Parameterfile1|section]]<br />
<br />
== Solving linear mixed model equations ==<br />
<br />
=== Estimating a mean in a uni-variate model ===<br />
<br />
Estimating a mean is equivalent to obtaining the generalized least square solution $$b=(X'R^{-1}X)^{-1}X'R^{-1}y$$ for model $$y=Xb+e$$, where $$y$$ is a vector of $$n$$ observations, $$X$$ is as single column matrix of $$1$$, $$b$$ is a fixed factor (mean), $$e$$ is the residual and $$y\sim N(Xb,R)$$ where $$R$$ is a $$n \times n$$ co-variance matrix.<br />
<br />
From the above it follows that for task of solving for $$b$$ {{lmt}} needs following information:<br />
<br />
the data<br />
the residual variance $$R$$<br />
the model<br />
the solver<br />
<br />
Assume we have a data file "data.csv" with content:<br />
#y,mu<br />
25.0,1<br />
33.1,1<br />
36.0,1<br />
28.3,1<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records.<br />
A valid {{lmt}} xml parameter file would look like:<br />
<syntaxhighlight lang="xml" line highlight="5,27"><br />
<root><br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: my_solver<br />
</solve><br />
</jobs><br />
<models><br />
<eqn attributes="strings"><br />
y=mu*b<br />
</eqn><br />
</models><br />
<data><br />
datafile: data.csv<br />
missingthreshold: -50.0<br />
</data><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
</vars><br />
<solvers><br />
solvers: my_solver<br />
<my_solver><br />
</my_solver><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
<br />
Following the introduced [[Parameterfile1|parameterfile terminology]] tags {{cc|<data>}}, {{cc|<vars>}}, {{cc|<model>}}, {{cc|<jobs>}} are automatic-compulsory. {{cc|<solvers>}} is an automatic-optional tag because not every {{lmt}} job requires a solver.<br />
<br />
The most important aspect is the model definition in tag {{cc|<eqn>}}, nested inside tag {{cc|<model>}} $$y=mu*b$$. The variable names used here are either defined by the data file header, or by the user. That is, $$y$$ and $$mu$$ are defined in the data file header, whereas $$b$$ is a user-defined factor name. Translated this means that the content of the data column named $$y$$ should be regressed on the content of the data column named $$mu$$ with the regression coefficient named $$b$$.<br />
<br />
Since there are no further specifications supplied about $$y$$, $$mu$$ and $$b$$, it is assumed that $$y$$ is a continuous variable, $$mu$$ is a classification variable, and $$b$$ is fixed factor.<br />
The necessary variances are defined by the content of the automatic-compulsory tag {{cc|<vars>}}. {{lmt}} requires one compulsory variance, the residual variance, which must be specified via tag {{cc|<res>}}. Therefore tag {{cc|res}} is automatic-compulsory.<br />
<br />
The default {{lmt}} variance structure is [https://en.wikipedia.org/wiki/Kronecker_product $$\Gamma\otimes\Sigma$$], where $$\Gamma$$ and $$\Sigma$$ are specified inside tags {{cc|<gamma>}} and {{cc|<sigma>}}, respectively.<br />
However, only tag {{cc|<sigma>}} is [[Parameterfile1#Parsing logic|automatic-compulsory]], whereas tag {{cc|<gamma>}} is [[Parameterfile1#Parsing logic|automatic-optional]]. A missing {{cc|<gamma>}} tag implies that [https://en.wikipedia.org/wiki/Identity_matrix $$\Gamma = I$$]. Note that for {{lmt}} $$\Sigma$$ is always a matrix, that is a scalar $$\sigma^2$$ is treated as a matrix $$1 \times 1$$ matrix.<br />
<br />
For the above example, the variance specification inside {{cc|<res>}} implies that $$\Gamma\otimes \Sigma \equiv I\otimes \Sigma$$. Since $$\Sigma$$ is a $$1\times 1$$ matrix with $$\Sigma[1,1]=\sigma_e^2$$, $$R$$ reduces to $$I\sigma_e^2$$.<br />
<br />
Note tag {{cc|<matrix>}} nested in tag {{cc|<sigma>}}. The content of tag {{cc|<matrix>}} does not comply with the formatting rules as pointed o ut [[Parameterfile1#Key strings|above]]. That is {{cc|5.0}} is not a valid key string. To let {{lmt}} know that the content of tag {{cc|<matrix>}} should not be evaluated as a key string, with a subsequent error message, [[Parameterfile1#Escaping tag content formatting rules|the tag must have attributes]]. In this example {{cc|1=matrix attributes="matrix"}} escapes the content of tag {{cc|<matrix>}} from the formatting rules.<br />
<br />
Further, tag {{cc|<matrix>}} is automatic-optional. This might be confusing because, as pointed out above, $$\Sigma$$ forms an indispensable part of $$\Gamma\otimes \Sigma$$. However, tag {{cc|<matrix>}} belongs to a [[Parameterfile1#Group of mutually exclusive information sources|group of mutually exclusive information sources]] of which members are tag {{cc|<matrix>}} and key string {{cc|file: yourfilename}}. That is, $$\Sigma$$ maybe either embedded in the parameter file or supplied via an external file.<br />
<br />
Note that the spelling of most tags used in the above parameter file is determined by {{lmt}} and must be abide by. However, for the sake of contrast, all words starting with {{cc|my_}} are user defined. For example the tag {{cc|solvers}} contains key string {{cc|solvers: my_solver}} which nominates a [[Parameterfile1#Parsing logic|nominated-compulsory]] tag {{cc|<my_solver>}} to be invoked by {{lmt}}. Since tag {{cc|<my_solver>}} contains no further tags or key strings the used solver will be the default solver running on default parameters. Subsequently the name "my_solver" is used in job solve to provide the job with a solver to fulfil the task.<br />
<br />
=== Estimating a fixed mean and a random genetic effect in a uni-variate model ===<br />
<br />
Consider the linear model $$y=Xb+Zu+e$$ where all variables are those declared in [[#Estimating a mean]], $$u$$ is vector of length $$m$$ of random direct genetic effects and $$Z$$ is a design matrix of dimension $$n \times m$$ linking genetic effects to their respective observations. Note that $$u\sim N(0,A\sigma_a^2)$$ where $$A$$ is the pedigree-derived relationship matrix and forms the $$\Gamma$$ part in $$\Gamma\otimes\Sigma$$. A possible data file for such mode may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
where the columns are comma-separated, the first row is commented out with “#” but contains the header, and all other rows contain data records. Further assume a pedigree in a file called "ped.csv" with content:<br />
1,0,0<br />
2,0,0<br />
3,1,0<br />
4,0,2<br />
5,3,4<br />
6,0,4<br />
7,5,4<br />
8,5,7<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y = mu*b + id*u(v(my_var(1)))<br />
</eqn><br />
</model><br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: my_solver<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: my_solver<br />
<my_solver><br />
</my_solver><br />
</solvers><br />
</root><br />
</syntaxhighlight><br />
<br />
Compared with the parameter file in example [[#Estimating a mean]] the one above contains only a few extra elements. One this the automatic-optional {{cc|<pedigrees>}} nested inside tag {{cc|<root>}}. This tag contains a keystring {{cc|pedigrees: myped}}, where the user-defined variable behind {{cc|pedigrees:}} is the name of a nominated-compulsory tag nested inside tag {cc|<pedigrees>}}. This concept allows to supply several pedigrees to lmt (e.g. a normal pedigree and a genetic group pedigree). In our example we have only one pedigree named my_ped, with tag {{cc|<my_ped>}} containing the information about this pedigree. Another additional element is the key string {{cc|vars: my_var}} nested in tag {{cc|<vars>}} where the variable of key string {{cc|vars: my_var}} provides the tag names of nominated-compulsory tags, in this example tag {{cc|<my_var>}}.<br />
<br />
Tag {{cc|<myvar>}} consist of two structural components: the automatic-compulsory tag {{cc|<sigma>}} and the automatic-optional {{cc|<gamma>}}. Since the the variance of $$u=A\sigma_a^2$$, where $$A=\Gamma$$ and $$\sigma_a^2=\Sigma$$, a {{cc|<gamma>}} tag must be supplied to fully specify the variance. '''Note that if the {{cc|<gamma>}} tag is missing or miss-spelled {{lmt}} will assume that the variance of $$u=I\sigma_a^2$$'''. Tag {{cc|<gamma>}} contains a automatic-compulsory tag {{cc|<A>}} which specifies the $$\Gamma=A$$. Since $$A$$ is build from a pedigree, tag {{cc|<A>}} contains a compulsory key string {{cc|pedigree: my_ped}} which nominates pedigree in tag {{cc|<my_ped>}} to be used for building $$A$$.<br />
<br />
Note the difference between the tags {{cc|<sigma>}} nested in tag {{cc|<res>}} and {{cc|<my_var>}}. The former specifies {{cc|<sigma>}} to be provided by tag {{cc|1=<matrix attributes="matrix">}}, whereas the latter specifies {{cc|<sigma>}} to be provided by a file.<br />
<br />
The model section in the above parameter file need to communicate to to {{lmt}} that $$u$$ is a random factor with a variance $$A\sigma_a^2$$. This is done by extending the u.d. factor name {{cc|u}} in {{cc|1=y = mu*b + id*u(v(my_var(1)))}} by a specifier {{cc|(v(my_var(1)))}}. Note that without a specifier {{cc|u}} would be regarded as a fixed factor. The specifier {{cc|u(v)}} communicates that {{cc|u}} has a variance assigned. Further, {{cc|v}} has a specifier assigned via {{cc|v(my_var)}} which communicates that the name of the variance is {{cc|my_var}}. The variance in tag {{cc|<my_var>}} contains a {{cc|<gamma>}} and a {{cc|<sigma>}} component. The integer number inside bracket {{cc|my_var(1)}} communicates that $$\sigma_a^2$$ of {{cc|u}} is located in the first diagonal element of $$\Sigma$$.<br />
<br />
In summary construct {{cc|u(v(my_var(1)))}} communicates that<br />
*{{cc|u}} has a variance assigned<br />
*the variance is named {{cc|my_var}}<br />
*the variance is located in the first diagonal element of the $$\Sigma$$ matrix specified in tag {{cc|<sigma>}} nested in tag {{cc|<my_var>>}}<br />
<br />
=== Estimating fixed means and a random genetic effects in a multi-variate model ===<br />
<br />
Consider the linear model <br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X_1 & 0 \\<br />
0 & X_2 \\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
Z & 0 \\<br />
0 & Z<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cc}<br />
I & 0 \\<br />
0 & I<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where all variables are those declared in [[#Estimating a mean and a random genetic effect in a uni-variate model|above]], and subscripts $$1$$ and $$2$$ index trait $$1$$ and $$2$$, respectively.<br />
<br />
Note that $$[u_1,u_2]\sim N([0,0],A\otimes \Sigma_a)$$ where $$A$$ is the pedigree-derived relationship matrix and <br />
$$<br />
\Sigma_a=<br />
\left(\begin{array}{cc}<br />
\sigma_{a_1}^2 & \sigma_{a_1,a_2}\\<br />
\sigma_{a_2,a_1} & \sigma_{a_2}^2<br />
\end{array}\right)<br />
$$<br />
Further, $$[e_1,e_2]\sim N([0,0],I\otimes \Sigma_e)$$ with<br />
$$<br />
\Sigma_e=<br />
\left(\begin{array}{cc}<br />
\sigma_{e_1}^2 & \sigma_{e_1,e_2}\\<br />
\sigma_{e_2,e_1} & \sigma_{e_2}^2<br />
\end{array}\right)<br />
$$.<br />
<br />
A possible data file for such mode may look like:<br />
#y1,y2,mu,id<br />
25.0,0.8,1,5<br />
33.1,0.5,1,6<br />
36.0,1.5,1,7<br />
28.3,3.6,1,8<br />
and the pedigree files is that provided in example [[#Estimating a mean and a random genetic effect in a uni-variate model]].<br />
<br />
<br />
and a valid {{lmt}} parameter file:<br />
<br />
<syntaxhighlight lang="xml" line highlight="6"><br />
<root><br />
<data><br />
file: data.csv<br />
</data><br />
<pedigrees><br />
pedigrees: my_ped<br />
<my_ped><br />
file: ped.csv<br />
</my_ped><br />
</pedigrees><br />
<vars><br />
<res><br />
<sigma><br />
<matrix attributes="matrix"><br />
5.0,0.8<br />
0.8,1.2<br />
</matrix><br />
</sigma><br />
</res><br />
vars: my_var<br />
<my_var><br />
<sigma><br />
file: sigma.csv<br />
</sigma><br />
<gamma><br />
<A><br />
pedigree: my_ped<br />
</A><br />
</gamma><br />
</my_var><br />
</vars><br />
<model><br />
<eqn attributes="strings"><br />
y1 = mu*b1 + id*u1(v(my_var(1)))<br />
y2 = mu*b2 + id*u2(v(my_var(2)))<br />
</eqn><br />
</model><br />
<jobs><br />
jobs: solve<br />
<solve><br />
solver: my_solver<br />
</solve><br />
</jobs><br />
<solvers><br />
solvers: my_solver<br />
<my_solver><br />
</my_solver><br />
</solvers><br />
</root><br />
</syntaxhighlight></div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=File_formats&diff=1416File formats2022-03-04T06:40:44Z<p>Boerner: </p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
*".coocsv" csv-format for storing sparse matrices in coordinate format.<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
"*.csv" files must contain rectangular arrays, that is every line must contain the same number of comma-separated records.<br />
<br />
lmt does not supports empty records, e.g.<br />
<br />
1,2,,4<br />
<br />
must be filled with some value (e.g zero).<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
== Block format ==<br />
<br />
Files in block format can contain multiple records of very different data. That is, a single file can contain several different matrices, vector, and scalars and a mixture of those. Block files are important for supplying sparse matrices, large arrays(e.g. genomic relationship matrices), block-diagonal matrices (e.g. when residual variances are heterogenous) etc. Further, lmt may write intermediate output to a block file for having connected information in the same file.<br />
<br />
The general structure of a single block is:<br />
<br />
BEGIN MYNAME<br />
DESCRIPTOR<br />
DATA<br />
END MYNAME<br />
<br />
where {{cc|MYNAME}} is a user-defined block name which must be unique, {{cc|DESCRIPTOR}} is a comma-separated sequence of data descriptors, and {{cc|DATA}} are the actual data.<br />
{{cc|DESCRIPTOR}} contains at least 3 values:<br />
<br />
*type<br />
*kind<br />
*size<br />
*dimension<br />
<br />
where {{cc|type}} is either {{cc|int}} for integer, {{cc|real}} for real or {{cc|char}} for character. {{cc|kind}} can be either {{cc|scalar}} or {{cc|array}}. {{cc|size}} is the storage size in bit for a single value, for integer and real it should be 64, for character it should be the storage size of the longest character string in an array of strings. If {{cc|kind}} is set to {{cc|array}}, dimension is a vector of comma-separated values containing the dimensions of the array, where the length of the vector determines the number of dimensions. That is, for a one-dimensional array the vector is of length one, for two-dimensional the length is two and for three-dimensional the length is three. Currently only one, two and three dimensional arrays are supported.<br />
<br />
A block file in csv format containing an integer scalar, an integer vector, a real matrix, and a real scalar maybe:<br />
<br />
BEGIN a <br />
int,scalar,64 <br />
5<br />
END a <br />
BEGIN b <br />
int,array,64,2 <br />
1<br />
2<br />
END b <br />
BEGIN c <br />
real,array,64,2,2 <br />
5,5<br />
5,5<br />
END c <br />
BEGIN d <br />
real,scalar,64 <br />
5<br />
END d<br />
<br />
where the above file can be produced in R<br />
<br />
<syntaxhighlight lang="R" line><br />
x<-list(a=as.integer(5),b=as.integer(c(1,2)),c=matrix(5,2,2),d=5)<br />
writelmtblockfile(x,"myfile.blkcsv","txt")<br />
</syntaxhighlight><br />
<br />
The R function {{cc|writelmtblockfile}} can be obtained from the author.<br />
<br />
In binary format, {{cc|BEGIN MYNAME}}, {{cc|END MYNAME}} and {{cc|DESCRIPTOR}} are stored in 50 byte character strings which '''must not''' be null terminated.<br />
<br />
lmt will assume block format for all files with file name suffix {{cc|.bin}} and {{cc|.blkcsv}}.<br />
<br />
<br />
== .coocsv format ==<br />
<br />
Comma-separated coordinate format is used to write out sparse matrices in acsii. The first line of the respective file contains the number of rows and columns of the sparse matrix. All subsequent rows contain tuples of three values which are<br />
*row number<br />
*column number<br />
*value</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=File_formats&diff=1415File formats2022-03-04T06:33:12Z<p>Boerner: </p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
*".coocsv" csv-format for storing sparse matrices in coordinate format.<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
"*.csv" files must contain rectangular arrays, that is every line must contain the same number of comma-separated records.<br />
<br />
lmt does not supports empty records, e.g.<br />
<br />
1,2,,4<br />
<br />
must be filled with some value (e.g zero).<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
== Block format ==<br />
<br />
Files in block format can contain multiple records of very different data. That is, a single file can contain several different matrices, vector, and scalars and a mixture of those. Block files are important for supplying sparse matrices, large arrays(e.g. genomic relationship matrices), block-diagonal matrices (e.g. when residual variances are heterogenous) etc. Further, lmt may write intermediate output to a block file for having connected information in the same file.<br />
<br />
The general structure of a single block is:<br />
<br />
BEGIN MYNAME<br />
DESCRIPTOR<br />
DATA<br />
END MYNAME<br />
<br />
where {{cc|MYNAME}} is a user-defined block name which must be unique, {{cc|DESCRIPTOR}} is a comma-separated sequence of data descriptors, and {{cc|DATA}} are the actual data.<br />
{{cc|DESCRIPTOR}} contains at least 3 values:<br />
<br />
*type<br />
*kind<br />
*size<br />
*dimension<br />
<br />
where {{cc|type}} is either {{cc|int}} for integer, {{cc|real}} for real or {{cc|char}} for character. {{cc|kind}} can be either {{cc|scalar}} or {{cc|array}}. {{cc|size}} is the storage size in bit for a single value, for integer and real it should be 64, for character it should be the storage size of the longest character string in an array of strings. If {{cc|kind}} is set to {{cc|array}}, dimension is a vector of comma-separated values containing the dimensions of the array, where the length of the vector determines the number of dimensions. That is, for a one-dimensional array the vector is of length one, for two-dimensional the length is two and for three-dimensional the length is three. Currently only one, two and three dimensional arrays are supported.<br />
<br />
A block file in csv format containing an integer scalar, an integer vector, a real matrix, and a real scalar maybe:<br />
<br />
BEGIN a <br />
int,scalar,64 <br />
5<br />
END a <br />
BEGIN b <br />
int,array,64,2 <br />
1<br />
2<br />
END b <br />
BEGIN c <br />
real,array,64,2,2 <br />
5,5<br />
5,5<br />
END c <br />
BEGIN d <br />
real,scalar,64 <br />
5<br />
END d<br />
<br />
In binary format, {{cc|BEGIN MYNAME}}, {{cc|END MYNAME}} and {{cc|DESCRIPTOR}} are stored in 50 byte character strings which '''must not''' be null terminated.<br />
<br />
lmt will assume block format for all files with file name suffix {{cc|.bin}} and {{cc|.blkcsv}}.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Input_files&diff=1414Input files2022-03-04T06:30:38Z<p>Boerner: </p>
<hr />
<div>lmt '''does not require''' the user to provide information about the file content. Depending on the prospective use lmt will expect a particular file content and will try to read the file accordingly. For example<br />
<br />
*the data file is supposed to contain only real/float numbers which are transferred to integer if required,<br />
*a file containing an ordinary pedigree is supposed to contain only integer numbers,<br />
*a file containing a missing value indicator matrix is supposed to contain only character strings, etc.<br />
<br />
== data file ==<br />
<br />
{{lmt}} accepts only a single file containing the actual data. A data file in ".csv" format must follow the following formatting rules:<br />
*file must have at least one commented line where the last commented line must containing the column names separated by comma,<br />
*the column names<br />
**must be alpha-numeric only<br />
**must not be quoted<br />
**must be unique<br />
*below the header the data file must contain only numeric values where the decimal separator is a dot(".").<br />
The content of a data file maybe named "mydata.csv" with three columns may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
<br />
== co-variance matrix file ==<br />
<br />
A co-variance matrix files must contain a single full squared symmetric positive definite matrix. The content of a co-variance file maybe named "sigma.csv" may look like<br />
1.5,0.8,0.1<br />
0.8,2.1,1.1<br />
0.1,1.1,1.9<br />
A co-variance matrix can be checked in [https://en.wikipedia.org/wiki/R_(programming_language) R] via<br />
<syntaxhighlight lang="R" line><br />
s<-as.matrix(read.table("sigma.csv",sep=","))<br />
if(nrow(s)!=ncol(s)) stop("matrix not squared")<br />
if(any(s[lower.tri(s)]!=t(s)[lower.tri(s)])) stop("matrix not symmetric")<br />
if(any(diag(s)<10e-12)) stop("diagonal element near zero")<br />
if(min(eigen(s)$values)<10e-5) stop("matrix near indefinite")<br />
</syntaxhighlight><br />
<br />
== co-variance mask files ==<br />
<br />
A co-variance mask file communicates to {{lmt}} which co-variances should remain constant when {{lmt}} is used to estimate variances. The mask file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for co-variances which must remain constant and "F" codes for variances which are allowed to float. The mask file must have the same dimensions as the associated co-variance matrix. For instance the above co-variance matrix file maybe accompanied by a mask file containing<br />
T,F,F<br />
F,T,F<br />
F,F,F<br />
which communicates to {{lmt}} that the first and second diagonal element should remain at their original values.<br />
<br />
== missing observations indicator file ==<br />
<br />
The pattern of missing observations maybe communicated via an indicator file, where the file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for an available observation and "F" codes for a missing observation. Further, similar to the data file, the missing value indicator file must contain a header with the same column names as the observation columns in the data file.<br />
<br />
An example data file "mydata.csv"<br />
#y1,y2,mu,id<br />
25.0,0.0,1,5<br />
0.0,0.8,1,6<br />
36.0,-1.5,1,7<br />
28.3,0.0,1,8<br />
maybe accompanied by a missing value indicator file "mymiss.csv"<br />
#y1,y2<br />
T,F<br />
F,T<br />
T,T<br />
T,F<br />
<br />
== pedigree file ==<br />
<br />
For all types of pedigree described below it is required that<br />
*all pedigree ids are positive integer numbers not larger than 9.223372e+18(i.e. the ids must fit in a 64 bit integer)<br />
*the pedigree is complete, that is all individuals occurring as parents must have a record as individuals,<br />
*missing parents are coded with zero<br />
*the pedigree must not contain cycle dependencies<br />
<br />
It is not necessary that the pedigree is sorted or that a sorting variable(e.g. date of birth) is supplied.<br />
<br />
=== ordinary pedigree file ===<br />
A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, where the number of unique ids in the first column must be equal to the row dimension of the pedigree.<br />
<br />
For instance a file maybe called "myped.csv" may contain<br />
1,0,0<br />
2,0,0<br />
3,1,2<br />
4,1,2<br />
5,3,4<br />
A consistency check for that pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d")<br />
if(length(unique(p$i))!=nrow(p)) stop("ids not unique")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
</syntaxhighlight><br />
<br />
=== probabilistic pedigree file ===<br />
Probabilistic pedigrees account for the possibility that an individual originates from more than one pair of parents. That is, an ordinary pedigree is just a special case of a probabilistic pedigree with all probabilities set to 1. In a probabilistic pedigree individual may have repeated records.<br />
A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, parentage probability. Within individuals parentage probabilities must sum up to 1. Further, repeated records of the same individual id must be adjacent. For instance<br />
1,0,0,1.0<br />
2,0,0,1.0<br />
3,1,2,1.0<br />
4,1,2,0.5<br />
4,0,0,0.5<br />
5,3,4,0.1<br />
5,1,3,0.2<br />
5,1,4,0.2<br />
5,1,2,0.5<br />
A consistency check for that pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d","p")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
if(any((abs(aggregate(p$p,by=list(p$i),sum)$x-1.0)>10e-12))) stop("probabilities do not sum up")<br />
</syntaxhighlight><br />
<br />
=== genetic group pedigree file ===<br />
Ordinary and probabilistic pedigrees can contain genetic groups. {{lmt}} assumes '''one phantom parent per genetic group''' where the phantom parents must be located at the top of pedigree and must have their parents set to zero. The number of phantom parents is communicated to {{lmt}} as an extra parameter at the appropriate location in the parameter file. Adding phantom parents to a pedigree requires to shift the numbering of the original pedigree by the number of phantom parents. For example the above ordinary pedigree can be transferred into a pedigree with 2 genetic groups, and therefore 2 phantom parents:<br />
1,0,0<br />
2,0,0<br />
3,1,1<br />
4,2,2<br />
5,3,4<br />
6,3,4<br />
7,5,6<br />
where the original founder individuals 1 and 2 are now coded as 3 and 4, and are off-spring of phantom parents 1 and 2 respectively.<br />
The genetic group methodology requires that in a genetic group pedigree the only individuals with unknown parents are the phantom parents. {{lmt}} is not enforcing this concept, that is the user may supply a genetic group pedigree where an individual has one or both parents unknown although the individual is not a phantom parent.<br />
<br />
A consistency check for the above pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d")<br />
if(length(unique(p$i))!=nrow(p)) stop("ids not unique")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
if(any(p[c(1:2),c("s","d")]!=0)) stop("some phantom parents have known parents")<br />
if(any(p[-c(1:2),c("s","d")]==0)) stop("some ordinary individuals have missing parents")<br />
</syntaxhighlight><br />
<br />
=== meta-founder pedigree file ===<br />
The meta-founder concept is very similar to the genetic group concept with the phantom parents becoming meta-founders, and therefore the same format requirements as for the genetic group pedigree apply. The number of meta-founders as well as the meta-founder co-variance matrix are communicated to {{lmt}} as extra parameters at the appropriate location in the parameter file.<br />
<br />
== Genotype cross-reference file ==<br />
The file contains the pedigree ids of the genotyped individuals as a single column vector. The genotype file and the cross-reference file must have the same number of lines. {{lmt}} will related the individual id and the genotype via the file line number, that is the pedigree id located in line #5 of the cross-reference file is that of an individual of which genotype is located in line #5 of the genotype file.<br />
<br />
== Genotype file ==<br />
<br />
A genotype file must be in ascii text format where each line contains a single genotype coded 0,1 or 2 for homozygous "aa", heterozygous "Aa" and homozygous "AA", respectively. Currently, missing values are not supported. A single genotype must not contain any space. The file must have a many lines as there are genotypes and each genotype must have the same number of markers. A file containing 10 genotypes of 40 markers each maybe<br />
0122221210011211221100021210220020021221<br />
1211121121111120110011110201121020111111<br />
0122211210012202222200022120220111021222<br />
0122211210012202222200022120220111021222<br />
0222220220020220220000020200220020022220<br />
1111122111102111111111111211121020110112<br />
2200022002202020000002200202022020200002<br />
1211111121112111111111111111121111111112<br />
2200022012202020000002200202012020200002<br />
1211121121111120110001110201111020111111<br />
Note that additional information about the genotypes, e.g. the pedigree ids of the related individuals, maybe supplied via an additional file.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=File_formats&diff=1413File formats2022-03-04T06:27:27Z<p>Boerner: /* ".csv" files */</p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
*".coocsv" csv-format for storing sparse matrices in coordinate format.<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
"*.csv" files must contain rectangular arrays, that is every line must contain the same number of comma-separated records.<br />
<br />
lmt supports empty records, e.g.<br />
<br />
1,2,,4<br />
<br />
which will be filled with zero.<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
== Block format ==<br />
<br />
Files in block format can contain multiple records of very different data. That is, a single file can contain several different matrices, vector, and scalars and a mixture of those. Block files are important for supplying sparse matrices, large arrays(e.g. genomic relationship matrices), block-diagonal matrices (e.g. when residual variances are heterogenous) etc. Further, lmt may write intermediate output to a block file for having connected information in the same file.<br />
<br />
The general structure of a single block is:<br />
<br />
BEGIN MYNAME<br />
DESCRIPTOR<br />
DATA<br />
END MYNAME<br />
<br />
where {{cc|MYNAME}} is a user-defined block name which must be unique, {{cc|DESCRIPTOR}} is a comma-separated sequence of data descriptors, and {{cc|DATA}} are the actual data.<br />
{{cc|DESCRIPTOR}} contains at least 3 values:<br />
<br />
*type<br />
*kind<br />
*size<br />
*dimension<br />
<br />
where {{cc|type}} is either {{cc|int}} for integer, {{cc|real}} for real or {{cc|char}} for character. {{cc|kind}} can be either {{cc|scalar}} or {{cc|array}}. {{cc|size}} is the storage size in bit for a single value, for integer and real it should be 64, for character it should be the storage size of the longest character string in an array of strings. If {{cc|kind}} is set to {{cc|array}}, dimension is a vector of comma-separated values containing the dimensions of the array, where the length of the vector determines the number of dimensions. That is, for a one-dimensional array the vector is of length one, for two-dimensional the length is two and for three-dimensional the length is three. Currently only one, two and three dimensional arrays are supported.<br />
<br />
A block file in csv format containing an integer scalar, an integer vector, a real matrix, and a real scalar maybe:<br />
<br />
BEGIN a <br />
int,scalar,64 <br />
5<br />
END a <br />
BEGIN b <br />
int,array,64,2 <br />
1<br />
2<br />
END b <br />
BEGIN c <br />
real,array,64,2,2 <br />
5,5<br />
5,5<br />
END c <br />
BEGIN d <br />
real,scalar,64 <br />
5<br />
END d<br />
<br />
In binary format, {{cc|BEGIN MYNAME}}, {{cc|END MYNAME}} and {{cc|DESCRIPTOR}} are stored in 50 byte character strings which '''must not''' be null terminated.<br />
<br />
lmt will assume block format for all files with file name suffix {{cc|.bin}} and {{cc|.blkcsv}}.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=File_formats&diff=1412File formats2022-03-04T06:23:27Z<p>Boerner: /* Block format */</p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
*".coocsv" csv-format for storing sparse matrices in coordinate format.<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
The type of the file content is determined by its prospective use, that is<br />
*the data file is supposed to contain only real/float numbers which are transferred to integer if required,<br />
*a file containing an ordinary pedigree is supposed to contain only integer numbers,<br />
*a file containing a missing value indicator matrix is supposed to contain only character strings.<br />
<br />
== Block format ==<br />
<br />
Files in block format can contain multiple records of very different data. That is, a single file can contain several different matrices, vector, and scalars and a mixture of those. Block files are important for supplying sparse matrices, large arrays(e.g. genomic relationship matrices), block-diagonal matrices (e.g. when residual variances are heterogenous) etc. Further, lmt may write intermediate output to a block file for having connected information in the same file.<br />
<br />
The general structure of a single block is:<br />
<br />
BEGIN MYNAME<br />
DESCRIPTOR<br />
DATA<br />
END MYNAME<br />
<br />
where {{cc|MYNAME}} is a user-defined block name which must be unique, {{cc|DESCRIPTOR}} is a comma-separated sequence of data descriptors, and {{cc|DATA}} are the actual data.<br />
{{cc|DESCRIPTOR}} contains at least 3 values:<br />
<br />
*type<br />
*kind<br />
*size<br />
*dimension<br />
<br />
where {{cc|type}} is either {{cc|int}} for integer, {{cc|real}} for real or {{cc|char}} for character. {{cc|kind}} can be either {{cc|scalar}} or {{cc|array}}. {{cc|size}} is the storage size in bit for a single value, for integer and real it should be 64, for character it should be the storage size of the longest character string in an array of strings. If {{cc|kind}} is set to {{cc|array}}, dimension is a vector of comma-separated values containing the dimensions of the array, where the length of the vector determines the number of dimensions. That is, for a one-dimensional array the vector is of length one, for two-dimensional the length is two and for three-dimensional the length is three. Currently only one, two and three dimensional arrays are supported.<br />
<br />
A block file in csv format containing an integer scalar, an integer vector, a real matrix, and a real scalar maybe:<br />
<br />
BEGIN a <br />
int,scalar,64 <br />
5<br />
END a <br />
BEGIN b <br />
int,array,64,2 <br />
1<br />
2<br />
END b <br />
BEGIN c <br />
real,array,64,2,2 <br />
5,5<br />
5,5<br />
END c <br />
BEGIN d <br />
real,scalar,64 <br />
5<br />
END d<br />
<br />
In binary format, {{cc|BEGIN MYNAME}}, {{cc|END MYNAME}} and {{cc|DESCRIPTOR}} are stored in 50 byte character strings which '''must not''' be null terminated.<br />
<br />
lmt will assume block format for all files with file name suffix {{cc|.bin}} and {{cc|.blkcsv}}.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=File_formats&diff=1411File formats2022-03-04T06:22:18Z<p>Boerner: /* Block format */</p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
*".coocsv" csv-format for storing sparse matrices in coordinate format.<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
The type of the file content is determined by its prospective use, that is<br />
*the data file is supposed to contain only real/float numbers which are transferred to integer if required,<br />
*a file containing an ordinary pedigree is supposed to contain only integer numbers,<br />
*a file containing a missing value indicator matrix is supposed to contain only character strings.<br />
<br />
== Block format ==<br />
<br />
Files in block format can contain multiple records of very different data. That is, a single file can contain several different matrices, vector, and scalars and a mixture of those. Block files are important for supplying sparse matrices, large arrays(e.g. genomic relationship matrices), block-diagonal matrices (e.g. when residual variances are heterogenous) etc. Further, lmt may write intermediate output to a block file for having connected information in the same file.<br />
<br />
The general structure of a single block is:<br />
<br />
BEGIN MYNAME<br />
DESCRIPTOR<br />
DATA<br />
END MYNAME<br />
<br />
where {{cc|MYNAME}} is a user-defined block name which must be unique, {{cc|DESCRIPTOR}} is a comma-separated sequence of data descriptors, and {{cc|DATA}} are the actual data.<br />
{{cc|DESCRIPTOR}} contains at least 3 values:<br />
<br />
*type<br />
*kind<br />
*size<br />
*dimension<br />
<br />
where {{cc|type}} is either {{cc|int}} for integer, {{cc|real}} for real or {{cc|char}} for character. {{cc|kind}} can be either {{cc|scalar}} or {{cc|array}}. {{cc|size}} is the storage size in bit for a single value, for integer and real it should be 64, for character it should be the storage size of the longest character string in an array of strings. If {{cc|kind}} is set to {{cc|array}}, dimension is a vector of comma-separated values containing the dimensions of the array, where the length of the vector determines the number of dimensions. That is, for a one-dimensional array the vector is of length one, for two-dimensional the length is two and for three-dimensional the length is three. Currently only one, two and three dimensional arrays are supported.<br />
<br />
A block file in csv format containing an integer scalar, an integer vector, a real matrix, and a real scalar maybe:<br />
<br />
BEGIN a <br />
int,scalar,64 <br />
5<br />
END a <br />
BEGIN b <br />
int,array,64,2 <br />
1<br />
2<br />
END b <br />
BEGIN c <br />
real,array,64,2,2 <br />
5,5<br />
5,5<br />
END c <br />
BEGIN d <br />
real,scalar,64 <br />
5<br />
END d<br />
<br />
In binary format, {{cc|BEGIN MYNAME}}, {{cc|END MYNAME}} and {{cc|DESCRIPTOR}} are stored in 50 byte character strings which '''must not''' be null terminated</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=File_formats&diff=1410File formats2022-03-04T06:19:19Z<p>Boerner: </p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
*".coocsv" csv-format for storing sparse matrices in coordinate format.<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
The type of the file content is determined by its prospective use, that is<br />
*the data file is supposed to contain only real/float numbers which are transferred to integer if required,<br />
*a file containing an ordinary pedigree is supposed to contain only integer numbers,<br />
*a file containing a missing value indicator matrix is supposed to contain only character strings.<br />
<br />
== Block format ==<br />
<br />
Files in block format can contain multiple records of very different data. That is, a single file can contain several different matrices, vector, and scalars and a mixture of those. Block files are important for supplying sparse matrices, large arrays(e.g. genomic relationship matrices), block-diagonal matrices (e.g. when residual variances are heterogenous) etc. Further, lmt may write intermediate output to a block file for having connected information in the same file.<br />
<br />
The general structure of a single block is:<br />
<br />
BEGIN MYNAME<br />
DESCRIPTOR<br />
DATA<br />
END MYNAME<br />
<br />
where {{cc|MYNAME}} is a user-defined block name which must be unique, {{cc|DESCRIPTOR}} is a comma-separated sequence of data descriptors, and {{cc|DATA}} are the actual data.<br />
{{cc|DESCRIPTOR}} contains at least 3 values:<br />
<br />
*type<br />
*kind<br />
*size<br />
*dimension<br />
<br />
where {{cc|type}} is either {{cc|int}} for integer, {{cc|real}} for real or {{cc|char}} for character. {{cc|kind}} can be either {{cc|scalar}} or {{cc|array}}. {{cc|size}} is the storage size in bit for a single value, for integer and real it should be 64, for character it should be the storage size of the longest character string in an array of strings. If {{cc|kind}} is set to {{cc|array}}, dimension is a vector of comma-separated values containing the dimensions of the array, where the length of the vector determines the number of dimensions. That is, for a one-dimensional array the vector is of length one, for two-dimensional the length is two and for three-dimensional the length is three. Currently only one, two and three dimensional arrays are supported.<br />
<br />
A block file in csv format containing an integer scalar, an integer vector, a real matrix, and a real scalar maybe:<br />
<br />
BEGIN a <br />
int,scalar,64 <br />
5<br />
END a <br />
BEGIN b <br />
int,array,64,2 <br />
1<br />
2<br />
END b <br />
BEGIN c <br />
real,array,64,2,2 <br />
5,5<br />
5,5<br />
END c <br />
BEGIN d <br />
real,scalar,64 <br />
5<br />
END d</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=File_formats&diff=1409File formats2022-03-04T05:52:09Z<p>Boerner: </p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
*".coocsv" csv-format for storing sparse matrices in coordinate format.<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
The type of the file content is determined by its prospective use, that is<br />
*the data file is supposed to contain only real/float numbers which are transferred to integer if required,<br />
*a file containing an ordinary pedigree is supposed to contain only integer numbers,<br />
*a file containing a missing value indicator matrix is supposed to contain only character strings.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=File_formats&diff=1408File formats2022-03-04T05:51:23Z<p>Boerner: Created page with "== File content determination via file name extensions == {{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are *".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files *".blkcsv" for comma separated value ascii text files in block format *".bin" for binary files in block format Note that this mechanism does..."</p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
The type of the file content is determined by its prospective use, that is<br />
*the data file is supposed to contain only real/float numbers which are transferred to integer if required,<br />
*a file containing an ordinary pedigree is supposed to contain only integer numbers,<br />
*a file containing a missing value indicator matrix is supposed to contain only character strings.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Input_files&diff=1407Input files2022-03-04T05:50:29Z<p>Boerner: </p>
<hr />
<div>== data file ==<br />
<br />
{{lmt}} accepts only a single file containing the actual data. A data file in ".csv" format must follow the following formatting rules:<br />
*file must have at least one commented line where the last commented line must containing the column names separated by comma,<br />
*the column names<br />
**must be alpha-numeric only<br />
**must not be quoted<br />
**must be unique<br />
*below the header the data file must contain only numeric values where the decimal separator is a dot(".").<br />
The content of a data file maybe named "mydata.csv" with three columns may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
<br />
== co-variance matrix file ==<br />
<br />
A co-variance matrix files must contain a single full squared symmetric positive definite matrix. The content of a co-variance file maybe named "sigma.csv" may look like<br />
1.5,0.8,0.1<br />
0.8,2.1,1.1<br />
0.1,1.1,1.9<br />
A co-variance matrix can be checked in [https://en.wikipedia.org/wiki/R_(programming_language) R] via<br />
<syntaxhighlight lang="R" line><br />
s<-as.matrix(read.table("sigma.csv",sep=","))<br />
if(nrow(s)!=ncol(s)) stop("matrix not squared")<br />
if(any(s[lower.tri(s)]!=t(s)[lower.tri(s)])) stop("matrix not symmetric")<br />
if(any(diag(s)<10e-12)) stop("diagonal element near zero")<br />
if(min(eigen(s)$values)<10e-5) stop("matrix near indefinite")<br />
</syntaxhighlight><br />
<br />
== co-variance mask files ==<br />
<br />
A co-variance mask file communicates to {{lmt}} which co-variances should remain constant when {{lmt}} is used to estimate variances. The mask file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for co-variances which must remain constant and "F" codes for variances which are allowed to float. The mask file must have the same dimensions as the associated co-variance matrix. For instance the above co-variance matrix file maybe accompanied by a mask file containing<br />
T,F,F<br />
F,T,F<br />
F,F,F<br />
which communicates to {{lmt}} that the first and second diagonal element should remain at their original values.<br />
<br />
== missing observations indicator file ==<br />
<br />
The pattern of missing observations maybe communicated via an indicator file, where the file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for an available observation and "F" codes for a missing observation. Further, similar to the data file, the missing value indicator file must contain a header with the same column names as the observation columns in the data file.<br />
<br />
An example data file "mydata.csv"<br />
#y1,y2,mu,id<br />
25.0,0.0,1,5<br />
0.0,0.8,1,6<br />
36.0,-1.5,1,7<br />
28.3,0.0,1,8<br />
maybe accompanied by a missing value indicator file "mymiss.csv"<br />
#y1,y2<br />
T,F<br />
F,T<br />
T,T<br />
T,F<br />
<br />
== pedigree file ==<br />
<br />
For all types of pedigree described below it is required that<br />
*all pedigree ids are positive integer numbers not larger than 9.223372e+18(i.e. the ids must fit in a 64 bit integer)<br />
*the pedigree is complete, that is all individuals occurring as parents must have a record as individuals,<br />
*missing parents are coded with zero<br />
*the pedigree must not contain cycle dependencies<br />
<br />
It is not necessary that the pedigree is sorted or that a sorting variable(e.g. date of birth) is supplied.<br />
<br />
=== ordinary pedigree file ===<br />
A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, where the number of unique ids in the first column must be equal to the row dimension of the pedigree.<br />
<br />
For instance a file maybe called "myped.csv" may contain<br />
1,0,0<br />
2,0,0<br />
3,1,2<br />
4,1,2<br />
5,3,4<br />
A consistency check for that pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d")<br />
if(length(unique(p$i))!=nrow(p)) stop("ids not unique")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
</syntaxhighlight><br />
<br />
=== probabilistic pedigree file ===<br />
Probabilistic pedigrees account for the possibility that an individual originates from more than one pair of parents. That is, an ordinary pedigree is just a special case of a probabilistic pedigree with all probabilities set to 1. In a probabilistic pedigree individual may have repeated records.<br />
A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, parentage probability. Within individuals parentage probabilities must sum up to 1. Further, repeated records of the same individual id must be adjacent. For instance<br />
1,0,0,1.0<br />
2,0,0,1.0<br />
3,1,2,1.0<br />
4,1,2,0.5<br />
4,0,0,0.5<br />
5,3,4,0.1<br />
5,1,3,0.2<br />
5,1,4,0.2<br />
5,1,2,0.5<br />
A consistency check for that pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d","p")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
if(any((abs(aggregate(p$p,by=list(p$i),sum)$x-1.0)>10e-12))) stop("probabilities do not sum up")<br />
</syntaxhighlight><br />
<br />
=== genetic group pedigree file ===<br />
Ordinary and probabilistic pedigrees can contain genetic groups. {{lmt}} assumes '''one phantom parent per genetic group''' where the phantom parents must be located at the top of pedigree and must have their parents set to zero. The number of phantom parents is communicated to {{lmt}} as an extra parameter at the appropriate location in the parameter file. Adding phantom parents to a pedigree requires to shift the numbering of the original pedigree by the number of phantom parents. For example the above ordinary pedigree can be transferred into a pedigree with 2 genetic groups, and therefore 2 phantom parents:<br />
1,0,0<br />
2,0,0<br />
3,1,1<br />
4,2,2<br />
5,3,4<br />
6,3,4<br />
7,5,6<br />
where the original founder individuals 1 and 2 are now coded as 3 and 4, and are off-spring of phantom parents 1 and 2 respectively.<br />
The genetic group methodology requires that in a genetic group pedigree the only individuals with unknown parents are the phantom parents. {{lmt}} is not enforcing this concept, that is the user may supply a genetic group pedigree where an individual has one or both parents unknown although the individual is not a phantom parent.<br />
<br />
A consistency check for the above pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d")<br />
if(length(unique(p$i))!=nrow(p)) stop("ids not unique")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
if(any(p[c(1:2),c("s","d")]!=0)) stop("some phantom parents have known parents")<br />
if(any(p[-c(1:2),c("s","d")]==0)) stop("some ordinary individuals have missing parents")<br />
</syntaxhighlight><br />
<br />
=== meta-founder pedigree file ===<br />
The meta-founder concept is very similar to the genetic group concept with the phantom parents becoming meta-founders, and therefore the same format requirements as for the genetic group pedigree apply. The number of meta-founders as well as the meta-founder co-variance matrix are communicated to {{lmt}} as extra parameters at the appropriate location in the parameter file.<br />
<br />
== Genotype cross-reference file ==<br />
The file contains the pedigree ids of the genotyped individuals as a single column vector. The genotype file and the cross-reference file must have the same number of lines. {{lmt}} will related the individual id and the genotype via the file line number, that is the pedigree id located in line #5 of the cross-reference file is that of an individual of which genotype is located in line #5 of the genotype file.<br />
<br />
== Genotype file ==<br />
<br />
A genotype file must be in ascii text format where each line contains a single genotype coded 0,1 or 2 for homozygous "aa", heterozygous "Aa" and homozygous "AA", respectively. Currently, missing values are not supported. A single genotype must not contain any space. The file must have a many lines as there are genotypes and each genotype must have the same number of markers. A file containing 10 genotypes of 40 markers each maybe<br />
0122221210011211221100021210220020021221<br />
1211121121111120110011110201121020111111<br />
0122211210012202222200022120220111021222<br />
0122211210012202222200022120220111021222<br />
0222220220020220220000020200220020022220<br />
1111122111102111111111111211121020110112<br />
2200022002202020000002200202022020200002<br />
1211111121112111111111111111121111111112<br />
2200022012202020000002200202012020200002<br />
1211121121111120110001110201111020111111<br />
Note that additional information about the genotypes, e.g. the pedigree ids of the related individuals, maybe supplied via an additional file.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Input_file_formats&diff=1404Input file formats2022-03-04T05:47:03Z<p>Boerner: Boerner moved page Input file formats to Input files</p>
<hr />
<div>#REDIRECT [[Input files]]</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Input_files&diff=1403Input files2022-03-04T05:47:03Z<p>Boerner: Boerner moved page Input file formats to Input files</p>
<hr />
<div>== File content determination via file name extensions ==<br />
{{lmt}} automatically detects the format of input files by the [https://en.wikipedia.org/wiki/Filename_extension filename extension]. Supported extensions are<br />
*".csv" for ordinary [https://en.wikipedia.org/wiki/Comma-separated_values comma separated values] ascii text files<br />
*".blkcsv" for comma separated value ascii text files in block format<br />
*".bin" for binary files in block format<br />
<br />
Note that this mechanism does not apply to files containing genotypes.<br />
<br />
== ".csv" files ==<br />
<br />
".csv" files may contain several commented lines at the top only where the comment character is "#".<br />
<br />
The type of the file content is determined by its prospective use, that is<br />
*the data file is supposed to contain only real/float numbers which are transferred to integer if required,<br />
*a file containing an ordinary pedigree is supposed to contain only integer numbers,<br />
*a file containing a missing value indicator matrix is supposed to contain only character strings.<br />
<br />
=== data file ===<br />
<br />
{{lmt}} accepts only a single file containing the actual data. A data file in ".csv" format must follow the following formatting rules:<br />
*file must have at least one commented line where the last commented line must containing the column names separated by comma,<br />
*the column names<br />
**must be alpha-numeric only<br />
**must not be quoted<br />
**must be unique<br />
*below the header the data file must contain only numeric values where the decimal separator is a dot(".").<br />
The content of a data file maybe named "mydata.csv" with three columns may look like:<br />
<br />
#y,mu,id<br />
25.0,1,5<br />
33.1,1,6<br />
36.0,1,7<br />
28.3,1,8<br />
<br />
=== co-variance matrix file ===<br />
<br />
A co-variance matrix files must contain a single full squared symmetric positive definite matrix. The content of a co-variance file maybe named "sigma.csv" may look like<br />
1.5,0.8,0.1<br />
0.8,2.1,1.1<br />
0.1,1.1,1.9<br />
A co-variance matrix can be checked in [https://en.wikipedia.org/wiki/R_(programming_language) R] via<br />
<syntaxhighlight lang="R" line><br />
s<-as.matrix(read.table("sigma.csv",sep=","))<br />
if(nrow(s)!=ncol(s)) stop("matrix not squared")<br />
if(any(s[lower.tri(s)]!=t(s)[lower.tri(s)])) stop("matrix not symmetric")<br />
if(any(diag(s)<10e-12)) stop("diagonal element near zero")<br />
if(min(eigen(s)$values)<10e-5) stop("matrix near indefinite")<br />
</syntaxhighlight><br />
<br />
=== co-variance mask files ===<br />
<br />
A co-variance mask file communicates to {{lmt}} which co-variances should remain constant when {{lmt}} is used to estimate variances. The mask file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for co-variances which must remain constant and "F" codes for variances which are allowed to float. The mask file must have the same dimensions as the associated co-variance matrix. For instance the above co-variance matrix file maybe accompanied by a mask file containing<br />
T,F,F<br />
F,T,F<br />
F,F,F<br />
which communicates to {{lmt}} that the first and second diagonal element should remain at their original values.<br />
<br />
=== missing observations indicator file ===<br />
<br />
The pattern of missing observations maybe communicated via an indicator file, where the file must contain characters which can be interpreted as a [https://en.wikipedia.org/wiki/Boolean_data_type boolean data type], and where "T" codes for an available observation and "F" codes for a missing observation. Further, similar to the data file, the missing value indicator file must contain a header with the same column names as the observation columns in the data file.<br />
<br />
An example data file "mydata.csv"<br />
#y1,y2,mu,id<br />
25.0,0.0,1,5<br />
0.0,0.8,1,6<br />
36.0,-1.5,1,7<br />
28.3,0.0,1,8<br />
maybe accompanied by a missing value indicator file "mymiss.csv"<br />
#y1,y2<br />
T,F<br />
F,T<br />
T,T<br />
T,F<br />
<br />
=== pedigree file ===<br />
<br />
For all types of pedigree described below it is required that<br />
*all pedigree ids are positive integer numbers not larger than 9.223372e+18(i.e. the ids must fit in a 64 bit integer)<br />
*the pedigree is complete, that is all individuals occurring as parents must have a record as individuals,<br />
*missing parents are coded with zero<br />
*the pedigree must not contain cycle dependencies<br />
<br />
It is not necessary that the pedigree is sorted or that a sorting variable(e.g. date of birth) is supplied.<br />
<br />
==== ordinary pedigree file ====<br />
A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, where the number of unique ids in the first column must be equal to the row dimension of the pedigree.<br />
<br />
For instance a file maybe called "myped.csv" may contain<br />
1,0,0<br />
2,0,0<br />
3,1,2<br />
4,1,2<br />
5,3,4<br />
A consistency check for that pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d")<br />
if(length(unique(p$i))!=nrow(p)) stop("ids not unique")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
</syntaxhighlight><br />
<br />
==== probabilistic pedigree file ====<br />
Probabilistic pedigrees account for the possibility that an individual originates from more than one pair of parents. That is, an ordinary pedigree is just a special case of a probabilistic pedigree with all probabilities set to 1. In a probabilistic pedigree individual may have repeated records.<br />
A file containing an ordinary pedigree must have three numeric columns: individual id,first parent id, second parent id, parentage probability. Within individuals parentage probabilities must sum up to 1. Further, repeated records of the same individual id must be adjacent. For instance<br />
1,0,0,1.0<br />
2,0,0,1.0<br />
3,1,2,1.0<br />
4,1,2,0.5<br />
4,0,0,0.5<br />
5,3,4,0.1<br />
5,1,3,0.2<br />
5,1,4,0.2<br />
5,1,2,0.5<br />
A consistency check for that pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d","p")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
if(any((abs(aggregate(p$p,by=list(p$i),sum)$x-1.0)>10e-12))) stop("probabilities do not sum up")<br />
</syntaxhighlight><br />
<br />
==== genetic group pedigree file ====<br />
Ordinary and probabilistic pedigrees can contain genetic groups. {{lmt}} assumes '''one phantom parent per genetic group''' where the phantom parents must be located at the top of pedigree and must have their parents set to zero. The number of phantom parents is communicated to {{lmt}} as an extra parameter at the appropriate location in the parameter file. Adding phantom parents to a pedigree requires to shift the numbering of the original pedigree by the number of phantom parents. For example the above ordinary pedigree can be transferred into a pedigree with 2 genetic groups, and therefore 2 phantom parents:<br />
1,0,0<br />
2,0,0<br />
3,1,1<br />
4,2,2<br />
5,3,4<br />
6,3,4<br />
7,5,6<br />
where the original founder individuals 1 and 2 are now coded as 3 and 4, and are off-spring of phantom parents 1 and 2 respectively.<br />
The genetic group methodology requires that in a genetic group pedigree the only individuals with unknown parents are the phantom parents. {{lmt}} is not enforcing this concept, that is the user may supply a genetic group pedigree where an individual has one or both parents unknown although the individual is not a phantom parent.<br />
<br />
A consistency check for the above pedigree in [https://en.wikipedia.org/wiki/R_(programming_language) R] may be<br />
<syntaxhighlight lang="R" line><br />
p<-read.table("myped.csv",sep=",")<br />
colnames(p)<-c("i","s","d")<br />
if(length(unique(p$i))!=nrow(p)) stop("ids not unique")<br />
if(any(!(p$s[p$s!=0] %in% p$i))) stop("some sires don't have records")<br />
if(any(!(p$d[p$d!=0] %in% p$i))) stop("some dams don't have records")<br />
if(any(p[c(1:2),c("s","d")]!=0)) stop("some phantom parents have known parents")<br />
if(any(p[-c(1:2),c("s","d")]==0)) stop("some ordinary individuals have missing parents")<br />
</syntaxhighlight><br />
<br />
==== meta-founder pedigree file ====<br />
The meta-founder concept is very similar to the genetic group concept with the phantom parents becoming meta-founders, and therefore the same format requirements as for the genetic group pedigree apply. The number of meta-founders as well as the meta-founder co-variance matrix are communicated to {{lmt}} as extra parameters at the appropriate location in the parameter file.<br />
<br />
=== Genotype cross-reference file ===<br />
The file contains the pedigree ids of the genotyped individuals as a single column vector. The genotype file and the cross-reference file must have the same number of lines. {{lmt}} will related the individual id and the genotype via the file line number, that is the pedigree id located in line #5 of the cross-reference file is that of an individual of which genotype is located in line #5 of the genotype file.<br />
<br />
== Genotype file ==<br />
<br />
A genotype file must be in ascii text format where each line contains a single genotype coded 0,1 or 2 for homozygous "aa", heterozygous "Aa" and homozygous "AA", respectively. Currently, missing values are not supported. A single genotype must not contain any space. The file must have a many lines as there are genotypes and each genotype must have the same number of markers. A file containing 10 genotypes of 40 markers each maybe<br />
0122221210011211221100021210220020021221<br />
1211121121111120110011110201121020111111<br />
0122211210012202222200022120220111021222<br />
0122211210012202222200022120220111021222<br />
0222220220020220220000020200220020022220<br />
1111122111102111111111111211121020110112<br />
2200022002202020000002200202022020200002<br />
1211111121112111111111111111121111111112<br />
2200022012202020000002200202012020200002<br />
1211121121111120110001110201111020111111<br />
Note that additional information about the genotypes, e.g. the pedigree ids of the related individuals, maybe supplied via an additional file.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Linear_mixed_models_in_lmt&diff=1381Linear mixed models in lmt2022-03-04T02:04:09Z<p>Boerner: /* Getting $$X$$ to full column rank */</p>
<hr />
<div>=== Matrix notation, factors and sub-factors ===<br />
<br />
Consider the multi-variate linear mixed model<br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2 \\<br />
y_3<br />
\end{array}<br />
\right)<br />
=<br />
\left(<br />
\begin{array}{ccc}<br />
X_1 & 0 & 0 \\<br />
0 & X_2 & 0 \\<br />
0 & 0 & X_3<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2 \\<br />
b_3<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{ccc}<br />
Z_1 & 0 & 0\\<br />
0 & Z_2 & 0\\<br />
0 & 0 & Z_3<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2 \\<br />
u_3<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2 \\<br />
e_3<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where $$(y_1,y_2,y_3)'$$, $$(b_1,b_2,b_3)'$$, $$(u_1,u_2,u_3)'$$ and $$(e_1,e_2,e_3)'$$ are vectors of response variables, effects of fixed factors, effects of random factors and effects of residuals respectively, and matrices<br />
$$\left(<br />
\begin{array}{ccc}<br />
X_1 & 0 & 0 \\<br />
0 & X_2 & 0 \\<br />
0 & 0 & X_3<br />
\end{array}<br />
\right)$$, and<br />
$$<br />
\left(<br />
\begin{array}{ccc}<br />
Z_1 & 0 & 0\\<br />
0 & Z_2 & 0\\<br />
0 & 0 & Z_3<br />
\end{array}<br />
\right)<br />
$$ are block-diagonal design matrices linking effects in the respective vectors to their related response variables. In usual mixed model terminology $$b_1$$, $$b_2$$ and $$b_3$$ are called fixed factors, and $$u_1$$, $$u_2$$ and $$u_3$$ are called random factors. Ignoring the residual the above model has in total 6 factors.<br />
<br />
However, the model maybe rewritten in matrix formulation as<br />
<br />
$$vec(Y)=Xvec(B)+Zvec(U)+vec(E)$$,<br />
<br />
where $$vec$$ is the [https://en.wikipedia.org/wiki/Vectorization_(mathematics) vectorization operator], $$Y=[y_1,y_2,y_3]$$, $$B=[b_1,b_2,b_3]$$, $$U=[u_1,u_2,u_3]$$ and $$E=[e_1,e_2,e_3]$$ are column matrices of response variables, the effects of the fixed and random factor, and the residuals, respectively, and<br />
$$X=\left(<br />
\begin{array}{ccc}<br />
X_1 & 0 & 0 \\<br />
0 & X_2 & 0 \\<br />
0 & 0 & X_3<br />
\end{array}<br />
\right)$$, and<br />
$$Z=<br />
\left(<br />
\begin{array}{ccc}<br />
Z_1 & 0 & 0\\<br />
0 & Z_2 & 0\\<br />
0 & 0 & Z_3<br />
\end{array}<br />
\right)<br />
$$. The distribution assumption for the random components in the model are $$vec(U^{'})\sim N((0,0,0)',\Gamma_u \otimes \Sigma_u)$$ and $$vec(E^{'})\sim N((0,0,0)',\Gamma_e \otimes \Sigma_e)$$. Note that the column and row dimensions of $$U$$ are determined by the column dimension of $$\Sigma_u$$ and $$\Gamma_u$$ respectively.<br />
<br />
Slightly different to the above terminology, {{lmt}} refers to $$B$$ and $$U$$ as factors, and therefore the model has only two factors, whereas the columns in $$B$$ and $$U$$ are referred to as '''sub-factors'''. <br />
<br />
Following the above matrix notation {{lmt}} will always invoke only one factor for all modelled fixed classification variables and only one factor for all modelled fixed continuous co-variables. Sub-factors are summarized into a single random factors if they share the same $$\Sigma$$ matrix. Thus, {{lmt}} will invoke as many random factors as there are different $$\Gamma \otimes \Sigma$$ constructs. That is, in {{lmt}} terminology the multi-variate model<br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2 \\<br />
y_3<br />
\end{array}<br />
\right)<br />
=<br />
\left(<br />
\begin{array}{ccc}<br />
X_1 & 0 & 0 \\<br />
0 & X_2 & 0 \\<br />
0 & 0 & X_3<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2 \\<br />
b_3<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cccccc}<br />
Z_{d,1} & 0 & 0 & Z_{m,1} & 0 & 0\\<br />
0 & Z_{d,2} & 0 & 0 & Z_{m,2} & 0\\<br />
0 & 0 & Z_{d,3} & 0 & 0 & Z_{m,3}\\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_{d,1} \\<br />
u_{d,2} \\<br />
u_{d,3} \\<br />
u_{m,1} \\<br />
u_{m,2} \\<br />
u_{m,3}<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{ccc}<br />
W_1 & 0 & 0\\<br />
0 & W_2 & 0\\<br />
0 & 0 & W_3<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
v_1 \\<br />
v_2 \\<br />
v_3<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2 \\<br />
e_3<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
with<br />
$$(u_{d,1},u_{d,2},u_{d,3},u_{m,1},u_{m,2},u_{m,3})'\sim N((0,0,0,0,0,0)',\Sigma_u \otimes \Gamma_u)$$ and $$(v_1,v_2,v_3)'\sim N((0,0,0)',\Sigma_v \otimes \Gamma_v)$$, rewritten as $$vec(Y)=Xvec(B)+Zvec(U)+Wvec(V)+vec(E)$$ will have only 3 factors, $$B$$, $$U$$ and $$V$$ with $$b_1,b_2,b_3$$, $$u_{d,1},u_{d,2},u_{d,3},u_{m,1},u_{m,2},u_{m,3}$$ and $$v_1,v_2,v_3$$ being subfactors of $$U$$ and $$V$$ respectively.<br />
<br />
=== Model syntax ===<br />
<br />
Thee syntax for communicating the model to {{lmt}} is effectively: "'''just write the model'''", where the model is written [[Parameter_file_elements#.3Ceqn.3E|into the space of a particular xml element of the parameter file]].<br />
<br />
<br />
Note that {{lmt}} will only check whether the specified model can be built, not whether the model is meaningful or allows for a statistical inference.<br />
<br />
==== An example ====<br />
An example for a valid {{lmt}} model string would be <br />
y=x*b+age(t(co(p(1,2))))*c+id*u(v(my_var(1))).<br />
<br />
The components of the model string are<br />
*the [[#Varibales|response variable]] {{cc|y}}, which must be a column name in the data file<br />
*[[#Variables|model variables]] {{cc|x}}, {{cc|age}} and {{cc|id}}, which must be a column names in the data file<br />
*[[#Sub-factors|sub-factors]] {{cc|b}}, {{cc|c}} and {{cc|u}} which are user-defined alpha-numeric character strings<br />
*[[#Relational operators|relation operators]] {{cc|1==}}, {{cc|*}} and {{cc|+}}<br />
*a [[#Variable specifiers|variable specifier]] {{cc|(t(co(p(1,2))))}} used to provide further information about variable {{cc|age}}<br />
*a [[#Sub-factor specifiers|sub-factor specifier]] {{cc|(v(my_var(1)))}} used to provide further information about sub-factor {{cc|u}}<br />
<br />
==== Variables ====<br />
Response variables and model variables are named using user-defined alpha-numeric character strings. These character strings must be column names in the data file. There is no size limitation for the variables names.<br />
<br />
Model variables can be used in several equations. That is, the bi-variate model<br />
y1=x*b1<br />
y2=x*b2,<br />
with variables {{cc|x, y1 and y2}} being column names in the data file, is equivalent to the model<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X & 0 \\<br />
0 & X<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)+<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
==== Sub-factors ====<br />
Sub-factors are named using user-defined alpha-numeric character strings. There is no size limitation for the variables names.<br />
<br />
Contrarily to using variables across traits, using a sub-factor across traits changes the model. That is model<br />
y1=x*b1<br />
y2=x*b1<br />
is equivalent to<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{c}<br />
X \\<br />
X <br />
\end{array}<br />
\right)<br />
\begin{array}{c}<br />
b_1 \\<br />
\end{array}<br />
+<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
==== Relational operators ====<br />
The rules for using relational operators are<br />
*{{cc|1==}} links a single response variable to the model<br />
*{{cc|*}} links a model variable to it's sub-factor, which together form a model term<br />
*{{cc|+}} concatenates different model terms.<br />
<br />
==== Specifiers ====<br />
Variables and sub-factors maybe accompanied by a specifier. A specifier is a [https://en.wikipedia.org/wiki/Tree_structure#Nested_parentheses tree diagramm] in [https://en.wikipedia.org/wiki/Newick_format Newick format] with all nodes named, but leaf nodes can be unnamed, and where the root node name is the variable or sub-factor name. The specifier provides additional information about a variable or sub-factor. The {{lmt}} version of the above [https://en.wikipedia.org/wiki/Newick_format tree diagram] differs in that<br />
*the parent nodes precede child nodes<br />
*child nodes within the same parent node are separated by semicolon<br />
*sibling nodes can be mutually exclusive, that is only one sibling node maybe allowed<br />
*leaf nodes maybe not named but contain additional, maybe comma-separated information<br />
*if a child node is marked as default, the child node and it's immediate parent node can be omitted<br />
*if a node is marked as optional it can be omitted. if an optional node is used it's compulsory child nodes must be included<br />
===== Variable specifiers =====<br />
Variable specifiers are used to communicate further information which may be that the variable<br />
*is continuous but real numbers<br />
*is continuous but integer numbers<br />
*is a genetic group regression matrix<br />
*undergoes a polynomial expansion<br />
*is associated to a nesting variable<br />
etc.<br />
<br />
The [https://en.wikipedia.org/wiki/Tree_structure tree diagram] for the variable specifier is<br />
<br />
[[File:variabletree.jpg|1000px|]]<br />
<br />
with the [https://en.wikipedia.org/wiki/Tree_structure#Nested_parentheses nested parentheses] representation written as<br />
<br />
''variable''('''t'''(<span style="color:red;">'''co'''</span>('''t'''(<span style="color:red;">'''i'''</span>;<span style="color:red;">'''r'''</span>);'''p'''(polynomial ids);'''n'''(''variable''));<span style="color:red;">'''cl'''</span>;<span style="color:red;">'''gg'''</span>(''pedigree'')))<br />
<br />
Note that the above representation would '''not''' yield a valid specifier useable in an equation as the diagram contains sibling nodes which are mutually exclusive, thus allowing only one of the sibling node to occur in the specifier. That is valid specifiers would be<br />
''variable''('''t'''('''cl'''))<br />
''variable''('''t'''('''co'''))<br />
''variable''('''t'''('''gg'''(''pedigree'')))<br />
''variable''('''t'''('''co'''('''t'''('''r''');'''p'''(polynomial id);'''n'''(''variable''))))<br />
''variable''('''t'''('''co'''('''t'''('''i''');'''p'''(polynomial id);'''n'''(''variable''))))<br />
Since a default-determining leave node and it's immediate parent node can be omitted the following equality holds:<br />
''variable''('''t'''('''cl'''))=''variable''<br />
''variable''('''t'''('''co'''('''t'''('''r'''))))=''variable''('''t'''('''co'''))<br />
<br />
A variable can have several different specifiers. Notwithstanding the statistical soundness, an example would be<br />
y=x(t(co))*b + x(t(co(n(g))))*c<br />
where {{cc| y, x and g}} are columns names in the data file. The equivalent model would be<br />
$$<br />
y=D_x ib+D_x X_gc + e<br />
$$<br />
where $$D_x$$ is a diagonal matrix constructed from {{cc|x}}, $$i$$ is a vector of ones, $$X_g$$ is a design matrix constructed from classification variable $$g$$, and $$b$$ and $$c$$ are the sub-factors.<br />
<br />
===== Sub-factor specifiers =====<br />
Sub-factor specifiers are used to communicate further information which may be that the sub-factor<br />
*is a random sub-factor<br />
*to which variance it is related to<br />
*which diagonal element in the $$\Sigma$$ matrix of the variance it is related to<br />
The [https://en.wikipedia.org/wiki/Tree_structure tree diagram] for the sub-factor specifier is<br />
<br />
[[File:subfactortree.jpg|500px|]]<br />
<br />
with the [https://en.wikipedia.org/wiki/Tree_structure#Nested_parentheses nested parentheses] representation written as<br />
''sub-factor''('''v'''(''variance name''(diagonal position)))<br />
<br />
According to the tree diagram the sub-factor specifier in the [[#An example|example model string]] translates to<br />
*sub-factor name is {{cc|u}}<br />
*the sub-factor has a variance<br />
*variance name is {{cc|my_var}}<br />
*the diagonal position in $$\Sigma$$ is #1.<br />
<br />
Contrarily to variables, a sub-factor can have only one specifier assigned. That is, {{lmt}} would not accept a bi-variate model<br />
y1=mu*b1+id*u1(v(myvar(1))<br />
y2=mu*b2+id*u1(v(myvar(2))<br />
because the two specifiers assigned to {{cc|u1}}, {{cc|(v(myvar(1))}} and {{cc|(v(myvar(2)}} differ.<br />
<br />
==== Polynomials ====<br />
{{lmt}} allows for random and fixed regression on polynomials of the general form $$y=f(x)b+e$$, where $$y$$ is the response variable, $$x$$ is the co-variable, $$f(x)$$ is the polynomial function of $$x$$, and $$e$$ is the residual. Polynomial functions are written [[Parameter_file_elements#.3Cpoly.3E|into the space of a particular xml element of the parameter file]]<br />
===== User defined polynomials =====<br />
Polynomials expressions can be freely defined by the user but must not have more than one variable, where that single variable '''must be x'''. That is polynomial expression<br />
3*x^2+exp(x)<br />
is a valid, whereas expressions<br />
3*y^2+exp(y)<br />
3*x^2+exp(y)<br />
are not valid as a variable named y is not supported.<br />
===== Hard-coded polynomials =====<br />
For convenience reasons complex polynomials are hard-coded and can be referenced by their hard-coded abbreviation.<br />
<br />
{|class="wikitable"<br />
!polynomial<br />
!abbreviation<br />
|-<br />
|Legendre order 0<br />
|l0<br />
|-<br />
|Legendre order 1<br />
|l1<br />
|-<br />
|Legendre order 2<br />
|l2<br />
|-<br />
|Legendre order 3<br />
|l3<br />
|-<br />
|Legendre order 4<br />
|l4<br />
|-<br />
|Legendre order 5<br />
|l5<br />
|-<br />
|Legendre order 6<br />
|l6<br />
|-<br />
|Legendre order 7<br />
|l7<br />
|}<br />
<br />
That is, instead of writing <code>0.5*(5*x^3-3*x)</code> one can simply write <code>l3</code>.<br />
<br />
=====Referencing polynomials in equations=====<br />
Including polynomials directly into the equation would have meant that for multi-trait models complex polynomials would have been written repeatedly into the respective variable specifier which is an error prone process. Therefore, as explained in [[#Variable specifier]] polynomials are referenced in the variable specifier via using [[Parameter_file_elements#.3Cpoly.3E|the number of that line inside the parameter file element in which they occur]].<br />
<br />
=====Polynomial variable expansion and $$\Sigma$$ dimensions in random regression models=====<br />
If a [[#Variables|variable]] has a [[#Variable specifiers|variable specifier]] assigned which contains polynomials, e.g<br />
z(t(co(t(i);p(1,2);n(id)))<br />
and the associated [[#Sub-factors|sub-factor]] has a [[#Sub-factor specifiers| sub-factor specifier]] assigned which declares the sub-factor to be random, e.g.<br />
z(t(co(t(i);p(1,2);n(id)))*u(v(myvar(2,3)),<br />
it must be assured that the number of referenced $$\Sigma$$ diagonal elements in the sub-factor specifier is equal to the number of referenced polynomials in the variable specifier. Further, the first referenced polynomial is related to the first referenced diagonal element, the second to the second and so forth.<br />
<br />
A miss-fit between the number of referenced polynomials and the number of referenced $$\Sigma$$ diagonal elements will cause an error stop.<br />
<br />
==={{lmt}}'s factor naming convention===<br />
<br />
{{lmt}} models as many factors as there are independent co-variance structures in the model, a factor for all fixed classification variables, and a factor for all fixed continuous co-variables. These factors are internally named, where the internal names are used in the output files, in output file names, and to override defaults in the parameter file. The convention used to name the factors is:<br />
<br />
*"fxco" is the default name for the factor modelling the fixed classification variables and fixed continuous variables<br />
*the names of random factors are user defined where the actual name is that of the variance<br />
<br />
===Treatment of fixed continuous variables===<br />
{{lmt}} will center fixed continuous variables. That is, the polynomial $$x+x^2$$ becomes $$x-\overline{x}+(x-\overline{x})^2$$. Nested variables will be centered within their nesting. Centering implies that one should not fit an intercept via $$x^0$$ as it will results in an error message. However, centering can be explicitly switched off in the specifier of each variable.<br />
<br />
===Column rank of $$X$$===<br />
lmt will try to find and remove linear dependencies in $$X$$. However, the respective computations are applied within trait and include only fixed classification variables. That means fitting classification variables implicitly via applying polynomials of power zero to a continuous co-varibales, or switching off the centering of continuous co-variables, can lead to linear dependencies in $$X$$ which are not accounted for. Then subsequent operations may fail or results maybe incorrect.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Linear_mixed_models_in_lmt&diff=1380Linear mixed models in lmt2022-03-04T02:02:19Z<p>Boerner: /* Getting $$X$$ to full column rank */</p>
<hr />
<div>=== Matrix notation, factors and sub-factors ===<br />
<br />
Consider the multi-variate linear mixed model<br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2 \\<br />
y_3<br />
\end{array}<br />
\right)<br />
=<br />
\left(<br />
\begin{array}{ccc}<br />
X_1 & 0 & 0 \\<br />
0 & X_2 & 0 \\<br />
0 & 0 & X_3<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2 \\<br />
b_3<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{ccc}<br />
Z_1 & 0 & 0\\<br />
0 & Z_2 & 0\\<br />
0 & 0 & Z_3<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_1 \\<br />
u_2 \\<br />
u_3<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2 \\<br />
e_3<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where $$(y_1,y_2,y_3)'$$, $$(b_1,b_2,b_3)'$$, $$(u_1,u_2,u_3)'$$ and $$(e_1,e_2,e_3)'$$ are vectors of response variables, effects of fixed factors, effects of random factors and effects of residuals respectively, and matrices<br />
$$\left(<br />
\begin{array}{ccc}<br />
X_1 & 0 & 0 \\<br />
0 & X_2 & 0 \\<br />
0 & 0 & X_3<br />
\end{array}<br />
\right)$$, and<br />
$$<br />
\left(<br />
\begin{array}{ccc}<br />
Z_1 & 0 & 0\\<br />
0 & Z_2 & 0\\<br />
0 & 0 & Z_3<br />
\end{array}<br />
\right)<br />
$$ are block-diagonal design matrices linking effects in the respective vectors to their related response variables. In usual mixed model terminology $$b_1$$, $$b_2$$ and $$b_3$$ are called fixed factors, and $$u_1$$, $$u_2$$ and $$u_3$$ are called random factors. Ignoring the residual the above model has in total 6 factors.<br />
<br />
However, the model maybe rewritten in matrix formulation as<br />
<br />
$$vec(Y)=Xvec(B)+Zvec(U)+vec(E)$$,<br />
<br />
where $$vec$$ is the [https://en.wikipedia.org/wiki/Vectorization_(mathematics) vectorization operator], $$Y=[y_1,y_2,y_3]$$, $$B=[b_1,b_2,b_3]$$, $$U=[u_1,u_2,u_3]$$ and $$E=[e_1,e_2,e_3]$$ are column matrices of response variables, the effects of the fixed and random factor, and the residuals, respectively, and<br />
$$X=\left(<br />
\begin{array}{ccc}<br />
X_1 & 0 & 0 \\<br />
0 & X_2 & 0 \\<br />
0 & 0 & X_3<br />
\end{array}<br />
\right)$$, and<br />
$$Z=<br />
\left(<br />
\begin{array}{ccc}<br />
Z_1 & 0 & 0\\<br />
0 & Z_2 & 0\\<br />
0 & 0 & Z_3<br />
\end{array}<br />
\right)<br />
$$. The distribution assumption for the random components in the model are $$vec(U^{'})\sim N((0,0,0)',\Gamma_u \otimes \Sigma_u)$$ and $$vec(E^{'})\sim N((0,0,0)',\Gamma_e \otimes \Sigma_e)$$. Note that the column and row dimensions of $$U$$ are determined by the column dimension of $$\Sigma_u$$ and $$\Gamma_u$$ respectively.<br />
<br />
Slightly different to the above terminology, {{lmt}} refers to $$B$$ and $$U$$ as factors, and therefore the model has only two factors, whereas the columns in $$B$$ and $$U$$ are referred to as '''sub-factors'''. <br />
<br />
Following the above matrix notation {{lmt}} will always invoke only one factor for all modelled fixed classification variables and only one factor for all modelled fixed continuous co-variables. Sub-factors are summarized into a single random factors if they share the same $$\Sigma$$ matrix. Thus, {{lmt}} will invoke as many random factors as there are different $$\Gamma \otimes \Sigma$$ constructs. That is, in {{lmt}} terminology the multi-variate model<br />
<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2 \\<br />
y_3<br />
\end{array}<br />
\right)<br />
=<br />
\left(<br />
\begin{array}{ccc}<br />
X_1 & 0 & 0 \\<br />
0 & X_2 & 0 \\<br />
0 & 0 & X_3<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2 \\<br />
b_3<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{cccccc}<br />
Z_{d,1} & 0 & 0 & Z_{m,1} & 0 & 0\\<br />
0 & Z_{d,2} & 0 & 0 & Z_{m,2} & 0\\<br />
0 & 0 & Z_{d,3} & 0 & 0 & Z_{m,3}\\<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
u_{d,1} \\<br />
u_{d,2} \\<br />
u_{d,3} \\<br />
u_{m,1} \\<br />
u_{m,2} \\<br />
u_{m,3}<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{ccc}<br />
W_1 & 0 & 0\\<br />
0 & W_2 & 0\\<br />
0 & 0 & W_3<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
v_1 \\<br />
v_2 \\<br />
v_3<br />
\end{array}<br />
\right)<br />
+<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2 \\<br />
e_3<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
with<br />
$$(u_{d,1},u_{d,2},u_{d,3},u_{m,1},u_{m,2},u_{m,3})'\sim N((0,0,0,0,0,0)',\Sigma_u \otimes \Gamma_u)$$ and $$(v_1,v_2,v_3)'\sim N((0,0,0)',\Sigma_v \otimes \Gamma_v)$$, rewritten as $$vec(Y)=Xvec(B)+Zvec(U)+Wvec(V)+vec(E)$$ will have only 3 factors, $$B$$, $$U$$ and $$V$$ with $$b_1,b_2,b_3$$, $$u_{d,1},u_{d,2},u_{d,3},u_{m,1},u_{m,2},u_{m,3}$$ and $$v_1,v_2,v_3$$ being subfactors of $$U$$ and $$V$$ respectively.<br />
<br />
=== Model syntax ===<br />
<br />
Thee syntax for communicating the model to {{lmt}} is effectively: "'''just write the model'''", where the model is written [[Parameter_file_elements#.3Ceqn.3E|into the space of a particular xml element of the parameter file]].<br />
<br />
<br />
Note that {{lmt}} will only check whether the specified model can be built, not whether the model is meaningful or allows for a statistical inference.<br />
<br />
==== An example ====<br />
An example for a valid {{lmt}} model string would be <br />
y=x*b+age(t(co(p(1,2))))*c+id*u(v(my_var(1))).<br />
<br />
The components of the model string are<br />
*the [[#Varibales|response variable]] {{cc|y}}, which must be a column name in the data file<br />
*[[#Variables|model variables]] {{cc|x}}, {{cc|age}} and {{cc|id}}, which must be a column names in the data file<br />
*[[#Sub-factors|sub-factors]] {{cc|b}}, {{cc|c}} and {{cc|u}} which are user-defined alpha-numeric character strings<br />
*[[#Relational operators|relation operators]] {{cc|1==}}, {{cc|*}} and {{cc|+}}<br />
*a [[#Variable specifiers|variable specifier]] {{cc|(t(co(p(1,2))))}} used to provide further information about variable {{cc|age}}<br />
*a [[#Sub-factor specifiers|sub-factor specifier]] {{cc|(v(my_var(1)))}} used to provide further information about sub-factor {{cc|u}}<br />
<br />
==== Variables ====<br />
Response variables and model variables are named using user-defined alpha-numeric character strings. These character strings must be column names in the data file. There is no size limitation for the variables names.<br />
<br />
Model variables can be used in several equations. That is, the bi-variate model<br />
y1=x*b1<br />
y2=x*b2,<br />
with variables {{cc|x, y1 and y2}} being column names in the data file, is equivalent to the model<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{cc}<br />
X & 0 \\<br />
0 & X<br />
\end{array}<br />
\right)<br />
\left(<br />
\begin{array}{c}<br />
b_1 \\<br />
b_2<br />
\end{array}<br />
\right)+<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
==== Sub-factors ====<br />
Sub-factors are named using user-defined alpha-numeric character strings. There is no size limitation for the variables names.<br />
<br />
Contrarily to using variables across traits, using a sub-factor across traits changes the model. That is model<br />
y1=x*b1<br />
y2=x*b1<br />
is equivalent to<br />
$$<br />
\left(<br />
\begin{array}{c}<br />
y_1 \\<br />
y_2<br />
\end{array}<br />
\right)=<br />
\left(<br />
\begin{array}{c}<br />
X \\<br />
X <br />
\end{array}<br />
\right)<br />
\begin{array}{c}<br />
b_1 \\<br />
\end{array}<br />
+<br />
\left(<br />
\begin{array}{c}<br />
e_1 \\<br />
e_2<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
==== Relational operators ====<br />
The rules for using relational operators are<br />
*{{cc|1==}} links a single response variable to the model<br />
*{{cc|*}} links a model variable to it's sub-factor, which together form a model term<br />
*{{cc|+}} concatenates different model terms.<br />
<br />
==== Specifiers ====<br />
Variables and sub-factors maybe accompanied by a specifier. A specifier is a [https://en.wikipedia.org/wiki/Tree_structure#Nested_parentheses tree diagramm] in [https://en.wikipedia.org/wiki/Newick_format Newick format] with all nodes named, but leaf nodes can be unnamed, and where the root node name is the variable or sub-factor name. The specifier provides additional information about a variable or sub-factor. The {{lmt}} version of the above [https://en.wikipedia.org/wiki/Newick_format tree diagram] differs in that<br />
*the parent nodes precede child nodes<br />
*child nodes within the same parent node are separated by semicolon<br />
*sibling nodes can be mutually exclusive, that is only one sibling node maybe allowed<br />
*leaf nodes maybe not named but contain additional, maybe comma-separated information<br />
*if a child node is marked as default, the child node and it's immediate parent node can be omitted<br />
*if a node is marked as optional it can be omitted. if an optional node is used it's compulsory child nodes must be included<br />
===== Variable specifiers =====<br />
Variable specifiers are used to communicate further information which may be that the variable<br />
*is continuous but real numbers<br />
*is continuous but integer numbers<br />
*is a genetic group regression matrix<br />
*undergoes a polynomial expansion<br />
*is associated to a nesting variable<br />
etc.<br />
<br />
The [https://en.wikipedia.org/wiki/Tree_structure tree diagram] for the variable specifier is<br />
<br />
[[File:variabletree.jpg|1000px|]]<br />
<br />
with the [https://en.wikipedia.org/wiki/Tree_structure#Nested_parentheses nested parentheses] representation written as<br />
<br />
''variable''('''t'''(<span style="color:red;">'''co'''</span>('''t'''(<span style="color:red;">'''i'''</span>;<span style="color:red;">'''r'''</span>);'''p'''(polynomial ids);'''n'''(''variable''));<span style="color:red;">'''cl'''</span>;<span style="color:red;">'''gg'''</span>(''pedigree'')))<br />
<br />
Note that the above representation would '''not''' yield a valid specifier useable in an equation as the diagram contains sibling nodes which are mutually exclusive, thus allowing only one of the sibling node to occur in the specifier. That is valid specifiers would be<br />
''variable''('''t'''('''cl'''))<br />
''variable''('''t'''('''co'''))<br />
''variable''('''t'''('''gg'''(''pedigree'')))<br />
''variable''('''t'''('''co'''('''t'''('''r''');'''p'''(polynomial id);'''n'''(''variable''))))<br />
''variable''('''t'''('''co'''('''t'''('''i''');'''p'''(polynomial id);'''n'''(''variable''))))<br />
Since a default-determining leave node and it's immediate parent node can be omitted the following equality holds:<br />
''variable''('''t'''('''cl'''))=''variable''<br />
''variable''('''t'''('''co'''('''t'''('''r'''))))=''variable''('''t'''('''co'''))<br />
<br />
A variable can have several different specifiers. Notwithstanding the statistical soundness, an example would be<br />
y=x(t(co))*b + x(t(co(n(g))))*c<br />
where {{cc| y, x and g}} are columns names in the data file. The equivalent model would be<br />
$$<br />
y=D_x ib+D_x X_gc + e<br />
$$<br />
where $$D_x$$ is a diagonal matrix constructed from {{cc|x}}, $$i$$ is a vector of ones, $$X_g$$ is a design matrix constructed from classification variable $$g$$, and $$b$$ and $$c$$ are the sub-factors.<br />
<br />
===== Sub-factor specifiers =====<br />
Sub-factor specifiers are used to communicate further information which may be that the sub-factor<br />
*is a random sub-factor<br />
*to which variance it is related to<br />
*which diagonal element in the $$\Sigma$$ matrix of the variance it is related to<br />
The [https://en.wikipedia.org/wiki/Tree_structure tree diagram] for the sub-factor specifier is<br />
<br />
[[File:subfactortree.jpg|500px|]]<br />
<br />
with the [https://en.wikipedia.org/wiki/Tree_structure#Nested_parentheses nested parentheses] representation written as<br />
''sub-factor''('''v'''(''variance name''(diagonal position)))<br />
<br />
According to the tree diagram the sub-factor specifier in the [[#An example|example model string]] translates to<br />
*sub-factor name is {{cc|u}}<br />
*the sub-factor has a variance<br />
*variance name is {{cc|my_var}}<br />
*the diagonal position in $$\Sigma$$ is #1.<br />
<br />
Contrarily to variables, a sub-factor can have only one specifier assigned. That is, {{lmt}} would not accept a bi-variate model<br />
y1=mu*b1+id*u1(v(myvar(1))<br />
y2=mu*b2+id*u1(v(myvar(2))<br />
because the two specifiers assigned to {{cc|u1}}, {{cc|(v(myvar(1))}} and {{cc|(v(myvar(2)}} differ.<br />
<br />
==== Polynomials ====<br />
{{lmt}} allows for random and fixed regression on polynomials of the general form $$y=f(x)b+e$$, where $$y$$ is the response variable, $$x$$ is the co-variable, $$f(x)$$ is the polynomial function of $$x$$, and $$e$$ is the residual. Polynomial functions are written [[Parameter_file_elements#.3Cpoly.3E|into the space of a particular xml element of the parameter file]]<br />
===== User defined polynomials =====<br />
Polynomials expressions can be freely defined by the user but must not have more than one variable, where that single variable '''must be x'''. That is polynomial expression<br />
3*x^2+exp(x)<br />
is a valid, whereas expressions<br />
3*y^2+exp(y)<br />
3*x^2+exp(y)<br />
are not valid as a variable named y is not supported.<br />
===== Hard-coded polynomials =====<br />
For convenience reasons complex polynomials are hard-coded and can be referenced by their hard-coded abbreviation.<br />
<br />
{|class="wikitable"<br />
!polynomial<br />
!abbreviation<br />
|-<br />
|Legendre order 0<br />
|l0<br />
|-<br />
|Legendre order 1<br />
|l1<br />
|-<br />
|Legendre order 2<br />
|l2<br />
|-<br />
|Legendre order 3<br />
|l3<br />
|-<br />
|Legendre order 4<br />
|l4<br />
|-<br />
|Legendre order 5<br />
|l5<br />
|-<br />
|Legendre order 6<br />
|l6<br />
|-<br />
|Legendre order 7<br />
|l7<br />
|}<br />
<br />
That is, instead of writing <code>0.5*(5*x^3-3*x)</code> one can simply write <code>l3</code>.<br />
<br />
=====Referencing polynomials in equations=====<br />
Including polynomials directly into the equation would have meant that for multi-trait models complex polynomials would have been written repeatedly into the respective variable specifier which is an error prone process. Therefore, as explained in [[#Variable specifier]] polynomials are referenced in the variable specifier via using [[Parameter_file_elements#.3Cpoly.3E|the number of that line inside the parameter file element in which they occur]].<br />
<br />
=====Polynomial variable expansion and $$\Sigma$$ dimensions in random regression models=====<br />
If a [[#Variables|variable]] has a [[#Variable specifiers|variable specifier]] assigned which contains polynomials, e.g<br />
z(t(co(t(i);p(1,2);n(id)))<br />
and the associated [[#Sub-factors|sub-factor]] has a [[#Sub-factor specifiers| sub-factor specifier]] assigned which declares the sub-factor to be random, e.g.<br />
z(t(co(t(i);p(1,2);n(id)))*u(v(myvar(2,3)),<br />
it must be assured that the number of referenced $$\Sigma$$ diagonal elements in the sub-factor specifier is equal to the number of referenced polynomials in the variable specifier. Further, the first referenced polynomial is related to the first referenced diagonal element, the second to the second and so forth.<br />
<br />
A miss-fit between the number of referenced polynomials and the number of referenced $$\Sigma$$ diagonal elements will cause an error stop.<br />
<br />
==={{lmt}}'s factor naming convention===<br />
<br />
{{lmt}} models as many factors as there are independent co-variance structures in the model, a factor for all fixed classification variables, and a factor for all fixed continuous co-variables. These factors are internally named, where the internal names are used in the output files, in output file names, and to override defaults in the parameter file. The convention used to name the factors is:<br />
<br />
*"fxco" is the default name for the factor modelling the fixed classification variables and fixed continuous variables<br />
*the names of random factors are user defined where the actual name is that of the variance<br />
<br />
===Treatment of fixed continuous variables===<br />
{{lmt}} will center fixed continuous variables. That is, the polynomial $$x+x^2$$ becomes $$x-\overline{x}+(x-\overline{x})^2$$. Nested variables will be centered within their nesting. Centering implies that one should not fit an intercept via $$x^0$$ as it will results in an error message. However, centering can be explicitly switched off in the specifier of each variable.<br />
<br />
===Getting $$X$$ to full column rank===<br />
lmt will try to find and remove linear dependencies in $$X$$. However, the respective algorithm is applied within trait and includes only fixed classification variables. That means that fitting classification variables implicitly via applying a polynomial of power zero to a continuous co-varibale, or switching off the centering of continuous co-variables can lead to linear dependecies in $$X$$ which are not accounted for. Then subsequent operations may fail or results maybe incorrect.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Genomic_data_in_lmt&diff=1379Genomic data in lmt2022-03-04T01:21:12Z<p>Boerner: /* Single step SNP-BLUP */</p>
<hr />
<div>lmt can account for genomic data via genomic relationship matrices $$G$$ and single step relationship matrices $$H$$ where single step G-BLUP, single step GT-BLUP, and single step SNP-BLUP are supported. lmt accepts plain marker data and will calculate all necessary derivatives required by the model. Genotypes can be scaled using average or marker specific allele content variance (2pq), and allele frequencies are either calculated from the data, or read from user specified input files. Futher, if requested $$G$$ can be adjusted to fit $$A$$, even for models where $$G$$ is not build(e.g. single step SNP-BLUP).<br />
<br />
==Single step SNP-BLUP==<br />
<br />
lmt's Single step SNP-BLUP model uses the approach described in Liu and Goddard 2014, where the adverse of the singe step SN-PBLUP variance structure can be written as<br />
<br />
$$<br />
\left(<br />
\begin{array}{ccc}<br />
(A^{n,n})^{-1}\otimes \Sigma_g +\xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & \xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma) & \xi M\zeta\gamma \\<br />
(A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma & M\zeta\gamma \\<br />
\gamma \zeta M^{'}\xi^{'} & \gamma \zeta M^{'}& \zeta\gamma<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where $$M$$ is a centered and scaled matrix of marker counts, $$\zeta = \Omega_{m}(\Gamma_m \otimes I)\Omega_{m}^{'}$$, $$\xi = A_{n,g}A_{g,g}^{-1}$$, $$\Sigma_g$$ is the global genetic co-variance matrix, $$\lambda$$ is the polygenic weight and $$\gamma$$ is the genomic weight. In most applications $$\gamma \zeta = \gamma I\otimes \Sigma_g$$. Note that in the instruction file $$\zeta$$ is parametrized independently of $$\Sigma_g$$, but it is advisable to ensure that the following equality holds $$\gamma 1'\zeta 1==\gamma \Sigma_g$$.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Genomic_data_in_lmt&diff=1378Genomic data in lmt2022-03-04T01:20:20Z<p>Boerner: /* Single step SNP-BLUP */</p>
<hr />
<div>lmt can account for genomic data via genomic relationship matrices $$G$$ and single step relationship matrices $$H$$ where single step G-BLUP, single step GT-BLUP, and single step SNP-BLUP are supported. lmt accepts plain marker data and will calculate all necessary derivatives required by the model. Genotypes can be scaled using average or marker specific allele content variance (2pq), and allele frequencies are either calculated from the data, or read from user specified input files. Futher, if requested $$G$$ can be adjusted to fit $$A$$, even for models where $$G$$ is not build(e.g. single step SNP-BLUP).<br />
<br />
==Single step SNP-BLUP==<br />
<br />
lmt's Single step SNP-BLUP model uses the approach described in Liu and Goddard 2014, where the adverse of the singe step SN-PBLUP variance structure can be written as<br />
<br />
$$<br />
\left(<br />
\begin{array}{ccc}<br />
(A^{n,n})^{-1}\otimes \Sigma_g +\xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & \xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma) & \xi M\zeta\gamma \\<br />
(A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma & M\zeta\gamma \\<br />
\gamma \zeta M^{'}\xi^{'} & \gamma \zeta M^{'}& \zeta\gamma<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where $$M$$ is a centered and scaled matrix of marker counts, $$\zeta = \Omega_{m}(\Gamma_m \otimes I)\Omega_{m}^{'}$$, $$\xi = A_{n,g}A_{g,g}^{-1}$$, $$\Sigma_g$$ is the global genetic co-variance matrix, $$\lambda$$ is the polygenic weight and $$\gamma$$ is the genomic weight. In most applications $$\gamma \zeta = \gamma I\otimes \Sigma_g$$. Note that in the instruction file $$\zeta$$ is parametrized independently of $$\Sigma_g$$, but it is advisable that the following equality holds $$\gamma 1'\zeta 1==\gamma \Sigma_g$$.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Genomic_data_in_lmt&diff=1377Genomic data in lmt2022-03-04T01:12:49Z<p>Boerner: /* Single step SNP-BLUP */</p>
<hr />
<div>lmt can account for genomic data via genomic relationship matrices $$G$$ and single step relationship matrices $$H$$ where single step G-BLUP, single step GT-BLUP, and single step SNP-BLUP are supported. lmt accepts plain marker data and will calculate all necessary derivatives required by the model. Genotypes can be scaled using average or marker specific allele content variance (2pq), and allele frequencies are either calculated from the data, or read from user specified input files. Futher, if requested $$G$$ can be adjusted to fit $$A$$, even for models where $$G$$ is not build(e.g. single step SNP-BLUP).<br />
<br />
==Single step SNP-BLUP==<br />
<br />
lmt's Single step SNP-BLUP model uses the approach described in Liu and Goddard 2014, where the adverse of the singe step SN-PBLUP variance structure can be written as<br />
<br />
$$<br />
\left(<br />
\begin{array}{ccc}<br />
(A^{n,n})^{-1}\otimes \Sigma_g +\xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & \xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma) & \xi M\zeta\gamma \\<br />
(A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma & M\zeta\gamma \\<br />
\gamma \zeta M^{'}\xi^{'} & \gamma \zeta M^{'}& \zeta\gamma<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where $$\zeta = \Omega_{m}(\Gamma_m \otimes I)\Omega_{m}^{'}$$ and $$\xi = A_{n,g}A_{g,g}^{-1}$$, $$\Sigma_g$$ is the global genetic co-variance matrix, $$\lambda$$ is the polygenic weight and $$\gamma$$ is the genomic weight. Note that when parametrizing this variance structure the following equality should hold $$\gamma 1'\zeta 1==\gamma \Sigma_g$$. Note that in most case $$\gamma \zeta == I\otimes \gamma \Sigma_g$$.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Genomic_data_in_lmt&diff=1376Genomic data in lmt2022-03-04T01:12:12Z<p>Boerner: </p>
<hr />
<div>lmt can account for genomic data via genomic relationship matrices $$G$$ and single step relationship matrices $$H$$ where single step G-BLUP, single step GT-BLUP, and single step SNP-BLUP are supported. lmt accepts plain marker data and will calculate all necessary derivatives required by the model. Genotypes can be scaled using average or marker specific allele content variance (2pq), and allele frequencies are either calculated from the data, or read from user specified input files. Futher, if requested $$G$$ can be adjusted to fit $$A$$, even for models where $$G$$ is not build(e.g. single step SNP-BLUP).<br />
<br />
==Single step SNP-BLUP==<br />
<br />
lmt's Single step SNP-BLUP model uses the approach described in Liu and Goddard 2014, where the adverse of the singe step SN-PBLUP variance structure can be written as<br />
<br />
$$<br />
\left(<br />
\begin{array}{ccc}<br />
(A^{n,n})^{-1}\otimes \Sigma_g +\xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & \xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma) & \xi M\zeta\gamma \\<br />
(A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma & M\zeta\gamma \\<br />
\gamma \zeta M^{'}\xi^{'} & \gamma \zeta M^{'}& \zeta\gamma<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where $$\zeta = \Omega_{m}(\Gamma_m \otimes I)\Omega_{m}^{'}$$ and $$\xi = A_{n,g}A_{g,g}^{-1}$$, $$\Sigma_g$$ is the global genetic co-variance matrix, $$\lambda$$ is the polygenic weight and $$\gamma$$ is the genomic weight. Note that when parametrizing this variance structure the following equality should hold $$\gamma 1'\zeta 1==\gamma \Sigma_g$$. Note that in most case $$\zeta == I\otimes \gamma \Sigma_g$$.</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Genomic_data_in_lmt&diff=1374Genomic data in lmt2022-03-04T01:07:43Z<p>Boerner: </p>
<hr />
<div>lmt can account for genomic data via genomic relationship matrices $$G$$ and single step relationship matrices $$H$$ where single step G-BLUP, single step GT-BLUP, and single step SNP-BLUP are supported. lmt accepts plain marker data and will calculate all necessary derivatives required by the model. Genotypes can be scaled using average or marker specific allele content variance (2pq), and allele frequencies are either calculated from the data, or read from user specified input files. Futher, if requested $$G$$ can be adjusted to fit $$A$$, even for models where $$G$$ is not build(e.g. single step SNP-BLUP).<br />
<br />
==Single step SNP-BLUP==<br />
<br />
lmt's Single step SNP-BLUP model uses the approach described in Liu and Goddard 2014, where the adverse of the singe step SN-PBLUP variance structure can be written as<br />
<br />
$$<br />
\left(<br />
\begin{array}{ccc}<br />
(A^{n,n})^{-1}\otimes \Sigma_g +\xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & \xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma) & \xi M\zeta\gamma \\<br />
(A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma & M\zeta\gamma \\<br />
\gamma \zeta M^{'}\xi^{'} & \gamma \zeta M^{'}& \zeta\gamma<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where $$\zeta = \Omega_{m}(\Gamma_m \otimes I)\Omega_{m}^{'}$$ and $$\xi = A_{n,g}A_{g,g}^{-1}$$, $$\Sigma_g$$ is the global genetic co-variance matrix, $$\lambda$$ is the polygenic weight and $$\gamma$$ is the genomic weight. Note that when parametrizing this variance structure the following equality should hold $$\gamma 1'\zeta 1==\gamma \Sigma_g$$</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Genomic_data_in_lmt&diff=1373Genomic data in lmt2022-03-04T00:20:53Z<p>Boerner: /* Single step SNP-BLUP */</p>
<hr />
<div>lmt can account for genomic data via genomic relationship matrices $$G$$ and single step relationship matrices $$H$$ where single step G-BLUP, single step GT-BLUP, and single step SNP-BLUP are supported<br />
<br />
==Single step SNP-BLUP==<br />
<br />
lmt's Single step SNP-BLUP model uses the approach described in Liu and Goddard 2014, where the adverse of the singe step SN-PBLUP variance structure can be written as<br />
<br />
$$<br />
\left(<br />
\begin{array}{ccc}<br />
(A^{n,n})^{-1}\otimes \Sigma_g +\xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & \xi (A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma) & \xi M\zeta\gamma \\<br />
(A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma)\xi^{'} & A_{g,g}\otimes \Sigma_g \lambda + M\zeta M^{'}\gamma & M\zeta\gamma \\<br />
\gamma \zeta M^{'}\xi^{'} & \gamma \zeta M^{'}& \zeta\gamma<br />
\end{array}<br />
\right)<br />
$$<br />
<br />
where $$\zeta = \Omega_{m}(\Gamma_m \otimes I)\Omega_{m}^{'}$$ and $$\xi = A_{n,g}A_{g,g}^{-1}$$, $$\Sigma_g$$ is the global genetic co-variance matrix, $$\lambda$$ is the polygenic weight and $$\gamma$$ is the genomic weight. Note that when parametrizing this variance structure the following equality should hold $$\gamma 1'\zeta 1==\gamma \Sigma_g$$</div>Boernerhttps://dmu.ghpc.au.dk/lmt/wiki/index.php?title=Genomic_data_in_lmt&diff=1372Genomic data in lmt2022-03-04T00:15:52Z<p>Boerner: Created page with "lmt can account for genomic data via genomic relationship matrices $$G$$ and single step relationship matrices $$H$$ where single step G-BLUP, single step GT-BLUP, and single step SNP-BLUP are supported ==Single step SNP-BLUP=="</p>
<hr />
<div>lmt can account for genomic data via genomic relationship matrices $$G$$ and single step relationship matrices $$H$$ where single step G-BLUP, single step GT-BLUP, and single step SNP-BLUP are supported<br />
<br />
==Single step SNP-BLUP==</div>Boerner