Parameter file elements

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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.

<model>[edit]

example host element element type purpose
<root>
 ..
 <model>
  <eqn attribute="strings">
   ..
  </eqn>
  <poly attribute="strings">
   ..
  </poly>
 </model>
</root>
root compulsory hosts information about the equations and the polynomials.

content:

  • compulsory element <eqn attributes="strings">
  • optional element <poly attributes="strings">

<eqn>[edit]

example host element element type purpose
<root>
 ..
 <model>
  <eqn attribute="strings">
   y1=x*b1+z*u1(v(g(1))
   y2=x*b2+z*u2(v(g(2))
   y3=x*b3+a(t(co(p(1,2);n(k))))*c1+z*u3(v(g(3)))
  </eqn>
  ..
 </model>
</root>
model compulsory hosts information about the equations.

content:

  • model strings which are escaped from the formatting rules by adding attributes="strings" to the start tag.

<poly>[edit]

example host element element type purpose
<root>
 ..
 <model>
  <poly attribute="strings">
   x^0
   x^2
   3*x^2+sqrt(sin(x))
  </poly>
  ..
 </model>
</root>
model optional 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.

content

  • polynomial strings which are escaped from the formatting rules by adding attributes="strings" to the start tag.

<pedigrees>[edit]

example host element element type purpose
<root>
 ..
 <pedigrees>
  pedigrees: a,b
  ...
 </pedigrees>
</root>
root automatic-optional hosts one to several elements each containing information about a specific pedigree

content:

  • key strings
word example type variable type variable values default explanation
pedigrees pedigrees: a,b compulsory csv word-list pedigree names none list content determines names of nominated-compulsory elements
  • nominated-compulsory elements

<pedigree name>[edit]

example host element element type purpose
<root>
 ..
 <pedigrees>
  pedigrees: myped
  ..
  <myped>
   file: myped.csv
   switch: selfing
   phantomparents: 2
  </myped>
  ..
 </pedigrees>
</root>
pedigrees nominated-compulsory hosts information about a specific pedigree identified by pedigree name

content:

  • key strings
word example type variable type variable values default explanation
file file: myped.csv compulsory word file name none list content determines the name of the file containing the pedigree
switch switch: selfing optional csv-word-list selfing,probabilistic none list content determines pedigree properties.
  • selfing: both parents can have the same id
  • probabilistic: each individual can have more than 1 pair of parents
phantomparents phantomparents: 2 optional single numeric value positive integer none integer number determines the number of individuals at the top of the pedigree which are phantom parents

<genotypes>[edit]

example host element element type purpose
<root>
 ..
 <genotypes>
  genotypes: a,b
  ...
 </genotypes>
</root>
root automatic-optional hosts one to several elements each containing information about different sets of genotypes

content:

  • key strings
word example type variable type variable values default explanation
genotypes genotypes: a,b compulsory csv word-list genotype names none list content determines names of nominated-compulsory elements
  • nominated-compulsory elements

<genotype name>[edit]

example host element element type purpose
<root>
 ..
 <genotypes>
  genotypes: mygn
  ..
  <mygn>
   file: genotypes.txt
   pedigree: myped
   cross: crossref.csv
  </mygn>
  ..
 </genotypes>
</root>
genotypes nominated-compulsory hosts information about a specific set of genotypes identified by genotype name

content:

  • key strings
word example type variable type variable values default explanation
file file: genotype.txt compulsory word file name none content determines the name of the file containing the genotypes
cross cross: mycross.csv optional word file name none content determines the name of the file containing the pedigree ids related to the genotypes
pedigree pedigree: myped optional word pedigree name none content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file
pqfile pqfile: mypq.csv optional word file name none 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.
switch switch: ignorefixed optional csv word-list ignorefixed,ignoremissing none
  • ignorefixed: fixed markers are ignored but may lead to program crash or spurious results latter on
  • ignoremissing: marker coded as missing(3) are set to 0.

<grms>[edit]

example host element element type purpose
<root>
 ..
 <grms>
  grms: a,b
  ...
 </grms>
</root>
root automatic-optional hosts one to several elements each containing information about a specific grm

content:

  • key strings
word example type variable type variable values default explanation
grms grms: x,y compulsory csv word-list grm names none list content determines names of nominated-compulsory elements
  • nominated-compulsory elements

<grm name>[edit]

example host element element type purpose
<root>
 ..
 <grms>
  grms: mygrm
  ..
  <mygrm>
   genotype: mygn
   method: YA
  </mygrm>
  ..
 </genotypes>
</root>
grms nominated-compulsory hosts information about a specific grm identified by grm name

content:

  • key strings
word example type variable type variable values default explanation
file file: mygrm.csv compulsory word file name none content determines the name of the file containing the grm. mutually exclusive with keyword genotype.
genotype genotype: mygn compulsory word genotype name none content determines the genotype element to be used for building the grm. mutually exclusive with keyword file.
cross cross: mycross.csv optional word file name none 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.
pedigree pedigree: myped optional word pedigree name none 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.
method method:YA optional alternative words VR|YA VR content determines the method to be used for building a grm from genotypes
  • VR: VanRaden Method 1 is used
  • YA: VanRaden Method 2(method Yang) is used

<vars>[edit]

example host element element type purpose
<root>
 ..
 <vars>
  vars: g,p
  ...
 </vars>
</root>
root compulsory hosts one to several elements each containing information about a specific variance.

content:

  • key strings
word example type variable type variable values default explanation
vars vars: g,p compulsory csv word-list variance names none list content determines names of nominated-compulsory elements
  • nominated-compulsory elements
  • compulsory element <res>

<Kronecker products>[edit]

<res>[edit]

example host element element type purpose
<root>
 ..
 <vars>
  ..
  <res>
   <sigma>
    ..
   </sigma>
  </res>
  ..
 </vars>
</root>
vars compulsory hosts information about the residual variance structure.

content:


<variance name>[edit]

example host element element type purpose
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <sigma>
    ..
   </sigma>
   <gamma>
    ..
   </gamma>
  </myvar>
  ..
 </vars>
</root>
vars nominated-compulsory hosts information about variance structure identified by variance name.

content:

  • key strings
word example type variable type variable values default explanation
type type: kronecker optional word kronecker,snpblup_1 kronecker determines whether the variance structure deviates from a Kronecker product.

<sigma>[edit]

example host element element type purpose
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <sigma>
    ..
   </sigma>
   ..
  </myvar>
  ..
 </vars>
</root>
variance name compulsory hosts information about $$\Sigma$$ as part of $$\Gamma \otimes \Sigma$$.

content:

  • key strings
word example type variable type variable values default explanation
file file: mymatrix.csv compulsory word file name none content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with <matrix attributes="array">.
type type: block optional word block none determines that $$\Sigma$$ is equal to $$\Theta$$
scale scale: 0.05 optional single numeric value real number>0.0 none multiplies $$\Sigma$$ once by the provided value after reading.
priordf priordf: 10 optional single numeric value real number>=0.0 0.0 prior degree of freedom when doing Gibbs sampling
  • optional element <matrix attributes="array">
<matrix attributes="array">[edit]
example host element element type purpose
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <sigma>
    <matrix attributes="array">
     5.0,0.5
     0.5,1.8
    </matrix>
   </sigma>
   ..
  </myvar>
  ..
 </vars>
</root>
sigma optional hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string file: .

<gamma>[edit]

example host element element type purpose
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <gamma>
    ..
   </gamma>
   ..
  </myvar>
  ..
 </vars>
</root>
variance name optional hosts information about $$\Gamma$$ as part of $$\Gamma \otimes \Sigma$$.

content:

  • mutually exclusive elements <A>, <H>, <G> and <E>
<A>[edit]
example host element element type purpose
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <gamma>
    <A>
     pedigree: myped
    </A>
   </gamma>
   ..
  </myvar>
  ..
 </vars>
</root>
gamma compulsory hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree pedigree name.

content:

  • key strings
word example type variable type variable values default explanation
pedigree pedigree: myped optional word pedigree name none content determines the name of a pedigree previously invoked to be used to construct A.
switch switch: gg optional csv word-list gg none
  • gg: the pedigree contains genetic groups which will be fitted as random
<H>[edit]
example host element element type purpose
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <gamma>
    <H>
     type: tblup
     pedigree: myped
     genotype: mygn
     aweight: 0.05
     switch: adjustg2a
    </H>
   </gamma>
   ..
  </myvar>
  ..
 </vars>
</root>
gamma compulsory 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
  • via a grm element for single step H-BLUP models
  • via a genotype element for single step T-BLUP models

Note that for type:tblup it is not necessary to have an automatic-optional <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.

content:

  • key strings
word example type variable type variable values default explanation
pedigree pedigree: myped compulsory word pedigree name none content determines the name of a pedigree element to be used to construct H.
type type: tblup optional word tblup|gblup gblup content determines the way the inverse of H is constructed.
grm grm: mygrm conditional-compulsory word pedigree name none content determines the grm element to be used to construct H. compulsory for type: hblup.
genotype genotype: mygn conditional-compulsory word genotype name none content determines the genotype element to be used to construct H. compulsory for type: tblup.
aweight aweight: 0.05 optional single numeric value 0.0<=aweight<=1.0 0.0 blending of $$G$$ with $$A_{gg}$$ by $$G_w=aweight\times A_{gg}+(1-aweight)\times G$$
switch switch: adjustg2a optional csv word-list adjustg2a,gg,diag none
  • adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method
  • gg: the pedigree contains genetic groups which will be fitted as random
  • diag: calculate H diagonal elements and write to file (only supported for gblup).
grmdadd grmdadd: 0.05 optional single numeric value real number >=0.0 none value added to the diagonal of $$G$$ to ensure invertibility. The policy is
  • if aweight>0.0, nothing will be added to the diagonals
  • if aweight is not supplied or is zero:
    • if grmdadd is not supplied 0.001 will be added to the diagonals
    • otherwise grmdadd will be used
<G>[edit]
example host element element type purpose
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <gamma>
    <G>
     grm: mygrm
    </G>
   </gamma>
   ..
  </myvar>
  ..
 </vars>
</root>
gamma compulsory hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix.

content:

  • key strings
word example type variable type variable values default explanation
grmdadd grmdadd: 0.05 optional single numeric value real number >=0.0 none value added to the diagonal of $$G$$ to ensure invertibility.
<E>[edit]
example host element element type purpose
<root>
 ..
 <vars>
  ..
  vars: myvar
  <myvar>
   <gamma>
    <E>
     file: mygamma.csv
    </E>
   </gamma>
   ..
  </myvar>
  ..
 </vars>
</root>
gamma compulsory hosts information about $$\Gamma^{-1}$$ being uploaded from a file.

content:

  • key strings
word example type variable type variable values default explanation
file file: mygamma.csv compulsory word file name none content determines the file which contains $$\Gamma^{-1}$$.
type type: dense optional word dense|sparse_csr_ut sparse_csr_ut content determines the file storage of $$\Gamma^{-1}$$
  • dense: full squared symmetric matrix
  • sparse_csr_ut: squared symmetric sparse upper triangular matrix in csr format

<jobs>[edit]

example host element element type purpose
<root>
 ..
 <jobs>
  jobs: solve,yh
  ...
 </jobs>
</root>
root compulsory hosts one to several elements each containing information about a specific job

content:

  • key strings
word example type variable type variable values default explanation
jobs jobs: solve,yhat compulsory csv word-list solve,sample,pevsample,mcemreml,yhat none job sequence is determined by the list sequence. list content determines nominated-compulsory elements
  • nominated-compulsory elements
    • <solve>
    • <sample>
    • <pevsample>
    • <pevsolve>
    • <mcemreml>
    • <yhat>

<solve>[edit]

example host element element type purpose
<root>
 ..
 <jobs>
  ..
  <solve>
   solver: mysolver
  </solve>
  ..
 </jobs>
 ..
</root>
jobs conditional-compulsory hosts information about job solve

content:

  • key strings
word example type variable type variable values default explanation
solver solver: mysolver compulsory word solver name none solver name must be the name of a previously defined solver

<sample>[edit]

example host element element type purpose
<root>
 ..
 <jobs>
  jobs: sample,..
  <sample>
   sampler: mysampler
  </sample>
  ..
 </jobs>
 ..
</root>
jobs conditional-compulsory hosts information about job sample

content:

  • key strings
word example type variable type variable values default explanation
sampler sampler: mysampler compulsory word sampler name none sampler name must be the name of a previously defined sampler

<pevsample>[edit]

example host element element type purpose
<root>
 ..
 <jobs>
  jobs: pevsample,..
  <pevsample>
   sampler: mysampler
  </pevsample>
  ..
 </jobs>
 ..
</root>
jobs conditional-compulsory hosts information about job pevsample

content:

  • key strings
word example type variable type variable values default explanation
sampler sampler: mysampler compulsory word sampler name none sampler name must be the name of a previously defined sampler of type pev

<pevsolve>[edit]

example host element element type purpose
<root>
 ..
 <jobs>
  jobs: pevsolve,..
  <pevsolve>
   solver: mysolver
  </pevsolver>
  ..
 </jobs>
 ..
</root>
jobs conditional-compulsory hosts information about job pevsolve

content:

  • key strings
word example type variable type variable values default explanation
solver solver: mysolver compulsory word solver name none solver name must be the name of a previously defined solver
factor factor: gen compulsory word factor name none factor name must be the name of a random factor
levels levels: 5,10,20 optional csv integer list factor level ids none 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.
levelfile levelfile: myfile.csv optional word file name none 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.
nrhs nrhs: 50 optional integer number of right-hand sides 1000 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.

<mcemreml>[edit]

example host element element type purpose
<root>
 ..
 <jobs>
  jobs: mcemreml,..
  <mcemreml>
   emrounds: 500
   sampler: mysampler
  </mcemreml>
  ..
 </jobs>
 ..
</root>
jobs conditional-compulsory hosts information about job mcemreml

content:

  • key strings
word example type variable type variable values default explanation
emrounds emrounds: 500 compulsory numeric value positive integer none provides the number of mcemreml-rounds to run
sampler sampler: mysampler compulsory word sampler name none sampler name must be the name of a previously defined sampler

<yhat>[edit]

example host element element type purpose
<root>
 ..
 <jobs>
  jobs: yhat,..
  <yhat>
  </yhat>
  ..
 </jobs>
 ..
</root>
jobs conditional-compulsory hosts information about job yhat

Currently yhat has no key strings or nested elements defined.

<samplers>[edit]

example host element element type purpose
<root>
 ..
 <samplers>
  samplers: a,b,..
  ...
 </samplers>
</root>
root optional hosts one to several elements each containing information about a specific sampler

content:

  • key strings
word example type variable type variable values default explanation
samplers samplers: a compulsory csv word-list sampler names none list content determines nominated-compulsory elements
  • conditional-compulsory elements

<sampler name>[edit]

example host element element type purpose
<root>
 ..
 <samplers>
  samplers: a,..
   <a>
    ..
   </a>
 </samplers>
</root>
samplers conditional-compulsory hosts one of several mutually exclusive elements defining the type of sampler sampler name

content:

  • compulsory mutually exclusive elements
    • <singlepass>
    • <blocked>
    • <pev>

<singlepass>[edit]

example host element element type purpose
<root>
 ..
 <samplers>
  samplers: a,..
   <a>
    <singlepass>
     samples: 10000
     burnin: 1000
    </singlepass>
   </a>
 </samplers>
</root>
sampler name compulsory defines parameters of a sampler of type singlepass
  • key strings
word example type variable type variable values default explanation
samples samples: 100000 optional numeric value positive integer 10000 provides the total number of samples to draw
burnin burnin: 1000 optional numeric value positive integer 0 provides the number of samples to be discarded as burnin

<blocked>[edit]

example host element element type purpose
<root>
 ..
 <samplers>
  samplers: a,..
   <a>
    <blocked>
     samples: 10000
     burnin: 1000
    </blocked>
   </a>
 </samplers>
</root>
sampler name compulsory defines parameters of a sampler of type blocked
  • key strings
word example type variable type variable values default explanation
samples samples: 100000 optional numeric value positive integer 10000 provides the total number of samples to draw
burnin burnin: 1000 optional numeric value positive integer 0 provides the number of samples to be discarded as burnin

<pev>[edit]

example host element element type purpose
<root>
 ..
 <samplers>
  samplers: a,..
   <a>
    <pev>
     samples: 10000
     burnin: 1000
     chains: 10
    </pev>
   </a>
 </samplers>
</root>
sampler name compulsory defines parameters of a sampler of type pev
  • key strings
word example type variable type variable values default explanation
samples samples: 100000 optional numeric value positive integer 10000 provides the total number of samples to draw
burnin burnin: 1000 optional numeric value positive integer 0 provides the number of samples to be discarded as burnin
chains chains: 10 optional numeric value positive integer 1 provides the number of parallel chains to run
switch switch: trace optional word trace none changes sampler from sampling prediction error variances to sampling traces required for emreml

<solvers>[edit]

example host element element type purpose
<root>
 ..
 <solvers>
  solvers: a,b,..
  ...
 </solvers>
</root>
root optional hosts one to several elements each containing information about a specific solver

content:

  • key strings
word example type variable type variable values default explanation
solvers solvers: a compulsory csv word-list solver names none list content determines nominated-compulsory elements
  • conditional-compulsory elements

<solver name>[edit]

example host element element type purpose
<root>
 ..
 <solvers>
  solvers: a,..
   <a>
    ..
   </a>
 </solvers>
</root>
solvers conditional-compulsory hosts one of several mutually exclusive elements defining the type of solver solver name

content:

  • compulsory mutually exclusive elements with default element
    • <pcgiod>, default
    • <direct>

<pcgiod>[edit]

example host element element type purpose
<root>
 ..
 <solvers>
  solvers: a,..
   <a>
    <pcgiod>
     rounds: 1000
     conv: -20.0
    </pcgiod>
   </a>
 </solvers>
</root>
solver name compulsory defines parameters of a solver of type pcgiod

content:

  • key strings
word example type variable type variable values default explanation
rounds rounds: 1000 optional numeric value positive integer 10000 provides the maximum number of rounds to run
conv conv: -15.0 optional numeric value any real number -18.42 provides the convergence threshold
convtype convtype: cd optional word cr|cd cr provides the convergence parameter type

<direct>[edit]

example host element element type purpose
<root>
 ..
 <solvers>
  solvers: a,..
   <a>
    <direct>
    </direct>
   </a>
 </solvers>
</root>
solver name compulsory defines parameters of a solver of type direct

content: no content defined