Difference between revisions of "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'''>= | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<model> | |||
<eqn attribute="strings"> | |||
.. | |||
</eqn> | |||
<poly attribute="strings"> | |||
.. | |||
</poly> | |||
</model> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''root''' | |||
{{!}}compulsory | |||
{{!}}hosts information about the equations and the polynomials. | |||
}} | |||
content: | |||
*compulsory element '''<eqn attributes="strings">''' | |||
*optional element '''<poly attributes="strings">''' | |||
==<'''eqn'''>== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<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> | |||
</syntaxhighlight> | |||
{{!}}'''model''' | |||
{{!}}compulsory | |||
{{!}}hosts information about the equations. | |||
}} | |||
content: | |||
*[[linear mixed models in lmt#Model_syntax|model strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag. | |||
==<'''poly'''>== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<model> | |||
<poly attribute="strings"> | |||
x^0 | |||
x^2 | |||
3*x^2+sqrt(sin(x)) | |||
</poly> | |||
.. | |||
</model> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''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 | |||
*[[linear mixed models in lmt#Polynomials|polynomial strings]] which are escaped from the formatting rules by adding '''attributes="strings"''' to the start tag. | |||
=<'''pedigrees'''>= | =<'''pedigrees'''>= | ||
{{tableele1| | {{tableele1| | ||
Line 37: | Line 111: | ||
switch: selfing | switch: selfing | ||
phantomparents: 2 | phantomparents: 2 | ||
qfile: myq.coocsv | |||
</myped> | </myped> | ||
.. | .. | ||
Line 74: | Line 149: | ||
{{!}}none | {{!}}none | ||
{{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents | {{!}}integer number determines the number of individuals at the top of the pedigree which are phantom parents | ||
{{!}}- | |||
{{!}}'''qfile''' | |||
{{!}}'''qfile''': myq.coocsv | |||
{{!}}optional | |||
{{!}}word | |||
{{!}}''file name'' | |||
{{!}}none | |||
{{!}}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. | |||
{{!}}- | |||
{{!}}'''metafile''' | |||
{{!}}'''metafile''': meta.csv | |||
{{!}}optional | |||
{{!}}word | |||
{{!}}''file name'' | |||
{{!}}none | |||
{{!}}provides name of the file containing the metafounder co-variance matrix. | |||
}} | }} | ||
Line 151: | Line 242: | ||
{{!}}none | {{!}}none | ||
{{!}}content determines the name of a pedigree previously invoked pedigree related to the content of the cross-reference file | {{!}}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. | |||
}} | }} | ||
Line 237: | Line 346: | ||
{{!}}- | {{!}}- | ||
{{!}}'''method''' | {{!}}'''method''' | ||
{{!}}'''method''':''' | {{!}}'''method''':'''vr1''' | ||
{{!}}optional | {{!}}optional | ||
{{!}}alternative words | {{!}}alternative words | ||
{{!}}''' | {{!}}'''vr1<nowiki>|</nowiki>vr2''' | ||
{{!}}''' | {{!}}'''vr1''' | ||
{{!}}content determines the method to be used for building a grm from genotypes | {{!}}content determines the method to be used for building a grm from genotypes | ||
*''' | *'''vr1''': VanRaden Method 1 is used | ||
*''' | *'''vr2''': VanRaden Method 2(method Yang) is used | ||
{{!}}- | |||
{{!}}'''outfile''' | |||
{{!}}'''outfile''': ''mygrm.bin'' | |||
{{!}}optional | |||
{{!}}word | |||
{{!}}''file name'' | |||
{{!}}none | |||
{{!}}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_'''. | |||
}} | }} | ||
Line 276: | Line 393: | ||
*nominated-compulsory elements | *nominated-compulsory elements | ||
*compulsory element '''<res>''' | *compulsory element '''<res>''' | ||
=='''<res>'''== | =='''Kronecker products'''== | ||
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no '''type''' keystring is provided this is the default. | |||
==='''<res>'''=== | |||
{{tableele1| | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | {{!}}<syntaxhighlight lang="xml" line> | ||
Line 299: | Line 418: | ||
content: | content: | ||
*compulsory element [[#<sigma>|'''<sigma>''']] | *compulsory element [[#<sigma>|'''<sigma>''']] | ||
*optional element '''<gamma>''' | *optional element [[#<gamma>|'''<gamma>''']] | ||
==''<variance name>''== | ===''<variance name>''=== | ||
{{tableele1| | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | {{!}}<syntaxhighlight lang="xml" line> | ||
Line 327: | Line 447: | ||
content: | content: | ||
*compulsory element '''<sigma>''' | *compulsory element [[#<sigma>|'''<sigma>''']] | ||
*optional element '''<gamma>''' | *optional element [[#<gamma>|'''<gamma>''']] | ||
*key strings | |||
{{tablekeys2| | |||
1={{!}}'''type''' | |||
{{!}}'''type''': ''kronecker'' | |||
{{!}}optional | |||
{{!}}word | |||
{{!}}''kronecker,snpblup_1'' | |||
{{!}}kronecker | |||
{{!}}determines whether the variance structure deviates from a Kronecker product. | |||
}} | |||
==='''<sigma>'''=== | ===='''<sigma>'''==== | ||
{{tableele1| | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | {{!}}<syntaxhighlight lang="xml" line> | ||
Line 357: | Line 488: | ||
*key strings | *key strings | ||
{{tablekeys2| | {{tablekeys2| | ||
{{!}}'''file''' | 1={{!}}'''file''' | ||
{{!}}'''file''': ''mymatrix.csv'' | {{!}}'''file''': ''mymatrix.csv'' | ||
{{!}}compulsory | {{!}}compulsory | ||
Line 372: | Line 503: | ||
{{!}}none | {{!}}none | ||
{{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]] | {{!}}determines that $$\Sigma$$ is equal to [[Supported_features#Supported_variance_structures|$$\Theta$$]] | ||
{{!}}- | |||
{{!}}'''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 | |||
{{!}}- | |||
{{!}}'''maskfile''' | |||
{{!}}'''maskfile''': ''mymatrixmask.csv'' | |||
{{!}}optional | |||
{{!}}word | |||
{{!}}''file name'' | |||
{{!}}none | |||
{{!}}content determines the name of the file containing a T/F matrix of the same dimension as the respective $$\Sigma$$ matrix. Is mutually exclusive with '''<nowiki><maskmatrix attributes="array"></nowiki>'''. | |||
}} | }} | ||
*optional element '''<matrix attributes="array">''' | *optional element '''<matrix attributes="array">''' | ||
=====<'''matrix attributes="array"'''>===== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<vars> | |||
.. | |||
vars: myvar | |||
<myvar> | |||
<sigma> | |||
<matrix attributes="array"> | |||
5.0,0.5 | |||
0.5,1.8 | |||
</matrix> | |||
</sigma> | |||
.. | |||
</myvar> | |||
.. | |||
</vars> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''sigma''' | |||
{{!}}optional | |||
{{!}}hosts the content of a single $$\Sigma$$ matrix. Is mutually exclusive with key string '''file: '''. | |||
}} | |||
=====<'''maskmatrix attributes="array"'''>===== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<vars> | |||
.. | |||
vars: myvar | |||
<myvar> | |||
<sigma> | |||
<maskmatrix attributes="array"> | |||
T,F | |||
F,T | |||
</matrix> | |||
</sigma> | |||
.. | |||
</myvar> | |||
.. | |||
</vars> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''sigma''' | |||
{{!}}optional | |||
{{!}}hosts the content of a single indicator matrix of the same dimensions as the respective $$\Sigma$$ matrix. Is mutually exclusive with key string '''maskfile: '''. | |||
}} | |||
==='''<gamma>'''=== | ===='''<gamma>'''==== | ||
{{tableele1| | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | {{!}}<syntaxhighlight lang="xml" line> | ||
Line 395: | Line 601: | ||
{{!}}''variance name'' | {{!}}''variance name'' | ||
{{!}}optional | {{!}}optional | ||
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. | {{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$. | ||
}} | }} | ||
content: | content: | ||
*mutually exclusive elements '''<A>, <H> and <E>''' | *mutually exclusive elements '''<A>, <H>, <G> and <E>''' | ||
===='''<A>'''==== | ====='''<A>'''===== | ||
{{tableele1| | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | {{!}}<syntaxhighlight lang="xml" line> | ||
Line 437: | Line 643: | ||
{{!}}none | {{!}}none | ||
{{!}}content determines the name of a pedigree previously invoked to be used to construct A. | {{!}}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>'''==== | ====='''<H>'''===== | ||
{{tableele1| | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | {{!}}<syntaxhighlight lang="xml" line> | ||
Line 468: | Line 684: | ||
*via a grm element for single step H-BLUP models | *via a grm element for single step H-BLUP models | ||
*via a genotype element for single step T-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>|<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. | |||
}} | }} | ||
Line 473: | Line 690: | ||
*key strings | *key strings | ||
{{tablekeys2| | {{tablekeys2| | ||
{{!}}'''pedigree''' | 1={{!}}'''pedigree''' | ||
{{!}}'''pedigree''': ''myped'' | {{!}}'''pedigree''': ''myped'' | ||
{{!}}compulsory | {{!}}compulsory | ||
Line 485: | Line 702: | ||
{{!}}optional | {{!}}optional | ||
{{!}}word | {{!}}word | ||
{{!}}'''tblup<nowiki>|</nowiki> | {{!}}'''tblup<nowiki>|</nowiki>gblup''' | ||
{{!}}''' | {{!}}'''gblup''' | ||
{{!}}content determines the way the inverse of H is constructed. | {{!}}content determines the way the inverse of H is constructed. | ||
{{!}}- | {{!}}- | ||
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{{!}}none | {{!}}none | ||
{{!}}content determines the grm element to be used to construct H. compulsory for '''type: hblup'''. | {{!}}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>'''===== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<vars> | |||
.. | |||
vars: myvar | |||
<myvar> | |||
<gamma> | |||
<G> | |||
grm: mygrm | |||
</G> | |||
</gamma> | |||
.. | |||
</myvar> | |||
.. | |||
</vars> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''gamma''' | |||
{{!}}compulsory | |||
{{!}}hosts information about $$\Gamma$$ being constructed from a genomic relationsship matrix. | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
1={{!}}'''grmdadd''' | |||
{{!}}'''grmdadd''': ''0.05'' | |||
{{!}}optional | |||
{{!}}single numeric value | |||
{{!}}real number >=0.0 | |||
{{!}}none | |||
{{!}} value added to the diagonal of $$G$$ to ensure invertibility. | |||
}} | |||
====='''<E>'''===== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<vars> | |||
.. | |||
vars: myvar | |||
<myvar> | |||
<gamma> | |||
<E> | |||
file: mygamma.csv | |||
</E> | |||
</gamma> | |||
.. | |||
</myvar> | |||
.. | |||
</vars> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''gamma''' | |||
{{!}}compulsory | |||
{{!}}hosts information about $$\Gamma^{-1}$$ being uploaded from a file. | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''file''' | |||
{{!}}'''file''': ''mygamma.csv'' | |||
{{!}}compulsory | |||
{{!}}word | |||
{{!}}''file name'' | |||
{{!}}none | |||
{{!}}content determines the file which contains $$\Gamma^{-1}$$. | |||
{{!}}- | |||
{{!}}'''type''' | |||
{{!}}'''type''': '''dense''' | |||
{{!}}optional | |||
{{!}}word | |||
{{!}}'''dense<nowiki>|</nowiki>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 [https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_(CSR,_CRS_or_Yale_format) csr] format | |||
}} | |||
=='''snpblup1'''== | |||
===''<variance name>''=== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<vars> | |||
.. | |||
vars: myvar | |||
<myvar> | |||
type: snpblup1 | |||
genotype: mygn | |||
aweight: 0.05 | |||
switch: adjustg2a | |||
<sigma> | |||
.. | |||
</sigma> | |||
<gamma> | |||
.. | |||
</gamma> | |||
</myvar> | |||
.. | |||
</vars> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''vars''' | |||
{{!}}nominated-compulsory | |||
{{!}}hosts information about variance structure identified by ''variance name''. | |||
}} | |||
content: | |||
*compulsory element '''<sigma>''' | |||
*compulsory element [[#<marker_sb1>|'''<marker_sb1>''']] | |||
*key strings | |||
{{tablekeys2| | |||
1={{!}}'''type''' | |||
{{!}}'''type''': ''kronecker'' | |||
{{!}}optional | |||
{{!}}word | |||
{{!}}''kronecker,snpblup_1'' | |||
{{!}}kronecker | |||
{{!}}determines whether the variance structure deviates from a Kronecker product. | |||
{{!}}- | |||
{{!}}'''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''' | ||
{{!}}'''aweight: 0.05''' | {{!}}'''aweight: 0.05''' | ||
{{!}}optional | {{!}}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 | {{!}}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). | |||
}} | |||
===='''<sigma>'''==== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<vars> | |||
.. | |||
vars: myvar | |||
<myvar> | |||
type: snpblup1 | |||
<sigma> | |||
.. | |||
</sigma> | |||
.. | |||
</myvar> | |||
.. | |||
</vars> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''variance name'' | |||
{{!}}compulsory | |||
{{!}}hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure. | |||
}} | |||
content: | |||
see [[#<sigma>|'''<sigma''']] | |||
===='''<marker_sb1>'''==== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<vars> | |||
.. | |||
vars: myvar | |||
<myvar> | |||
type: snpblup1 | |||
.. | |||
<marker_sb1> | |||
.. | |||
</marker_sb1> | |||
.. | |||
</myvar> | |||
.. | |||
</vars> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''marker'' | |||
{{!}}compulsory | |||
{{!}}hosts information about the co-variance between and within markers following [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. | |||
}} | |||
content: | |||
*compulsory element '''<sigma>''' | |||
*optional element '''<gamma>''' | |||
====='''<sigma>'''===== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<vars> | |||
.. | |||
vars: myvar | |||
<myvar> | |||
type: snpblup1 | |||
.. | |||
<marker_sb1> | |||
<sigma> | |||
.. | |||
</sigma> | |||
.. | |||
</marker_sb1> | |||
.. | |||
</myvar> | |||
.. | |||
</vars> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''marker'' | |||
{{!}}compulsory | |||
{{!}}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). | |||
}} | }} | ||
see [[#<sigma>|'''<sigma>''']] | |||
=<'''jobs'''>= | =<'''jobs'''>= | ||
<syntaxhighlight lang="xml" line> | {{tableele2| | ||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | <root> | ||
.. | .. | ||
Line 523: | Line 1,015: | ||
</root> | </root> | ||
</syntaxhighlight> | </syntaxhighlight> | ||
{{!}}'''root''' | |||
{{!}}optional | |||
{{!}}hosts one to several elements each containing information about a specific job | |||
{{!}}run default job(solve) in default parameterization(default pcgiod parameterization) | |||
}} | |||
content: | content: | ||
*key strings | *key strings | ||
{| | {{tablekeys2| | ||
{{!}}'''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 | *nominated-compulsory elements | ||
**'''<default>''' | |||
**'''<solve>''' | |||
**'''<sample>''' | |||
**'''<pevsample>''' | |||
**'''<pevsolve>''' | |||
**'''<mcemreml>''' | |||
**'''<airemlc>''' | |||
**'''<yhat>''' | |||
==<'''default'''>== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<jobs> | |||
.. | |||
<default> | |||
conv: -18.42 | |||
</default> | |||
.. | |||
</jobs> | |||
.. | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''jobs''' | |||
{{!}}conditional-compulsory | |||
{{!}}hosts information about job '''default''' | |||
}} | |||
content: see [[#<pcgiod>|<pcgiod>]] for a list of all possible key strings | |||
==<'''solve'''>== | ==<'''solve'''>== | ||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<syntaxhighlight lang="xml" line> | |||
<root> | <root> | ||
.. | .. | ||
Line 560: | Line 1,080: | ||
</root> | </root> | ||
</syntaxhighlight> | </syntaxhighlight> | ||
{{!}}'''jobs''' | |||
{{!}}conditional-compulsory | |||
{{!}}hosts information about job '''solve''' | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''solver''' | |||
{{!}}'''solver''': ''mysolver'' | |||
{{!}}compulsory | |||
{{!}}word | |||
{{!}}''solver name'' | |||
{{!}}none | |||
{{!}}''solver name'' must be the name of a previously defined solver | |||
}} | |||
==<'''sample'''>== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<jobs> | |||
jobs: sample,.. | |||
<sample> | |||
sampler: mysampler | |||
</sample> | |||
.. | |||
</jobs> | |||
.. | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''jobs''' | |||
{{!}}conditional-compulsory | |||
{{!}}hosts information about job '''sample''' | |||
}} | |||
content: | content: | ||
*key strings | *key strings | ||
{| | {{tablekeys2| | ||
{{!}}'''sampler''' | |||
{{!}}'''sampler''': ''mysampler'' | |||
{{!}}compulsory | |||
{{!}}word | |||
{{!}}''sampler name'' | |||
{{!}}none | |||
{{!}}''sampler name'' must be the name of a previously defined sampler | |||
}} | |||
==<'''pevsample'''>== | ==<'''pevsample'''>== | ||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<jobs> | |||
jobs: pevsample,.. | |||
<pevsample> | |||
sampler: mysampler | |||
</pevsample> | |||
.. | |||
</jobs> | |||
.. | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''jobs''' | |||
{{!}}conditional-compulsory | |||
{{!}}hosts information about job '''pevsample''' | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''sampler''' | |||
{{!}}'''sampler''': ''mysampler'' | |||
{{!}}compulsory | |||
{{!}}word | |||
{{!}}''sampler name'' | |||
{{!}}none | |||
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev | |||
}} | |||
==<'''pevsolve'''>== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<jobs> | |||
jobs: pevsolve,.. | |||
<pevsolve> | |||
solver: mysolver | |||
</pevsolver> | |||
.. | |||
</jobs> | |||
.. | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''jobs''' | |||
{{!}}conditional-compulsory | |||
{{!}}hosts information about job '''pevsolve''' | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
1={{!}}'''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. | |||
}} | |||
==<'''airemlc'''>== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<jobs> | |||
jobs: airemlc,.. | |||
<airemlc> | |||
rounds: 50 | |||
.. | |||
</airemlc> | |||
.. | |||
</jobs> | |||
.. | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''jobs''' | |||
{{!}}conditional-compulsory | |||
{{!}}hosts information about job '''airemlc''' | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''rounds''' | |||
{{!}}'''rounds''': ''10'' | |||
{{!}}optional | |||
{{!}}numeric value | |||
{{!}}positive integer | |||
{{!}}20 | |||
{{!}}provides the number of aireml-rounds to run | |||
{{!}}- | |||
{{!}}'''convtype''' | |||
{{!}}'''convtype''': '''ng''' | |||
{{!}}optional | |||
{{!}}word | |||
{{!}}'''cd<nowiki>|</nowiki>ng<nowiki>|</nowiki>ll<nowiki>|</nowiki>any<nowiki>|</nowiki>all''' | |||
{{!}}'''cd''' | |||
{{!}}provides the convergence criterion to use | |||
* ll: log of relative change in log-likelihood | |||
* ng: log of the norm of the gradient vector | |||
* cd: log of the relative change of the parameter vector | |||
* all: all of the above | |||
* any: any of the above | |||
{{!}}- | |||
{{!}}'''convll''' | |||
{{!}}'''convll''': ''-10.5'' | |||
{{!}}optional | |||
{{!}}numeric value | |||
{{!}}any real number | |||
{{!}}''-6.907755'' | |||
{{!}}provides the convergence threshold for convergence criterion '''ll''' | |||
{{!}}- | |||
{{!}}'''convng''' | |||
{{!}}'''convng''': ''-10.5'' | |||
{{!}}optional | |||
{{!}}numeric value | |||
{{!}}any real number | |||
{{!}}''-16.1181'' | |||
{{!}}provides the convergence threshold for convergence criterion '''ng''' | |||
{{!}}- | |||
{{!}}'''convcd''' | |||
{{!}}'''convcd''': ''-10.5'' | |||
{{!}}optional | |||
{{!}}numeric value | |||
{{!}}any real number | |||
{{!}}''-16.1181'' | |||
{{!}}provides the convergence threshold for convergence criterion '''cd''' | |||
{{!}}- | |||
{{!}}'''nscale''' | |||
{{!}}'''nscale''': ''0.5'' | |||
{{!}}optional | |||
{{!}}numeric value | |||
{{!}}any real number | |||
{{!}}''1.0'' | |||
{{!}}scales the length of the Newton step. | |||
{{!}}- | |||
{{!}}'''switch''' | |||
{{!}}'''switch''': '''residuals''' | |||
{{!}}optional | |||
{{!}}csv word-list | |||
{{!}}any real number | |||
{{!}}'''writeai,residuals,solutions''' | |||
{{!}} | |||
*'''writeai''': write ai matrix and gradient vector to files ai_ai.csv and ai_ja.csv. | |||
*'''residuals''': after convergence write the residuals to file aic_residuals.csv | |||
*'''solutions''': after convergence write the MME solutions to file results.csv | |||
}} | |||
==<'''mcemreml'''>== | ==<'''mcemreml'''>== | ||
==<''' | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<jobs> | |||
jobs: mcemreml,.. | |||
<mcemreml> | |||
rounds: 500 | |||
sampler: mysampler | |||
solver: mysolver | |||
</mcemreml> | |||
.. | |||
</jobs> | |||
.. | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''jobs''' | |||
{{!}}conditional-compulsory | |||
{{!}}hosts information about job '''mcemreml''' | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''rounds''' | |||
{{!}}'''rounds''': ''1000'' | |||
{{!}}optional | |||
{{!}}numeric value | |||
{{!}}positive integer | |||
{{!}}500 | |||
{{!}}provides maximum the number of mcemreml-rounds to run | |||
{{!}}- | |||
{{!}}'''conv''' | |||
{{!}}'''conv''': ''-16.21'' | |||
{{!}}optional | |||
{{!}}numeric value | |||
{{!}}real number | |||
{{!}} -6.907755 | |||
{{!}}provides the convergence threshold | |||
{{!}}- | |||
{{!}}'''sampler''' | |||
{{!}}'''sampler''': ''mysampler'' | |||
{{!}}compulsory | |||
{{!}}word | |||
{{!}}''sampler name'' | |||
{{!}}none | |||
{{!}}''sampler name'' must be the name of a previously defined sampler | |||
{{!}}- | |||
{{!}}'''solver''' | |||
{{!}}'''solver''': ''mysolver'' | |||
{{!}}compulsory | |||
{{!}}word | |||
{{!}}''solver name'' | |||
{{!}}none | |||
{{!}}''solver name'' must be the name of a previously defined solver | |||
}} | |||
==<'''yhat'''>== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<jobs> | |||
jobs: yhat,.. | |||
<yhat> | |||
</yhat> | |||
.. | |||
</jobs> | |||
.. | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''jobs''' | |||
{{!}}conditional-compulsory | |||
{{!}}hosts information about job '''yhat''' | |||
}} | |||
Currently '''yhat''' has no key strings or nested elements defined. | |||
=<'''samplers'''>= | =<'''samplers'''>= | ||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<samplers> | |||
samplers: a,b,.. | |||
... | |||
</samplers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''root''' | |||
{{!}}optional | |||
{{!}}hosts one to several elements each containing information about a specific sampler | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''samplers''' | |||
{{!}}'''samplers''': ''a'' | |||
{{!}}compulsory | |||
{{!}}csv word-list | |||
{{!}}''sampler names'' | |||
{{!}}none | |||
{{!}}list content determines nominated-compulsory elements | |||
}} | |||
*conditional-compulsory elements | |||
==<''sampler name''>== | ==<''sampler name''>== | ||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<samplers> | |||
samplers: a,.. | |||
<a> | |||
.. | |||
</a> | |||
</samplers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''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'''>=== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<samplers> | |||
samplers: a,.. | |||
<a> | |||
<singlepass> | |||
samples: 10000 | |||
burnin: 1000 | |||
</singlepass> | |||
</a> | |||
</samplers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''sampler name'' | |||
{{!}}compulsory | |||
{{!}}defines parameters of a sampler of type '''singlepass''' | |||
}} | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''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'''>=== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<samplers> | |||
samplers: a,.. | |||
<a> | |||
<blocked> | |||
samples: 10000 | |||
burnin: 1000 | |||
</blocked> | |||
</a> | |||
</samplers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''sampler name'' | |||
{{!}}compulsory | |||
{{!}}defines parameters of a sampler of type '''blocked''' | |||
}} | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''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'''>=== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<samplers> | |||
samplers: a,.. | |||
<a> | |||
<pev> | |||
samples: 10000 | |||
burnin: 1000 | |||
chains: 10 | |||
</pev> | |||
</a> | |||
</samplers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''sampler name'' | |||
{{!}}compulsory | |||
{{!}}defines parameters of a sampler of type '''pev''' | |||
}} | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''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'''>= | =<'''solvers'''>= | ||
* | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<solvers> | |||
solvers: a,b,.. | |||
... | |||
</solvers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''root''' | |||
{{!}}optional | |||
{{!}}hosts one to several elements each containing information about a specific solver | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''solvers''' | |||
{{!}}'''solvers''': ''a'' | |||
{{!}}compulsory | |||
{{!}}csv word-list | |||
{{!}}''solver names'' | |||
{{!}}none | |||
{{!}}list content determines nominated-compulsory elements | |||
}} | |||
*conditional-compulsory elements | |||
==<''solver name''>== | ==<''solver name''>== | ||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<solvers> | |||
solvers: a,.. | |||
<a> | |||
.. | |||
</a> | |||
</solvers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}'''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'''>=== | ===<'''pcgiod'''>=== | ||
{| | {{tableele1| | ||
{{!}}<syntaxhighlight lang="xml" line> | |||
! | <root> | ||
! | .. | ||
! | <solvers> | ||
solvers: a,.. | |||
<a> | |||
<pcgiod> | |||
rounds: 1000 | |||
conv: -20.0 | |||
</pcgiod> | |||
| | </a> | ||
</solvers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''solver name'' | |||
{{!}}compulsory | |||
{{!}}defines parameters of a solver of type '''pcgiod''' | |||
}} | |||
content: | |||
*key strings | |||
{{tablekeys2| | |||
{{!}}'''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<nowiki>|</nowiki>cd''' | |||
{{!}} '''cr''' | |||
{{!}}provides the convergence parameter type | |||
}} | |||
===<'''direct'''>=== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<solvers> | |||
solvers: a,.. | |||
<a> | |||
<direct> | |||
</direct> | |||
</a> | |||
</solvers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''solver name'' | |||
{{!}}compulsory | |||
{{!}}defines parameters of a solver of type '''direct''' | |||
}} | |||
content: no content defined |
Latest revision as of 23:44, 31 August 2022
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>
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>
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>
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>
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>
example | host element | element type | purpose |
<root>
..
<pedigrees>
pedigrees: myped
..
<myped>
file: myped.csv
switch: selfing
phantomparents: 2
qfile: myq.coocsv
</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.
|
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 |
qfile | qfile: myq.coocsv | optional | word | file name | none | 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. |
metafile | metafile: meta.csv | optional | word | file name | none | provides name of the file containing the metafounder co-variance matrix. |
<genotypes>
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>
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 |
|
<grms>
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>
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:vr1 | optional | alternative words | vr1|vr2 | vr1 | content determines the method to be used for building a grm from genotypes
|
outfile | outfile: mygrm.bin | optional | word | file name | none | 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_. |
<vars>
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
Variance structures below are Kronecker products $$\Gamma \otimes \Sigma$$. If no type keystring is provided this is the default.
<res>
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>
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>
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 |
maskfile | maskfile: mymatrixmask.csv | optional | word | file name | none | content determines the name of the file containing a T/F matrix of the same dimension as the respective $$\Sigma$$ matrix. Is mutually exclusive with <maskmatrix attributes="array">. |
- optional element <matrix attributes="array">
<matrix attributes="array">
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: . |
<maskmatrix attributes="array">
example | host element | element type | purpose |
<root>
..
<vars>
..
vars: myvar
<myvar>
<sigma>
<maskmatrix attributes="array">
T,F
F,T
</matrix>
</sigma>
..
</myvar>
..
</vars>
</root> |
sigma | optional | hosts the content of a single indicator matrix of the same dimensions as the respective $$\Sigma$$ matrix. Is mutually exclusive with key string maskfile: . |
<gamma>
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 $$\Gamma \otimes \Sigma$$. If absent $$\Gamma$$ defaults to $$I$$. |
content:
- mutually exclusive elements <A>, <H>, <G> and <E>
<A>
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 |
|
<H>
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
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 |
|
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
|
<G>
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>
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 $$\Gamma^{-1}$$
|
snpblup1
<variance name>
example | host element | element type | purpose |
<root>
..
<vars>
..
vars: myvar
<myvar>
type: snpblup1
genotype: mygn
aweight: 0.05
switch: adjustg2a
<sigma>
..
</sigma>
<gamma>
..
</gamma>
</myvar>
..
</vars>
</root> |
vars | nominated-compulsory | hosts information about variance structure identified by variance name. |
content:
- compulsory element <sigma>
- compulsory element <marker_sb1>
- 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. |
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 |
|
<sigma>
example | host element | element type | purpose |
<root>
..
<vars>
..
vars: myvar
<myvar>
type: snpblup1
<sigma>
..
</sigma>
..
</myvar>
..
</vars>
</root> |
variance name | compulsory | hosts information about $$\Sigma$$ for the poly-genetic part of the variance structure. |
content:
see <sigma
<marker_sb1>
example | host element | element type | purpose |
<root>
..
<vars>
..
vars: myvar
<myvar>
type: snpblup1
..
<marker_sb1>
..
</marker_sb1>
..
</myvar>
..
</vars>
</root> |
marker | compulsory | hosts information about the co-variance between and within markers following $$\Gamma \otimes \Sigma$$. |
content:
- compulsory element <sigma>
- optional element <gamma>
<sigma>
example | host element | element type | purpose |
<root>
..
<vars>
..
vars: myvar
<myvar>
type: snpblup1
..
<marker_sb1>
<sigma>
..
</sigma>
..
</marker_sb1>
..
</myvar>
..
</vars>
</root> |
marker | compulsory | hosts information about $$\Sigma$$ as part of $$\Gamma \otimes \Sigma$$ for the marker part of the variance structure. Note that $$\Sigma$$ will be scaled by (1-aweight). |
see <sigma>
<jobs>
example | host element | element type | purpose | default |
<root>
..
<jobs>
jobs: solve,yh
...
</jobs>
</root> |
root | optional | hosts one to several elements each containing information about a specific job | run default job(solve) in default parameterization(default pcgiod parameterization) |
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
- <default>
- <solve>
- <sample>
- <pevsample>
- <pevsolve>
- <mcemreml>
- <airemlc>
- <yhat>
<default>
example | host element | element type | purpose |
<root>
..
<jobs>
..
<default>
conv: -18.42
</default>
..
</jobs>
..
</root> |
jobs | conditional-compulsory | hosts information about job default |
content: see <pcgiod> for a list of all possible key strings
<solve>
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>
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>
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>
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. |
<airemlc>
example | host element | element type | purpose |
<root>
..
<jobs>
jobs: airemlc,..
<airemlc>
rounds: 50
..
</airemlc>
..
</jobs>
..
</root> |
jobs | conditional-compulsory | hosts information about job airemlc |
content:
- key strings
word | example | type | variable type | variable values | default | explanation |
rounds | rounds: 10 | optional | numeric value | positive integer | 20 | provides the number of aireml-rounds to run |
convtype | convtype: ng | optional | word | cd|ng|ll|any|all | cd | provides the convergence criterion to use
|
convll | convll: -10.5 | optional | numeric value | any real number | -6.907755 | provides the convergence threshold for convergence criterion ll |
convng | convng: -10.5 | optional | numeric value | any real number | -16.1181 | provides the convergence threshold for convergence criterion ng |
convcd | convcd: -10.5 | optional | numeric value | any real number | -16.1181 | provides the convergence threshold for convergence criterion cd |
nscale | nscale: 0.5 | optional | numeric value | any real number | 1.0 | scales the length of the Newton step. |
switch | switch: residuals | optional | csv word-list | any real number | writeai,residuals,solutions |
|
<mcemreml>
example | host element | element type | purpose |
<root>
..
<jobs>
jobs: mcemreml,..
<mcemreml>
rounds: 500
sampler: mysampler
solver: mysolver
</mcemreml>
..
</jobs>
..
</root> |
jobs | conditional-compulsory | hosts information about job mcemreml |
content:
- key strings
word | example | type | variable type | variable values | default | explanation |
rounds | rounds: 1000 | optional | numeric value | positive integer | 500 | provides maximum the number of mcemreml-rounds to run |
conv | conv: -16.21 | optional | numeric value | real number | -6.907755 | provides the convergence threshold |
sampler | sampler: mysampler | compulsory | word | sampler name | none | sampler name must be the name of a previously defined sampler |
solver | solver: mysolver | compulsory | word | solver name | none | solver name must be the name of a previously defined solver |
<yhat>
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>
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>
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>
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>
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>
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>
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>
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>
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>
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