Difference between revisions of "Parameter file elements"

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='''pedigrees'''=
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.
='''genotypes'''=
='''grms'''=
='''model'''=
=='''eqn'''==
=='''poly'''==
='''jobs'''=
Example:


<syntaxhighlight lang="xml" line>
=<'''model'''>=
<jobs>
{{tableele1|
   jobs: solve,yh
{{!}}<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'''>=
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<pedigrees>
  pedigrees: a,b
  ...
</pedigrees>
</root>
</syntaxhighlight>
{{!}}'''root'''
{{!}}automatic-optional
{{!}}hosts one to several elements each containing information about a specific pedigree}}
 
content:
*key strings
{{tablekeys2|
{{!}}'''pedigrees'''
{{!}}'''pedigrees''': ''a,b''
{{!}}compulsory
{{!}}csv word-list
{{!}}''pedigree names''
{{!}}none
{{!}}list content determines names of nominated-compulsory elements}}
*nominated-compulsory elements
==<''pedigree name''>==
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<pedigrees>
  pedigrees: myped
  ..
  <myped>
  file: myped.csv
  switch: selfing
  phantomparents: 2
  qfile: myq.coocsv
  </myped>
  ..
</pedigrees>
</root>
</syntaxhighlight>
{{!}}'''pedigrees'''
{{!}}nominated-compulsory
{{!}}hosts information about a specific pedigree identified by ''pedigree name''
}}
content:
*key strings
{{tablekeys2|
{{!}}'''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
{{!}}-
{{!}}'''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'''>=
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<genotypes>
  genotypes: a,b
  ...
</genotypes>
</root>
</syntaxhighlight>
{{!}}'''root'''
{{!}}automatic-optional
{{!}}hosts one to several elements each containing information about different sets of genotypes
}}
 
content:
*key strings
{{tablekeys2|
{{!}}'''genotypes'''
{{!}}'''genotypes''': ''a,b''
{{!}}compulsory
{{!}}csv word-list
{{!}}''genotype names''
{{!}}none
{{!}}list content determines names of nominated-compulsory elements
}}
*nominated-compulsory elements
==<''genotype name''>==
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<genotypes>
  genotypes: mygn
  ..
  <mygn>
  file: genotypes.txt
  pedigree: myped
  cross: crossref.csv
  </mygn>
  ..
</genotypes>
</root>
</syntaxhighlight>
{{!}}'''genotypes'''
{{!}}nominated-compulsory
{{!}}hosts information about a specific set of genotypes identified by ''genotype name''
}}
content:
*key strings
{{tablekeys2|
{{!}}'''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'''>=
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<grms>
   grms: a,b
   ...
   ...
</jobs>
</grms>
</root>
</syntaxhighlight>
</syntaxhighlight>
{{!}}'''root'''
{{!}}automatic-optional
{{!}}hosts one to several elements each containing information about a specific grm
}}


host: '''root'''
content:
*key strings
{{tablekeys2|
{{!}}'''grms'''
{{!}}'''grms''': ''x,y''
{{!}}compulsory
{{!}}csv word-list
{{!}}''grm names''
{{!}}none
{{!}}list content determines names of nominated-compulsory elements
}}
*nominated-compulsory elements
==<''grm name''>==
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<grms>
  grms: mygrm
  ..
  <mygrm>
  genotype: mygn
  method: YA
  </mygrm>
  ..
</genotypes>
</root>
</syntaxhighlight>
{{!}}'''grms'''
{{!}}nominated-compulsory
{{!}}hosts information about a specific grm identified by ''grm name''
}}
content:
*key strings
{{tablekeys2|
{{!}}'''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<nowiki>|</nowiki>vr2'''
{{!}}'''vr1'''
{{!}}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_'''.
}}
 
=<'''vars'''>=
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<vars>
  vars: g,p
  ...
</vars>
</root>
</syntaxhighlight>
{{!}}'''root'''
{{!}}compulsory
{{!}}hosts one to several elements each containing information about a specific variance.
}}


content:
content:
*key strings
*key strings
{| class="wikitable"
{{tablekeys2|
|example
{{!}}'''vars'''
|type
{{!}}'''vars''': ''g,p''
|variable type
{{!}}compulsory
|variable values
{{!}}csv word-list
|default
{{!}}''variance names''
|explanation
{{!}}none
|-
{{!}}list content determines names of nominated-compulsory elements
|'''jobs''': '''solve,yh'''
}}
|compulsory
|csv word-list
|'''solve,sample,pevsample,mcemreml,yh'''
|none
|job sequence is determined by the list sequence. list content determines nominated-compulsory elements
|}
*nominated-compulsory elements
*nominated-compulsory elements
=='''solve'''==
*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>'''===
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<vars>
  ..
  <res>
  <sigma>
    ..
  </sigma>
  </res>
  ..
</vars>
</root>
</syntaxhighlight>
{{!}}'''vars'''
{{!}}compulsory
{{!}}hosts information about the residual variance structure.
}}
 
content:
*compulsory element [[#<sigma>|'''<sigma>''']]
*optional element [[#<gamma>|'''<gamma>''']]
 
 
===''<variance name>''===
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<vars>
  ..
  vars: myvar
  <myvar>
  <sigma>
    ..
  </sigma>
  <gamma>
    ..
  </gamma>
  </myvar>
  ..
</vars>
</root>
</syntaxhighlight>
{{!}}'''vars'''
{{!}}nominated-compulsory
{{!}}hosts information about variance structure identified by ''variance name''.
}}
 
content:
*compulsory element [[#<sigma>|'''<sigma>''']]
*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>'''====
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<vars>
  ..
  vars: myvar
  <myvar>
  <sigma>
    ..
  </sigma>
  ..
  </myvar>
  ..
</vars>
</root>
</syntaxhighlight>
{{!}}''variance name''
{{!}}compulsory
{{!}}hosts information about $$\Sigma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]].
}}
 
content:
 
*key strings
{{tablekeys2|
1={{!}}'''file'''
{{!}}'''file''': ''mymatrix.csv''
{{!}}compulsory
{{!}}word
{{!}}''file name''
{{!}}none
{{!}}content determines the name of the file containing the $$\Sigma$$ matrix. is mutually exclusive with '''<nowiki><matrix attributes="array"></nowiki>'''.
{{!}}-
{{!}}'''type'''
{{!}}'''type''': '''block'''
{{!}}optional
{{!}}word
{{!}}'''block'''
{{!}}none
{{!}}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">'''
=====<'''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>'''====
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<vars>
  ..
  vars: myvar
  <myvar>
  <gamma>
    ..
  </gamma>
  ..
  </myvar>
  ..
</vars>
</root>
</syntaxhighlight>
{{!}}''variance name''
{{!}}optional
{{!}}hosts information about $$\Gamma$$ as part of [[Supported_features#Supported_variance_structures|$$\Gamma \otimes \Sigma$$]]. If absent $$\Gamma$$ defaults to $$I$$.
}}
 
content:
 
*mutually exclusive elements '''<A>, <H>, <G> and <E>'''
 
====='''<A>'''=====
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<vars>
  ..
  vars: myvar
  <myvar>
  <gamma>
    <A>
    pedigree: myped
    </A>
  </gamma>
  ..
  </myvar>
  ..
</vars>
</root>
</syntaxhighlight>
{{!}}'''gamma'''
{{!}}compulsory
{{!}}hosts information about $$\Gamma$$ being constructed as the numerator relationship matrix A using pedigree ''pedigree name''.
}}
 
content:
*key strings
{{tablekeys2|
{{!}}'''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>'''=====
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<vars>
  ..
  vars: myvar
  <myvar>
  <gamma>
    <H>
    type: tblup
    pedigree: myped
    genotype: mygn
    aweight: 0.05
    switch: adjustg2a
    </H>
  </gamma>
  ..
  </myvar>
  ..
</vars>
</root>
</syntaxhighlight>
{{!}}'''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>|<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
{{tablekeys2|
1={{!}}'''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<nowiki>|</nowiki>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>'''=====
{{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: 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).
}}
 
===='''<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''']]
 


<syntaxhighlight lang="xml" line>
===='''<marker_sb1>'''====
<jobs>
{{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'''>=
 
{{tableele2|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<jobs>
  jobs: solve,yh
   ...
   ...
</jobs>
</root>
</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:
*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
**'''<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'''>==
{{tableele1|
{{!}}<syntaxhighlight lang="xml" line>
<root>
..
<jobs>
  ..
   <solve>
   <solve>
    solver: mysolver
  solver: mysolver
   </solver>
   </solve>
</jobs>
  ..
</jobs>
..
</root>
</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>
</syntaxhighlight>
{{!}}'''jobs'''
{{!}}conditional-compulsory
{{!}}hosts information about job '''sample'''
}}


host: '''jobs'''
content:
 
*key strings
{{tablekeys2|
{{!}}'''sampler'''
{{!}}'''sampler''': ''mysampler''
{{!}}compulsory
{{!}}word
{{!}}''sampler name''
{{!}}none
{{!}}''sampler name'' must be the name of a previously defined sampler
}}
 
==<'''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:
content:


*key strings
*key strings
{| class="wikitable"
{{tablekeys2|
|example
{{!}}'''sampler'''
|type
{{!}}'''sampler''': ''mysampler''
|variable type
{{!}}compulsory
|variable values
{{!}}word
|default
{{!}}''sampler name''
|explanation
{{!}}none
|-
{{!}}''sampler name'' must be the name of a previously defined sampler of type pev
|'''solver''': ''mysolver''
}}
|compulsory
|word
|''solver name''
|none
|''solver name'' must be the name of a previously defined solver
|}


=='''sample'''==
==<'''pevsolve'''>==
=='''pevsample'''==
{{tableele1|
=='''mcemreml'''==
{{!}}<syntaxhighlight lang="xml" line>
=='''yh'''==
<root>
..
<jobs>
  jobs: pevsolve,..
  <pevsolve>
  solver: mysolver
  </pevsolver>
  ..
</jobs>
..
</root>
</syntaxhighlight>
{{!}}'''jobs'''
{{!}}conditional-compulsory
{{!}}hosts information about job '''pevsolve'''
}}


='''samplers'''=
content:
==''sampler name''==
 
='''solvers'''=
*key strings
*host: '''root'''
{{tablekeys2|
==''solver name''==
1={{!}}'''solver'''
*host: '''solvers'''
{{!}}'''solver''': ''mysolver''
*hosts mutually exclusive elements of which hard-coded names define the solver type
{{!}}compulsory
==='''pcgiod'''===
{{!}}word
*host: ''solver name''
{{!}}''solver name''
*defines the solver is an iteration-on-data preconditioned gradient solver
{{!}}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'''>==
{{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'''>=
 
{{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''>==
 
{{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'''>=
{{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''>==
 
{{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'''>===
 
{{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'''
}}


{| class="wikitable sortable"
content: no content defined
|-
! element name
! element type
! host element
! hosts elements
! element function
! key string key word
! key string variable
! key string function
! key string type
|-
|| '''pedigrees'''
|| Automatic-optional
|| '''root'''
|| yes
|| host elements of specific pedigrees
|| '''pedigrees'''
|| ''pedigree names''
|| nominates further elements
|| compulsory
|-
| rowspan="4"|''pedigree name''
| rowspan="4"| Nominated-compulsory
| rowspan="4"| '''pedigrees'''
| rowspan="4"| no
| rowspan="4"| host information about a specific pedigree
|| '''file'''
|| ''pedigree file name''
|| provides pedigree file name
|| compulsory
|-
| rowspan="2"| '''switch'''
|| '''probabilistic'''
|| pedigree is probabilistic
| rowspan="2"| optional
|-
|| '''selfing'''
|| pedigree contains selfing
|-
|| '''phantomparents'''
|| integer
|| provides the number of individuals at the top of the pedigree which are phantom parents
|| optional
|-
|}

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.
  • 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
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
  • 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>

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
  • 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_.

<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
  • gg: the pedigree contains genetic groups which will be fitted as random
<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
  • 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>
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 $$\Gamma^{-1}$$
  • dense: full squared symmetric matrix
  • sparse_csr_ut: squared symmetric sparse upper triangular matrix in csr format

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:

  • 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
  • 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>

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
  • 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>

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

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