Parameter file elements

<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 </myped> .. </pedigrees> </root>	pedigrees	nominated-compulsory	hosts information about a specific pedigree identified by pedigree name

content:

• key strings

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

<genotypes>

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

<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:YA	optional	alternative words	VR|YA	VR	content determines the method to be used for building a grm from genotypes VR: VanRaden Method 1 is used YA: VanRaden Method 2(method Yang) is used

<vars>

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>

<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:

• compulsory element <sigma>
• optional element <gamma>

<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:

• compulsory element <sigma>
• optional element <gamma>

<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 $$\Theta$$

• optional element <matrix attributes="array">

<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 $$\Gamma \otimes \Sigma$$.

content:

• mutually exclusive elements <A>, <H> 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.

<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|hblup	hblup	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	none	adjustg2a: adjustment of $$G$$ towards $$A_{gg}$$ using method

<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	optional	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

<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.

<jobs>

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

content:

• key strings

word	example	type	variable type	variable values	default	explanation
jobs	jobs: solve,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
  • <solve>
  • <sample>
  • <pevsample>
  • <mcemreml>
  • <yh>

<solve>

Example:

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

<solvers>

• host: root

<solver name>

• host: solvers
• hosts mutually exclusive elements of which hard-coded names define the solver type

<pcgiod>

• host: solver name
• defines the solver is an iteration-on-data preconditioned gradient solver

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
pedigree name	Nominated-compulsory	pedigrees	no	host information about a specific pedigree	file	pedigree file name	provides pedigree file name	compulsory
					switch	probabilistic	pedigree is probabilistic	optional
						selfing	pedigree contains selfing
					phantomparents	integer	provides the number of individuals at the top of the pedigree which are phantom parents	optional