Parameter file elements

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.

<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: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
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:

• 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>

• 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

• 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: .

<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:

• 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	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>
  • <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 model strings 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.

<mcemreml>

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

content:

• key strings

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

<yhat>

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