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<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:
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:
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:
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:
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:
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:
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:
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:
<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:
<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:
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:
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:
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:
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:
word
|
example
|
type
|
variable type
|
variable values
|
default
|
explanation
|
jobs
|
jobs: solve,yhat
|
compulsory
|
csv word-list
|
solve,sample,pevsample,mcemreml,yhat
|
none
|
job sequence is determined by the list sequence. list content determines nominated-compulsory elements
|
- nominated-compulsory elements
- <solve>
- <sample>
- <pevsample>
- <mcemreml>
- <yhat>
<solve>
example
|
host element
|
element type
|
purpose
|
<root>
..
<jobs>
..
<solve>
solver: mysolver
</solve>
..
</jobs>
..
</root>
|
jobs
|
conditional-compulsory
|
hosts information about job solve
|
content:
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:
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:
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
|
<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:
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:
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
|
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
|
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
|
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>