Difference between revisions of "Parameter file elements"
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{{!}}defines parameters of a solver of type '''pcgiod''' | {{!}}defines parameters of a solver of type '''pcgiod''' | ||
}} | }} | ||
content: | |||
*key strings | *key strings | ||
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{{!}}provides the convergence threshold | {{!}}provides the convergence threshold | ||
}} | }} | ||
===<'''direct'''>=== | |||
{{tableele1| | |||
{{!}}<syntaxhighlight lang="xml" line> | |||
<root> | |||
.. | |||
<solvers> | |||
solvers: a,.. | |||
<a> | |||
<direct> | |||
</direct> | |||
</a> | |||
</solvers> | |||
</root> | |||
</syntaxhighlight> | |||
{{!}}''solver name'' | |||
{{!}}compulsory | |||
{{!}}defines parameters of a solver of type '''direct''' | |||
}} | |||
content: no content defined |
Revision as of 11:48, 4 January 2021
<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.
|
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
|
<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:
<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:
- 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
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 |
|
<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 $$\Gamma^{-1}$$
|
<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,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:
- 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 |
<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 |
<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