Difference between revisions of "Parameter file elements"
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| Line 23: | Line 23: | ||
*key strings | *key strings | ||
{| class="wikitable" | {| class="wikitable" | ||
|word | |||
|example | |example | ||
|type | |type | ||
| Line 30: | Line 31: | ||
|explanation | |explanation | ||
|- | |- | ||
|'''pedigrees''' | |||
|'''pedigrees''': ''a,b'' | |'''pedigrees''': ''a,b'' | ||
|compulsory | |compulsory | ||
Revision as of 11:42, 3 January 2021
<pedigrees>
| Example | host | type | purpose |
<root>
..
<pedigrees>
pedigrees: a,b
...
</pedigrees>
</root> |
root | automatic-optional | hosts one to several elements each containing information about specific pedigrees |
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 nominated-compulsory elements |
- nominated-compulsory elements
<genotypes>
<grms>
<model>
<eqn>
<poly>
<jobs>
Example:
<root>
..
<jobs>
jobs: solve,yh
...
</jobs>
</root>host: root
content:
- key strings
| example | type | variable type | variable values | default | explanation |
| 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>
Example:
<root>
..
<jobs>
..
<solve>
solver: mysolver
</solve>
..
</jobs>
..
</root>host: jobs
content:
- key strings
| example | type | variable type | variable values | default | explanation |
| solver: mysolver | compulsory | word | solver name | none | solver name must be the name of a previously defined solver |
<sample>
<pevsample>
<mcemreml>
<yh>
<samplers>
<sampler name>
<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 |