Difference between revisions of "Parameter file elements"
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|} | |} | ||
*nominated-compulsory elements | *nominated-compulsory elements | ||
='''genotypes'''= | =<'''genotypes'''>= | ||
='''grms'''= | =<'''grms'''>= | ||
='''model'''= | =<'''model'''>= | ||
=='''eqn'''== | ==<'''eqn'''>== | ||
=='''poly'''== | ==<'''poly'''>== | ||
='''jobs'''= | =<'''jobs'''>= | ||
Example: | Example: | ||
| Line 70: | Line 70: | ||
|} | |} | ||
*nominated-compulsory elements | *nominated-compulsory elements | ||
=='''solve'''== | ==<'''solve'''>== | ||
Example: | Example: | ||
| Line 108: | Line 108: | ||
|} | |} | ||
=='''sample'''== | ==<'''sample'''>== | ||
=='''pevsample'''== | ==<'''pevsample'''>== | ||
=='''mcemreml'''== | ==<'''mcemreml'''>== | ||
=='''yh'''== | ==<'''yh'''>== | ||
='''samplers'''= | =<'''samplers'''>= | ||
==''sampler name''== | ==<''sampler name''>== | ||
='''solvers'''= | =<'''solvers'''>= | ||
*host: '''root''' | *host: '''root''' | ||
==''solver name''== | ==<''solver name''>== | ||
*host: '''solvers''' | *host: '''solvers''' | ||
*hosts mutually exclusive elements of which hard-coded names define the solver type | *hosts mutually exclusive elements of which hard-coded names define the solver type | ||
==='''pcgiod'''=== | ===<'''pcgiod'''>=== | ||
*host: ''solver name'' | *host: ''solver name'' | ||
*defines the solver is an iteration-on-data preconditioned gradient solver | *defines the solver is an iteration-on-data preconditioned gradient solver | ||
Revision as of 11:32, 3 January 2021
<pedigrees>
Example:
<root>
..
<pedigrees>
pedigrees: a,b
...
</pedigrees>
</root>host: root
content:
- key strings
| example | type | variable type | variable values | default | explanation |
| 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 |