readme.renumf90
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readme.renumf90 [2012/05/29 12:14] – [Fields in the parameter file] ignacio | readme.renumf90 [2012/05/29 12:27] – [Combining fields or interactions] ignacio | ||
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</ | </ | ||
- | optional for animal effect only; p specifies the depth of pedigree search; | + | optional\\ |
+ | for animal effect only;\\ | ||
+ | p specifies the depth of pedigree search;\\ | ||
the default is 3; all pedigrees are loaded if p=0. | the default is 3; all pedigrees are loaded if p=0. | ||
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min avg max | min avg max | ||
</ | </ | ||
- | optional; specifies minimum, average and maximum generation interval; | + | optional\\ |
+ | specifies minimum, average and maximum generation interval;\\ | ||
applicable only if year of birth present; minimum and maximum used for | applicable only if year of birth present; minimum and maximum used for | ||
- | pedigree checks; average used to predict year of birth of parent with missing | + | pedigree checks;\\ |
+ | average used to predict year of birth of parent with missing | ||
pedigree. | pedigree. | ||
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i | i | ||
</ | </ | ||
- | optional; if only one sex has records, specifies which parent it is; used for | + | optional\\ |
- | pedigree checks. | + | if only one sex has records, specifies which parent it is;\\ |
+ | used for pedigree checks. | ||
< | < | ||
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t | t | ||
</ | </ | ||
- | optional; | + | optional\\ |
- | if t is ' | + | |
- | subsequent line should contain list of years to separate different UPG; | + | |
- | if t is ' | + | * if t is ' |
- | UPG number that this missing parent should be allocated to; in this option, | + | |
- | all known parents should have pedigree lines, i.e., each parent field should | + | |
- | contain either the ID of a real parent, or a negative UPG number. | + | |
- | if t is ' | + | * if t is ' |
- | custom_upg(year_of_birth, | + | |
< | < | ||
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</ | </ | ||
Specifies that random regressions should be applied to the animal and | Specifies that random regressions should be applied to the animal and | ||
- | corresponding effects (mat, pe and mpe), this keyword also could be | + | corresponding effects (mat, pe and mpe),\\ |
- | applied to set covariables for fixed effects; r_type is ' | + | this keyword also could be applied to set covariables for fixed effects;\\ |
- | random regressions are in the data, or " | + | r_type is ' |
to be generated from a single data variable; not yet implemented | to be generated from a single data variable; not yet implemented | ||
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</ | </ | ||
- | //g// are (co)variances for the animal effect; the dimensions of g should | + | //g// are (co)variances for the animal effect;\\ |
- | account for the maternal effect if present | + | the dimensions of g should account for the maternal effect if present |
< | < | ||
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- | ---- | + | =====Extra comments===== |
- | Sections starting from EFFECTS can be repeated any number of types. | + | Sections starting from EFFECTS can be repeated any number of types.\\ |
If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 | If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 | ||
on diagonals and 0.1 on off-diagonals. | on diagonals and 0.1 on off-diagonals. | ||
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The sequence of keywords should be as above although optional fields can be | The sequence of keywords should be as above although optional fields can be | ||
- | skipped. Keywords out of order may not be recognized. | + | skipped. |
- | =====OPTIONS===== | + | Keywords out of order may not be recognized. |
+ | |||
+ | =====Options===== | ||
The following options can added at the end of the parameter file to redefine | The following options can added at the end of the parameter file to redefine | ||
- | parameter | + | parameters |
- the default size of character fields | - the default size of character fields | ||
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OPTION alpha size nn | OPTION alpha size nn | ||
</ | </ | ||
- | where nn is the new size. | + | where //nn// is the new size. |
- the size of th record length | - the size of th record length | ||
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OPTION max_string_readline nn | OPTION max_string_readline nn | ||
</ | </ | ||
- | where nn is the new size. | + | where //nn// is the new size. |
- the maximun number of fields | - the maximun number of fields | ||
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OPTION max_field_readline nn | OPTION max_field_readline nn | ||
</ | </ | ||
- | where nn is the number of fields. | + | where //nn// is the number of fields. |
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=====Combining fields or interactions====== | =====Combining fields or interactions====== | ||
- | Several fields in the data file can be combined into one using a COMBINE keyword. | + | Several fields in the data file can be combined into one using a '' |
< | < | ||
COMBINE a b c .... | COMBINE a b c .... | ||
</ | </ | ||
- | catenates b c ... into c. Keywords COMBINE need to be on top of the parameter | + | catenates |
- | file, but possibly after comments. There may be many combined fields. | + | Keywords COMBINE need to be on top of the parameter file, but possibly after comments. |
+ | |||
+ | There may be many combined fields. | ||
For example: | For example: | ||
- | </file> | + | < |
COMBINE 7 2 3 4 | COMBINE 7 2 3 4 | ||
</ | </ | ||
- | combines content of fields 2 3 4 into field 7; the data file is not changed, | + | |
- | only the program treats field 7 as fields 2 3 4 put together (without spaces). | + | combines content of fields 2 3 4 into field 7; |
- | The combined fields can be treated as " | + | |
- | and if their total length is <9. Otherwise, they need to be used as " | + | the data file is not changed, only the program treats field 7 as fields 2 3 4 put together (without spaces). |
- | Please note that the maximum size of the combined variable is limited by the | + | |
- | largest size of the " | + | |
+ | The combined fields can be treated as " | ||
+ | |||
+ | Please note that the maximum size of the combined variable is limited by the largest size of the " | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani