readme.renumf90
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readme.renumf90 [2012/05/29 12:14] – [Fields in the parameter file] ignacio | readme.renumf90 [2012/05/29 12:22] – [Fields in the parameter file] 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. |
+ | |||
+ | Keywords out of order may not be recognized. | ||
=====OPTIONS===== | =====OPTIONS===== |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani