readme.renumf90
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readme.renumf90 [2012/11/18 21:43] – ignacio | readme.renumf90 [2018/05/18 23:36] – yutaka | ||
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for animal effect only; | for animal effect only; | ||
- | specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam | + | specifies positions in the pedigree file of animal |
missing alt_dam or yob can be replaced by 0 | missing alt_dam or yob can be replaced by 0 | ||
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* if t is ' | * if t is ' | ||
+ | < | ||
+ | INBREEDING | ||
+ | inb_type | ||
+ | </ | ||
+ | optional\\ | ||
+ | use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file | ||
+ | |||
+ | // | ||
+ | * ' | ||
+ | * ' | ||
+ | |||
+ | < | ||
+ | FIXED_REGRESSION | ||
+ | r_type | ||
+ | </ | ||
+ | It is the same as '' | ||
< | < | ||
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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) | + | corresponding |
this keyword also could be applied to set covariables for fixed effects; | this keyword also could be applied to set covariables for fixed effects; | ||
Line 248: | Line 265: | ||
</ | </ | ||
//gmpe// are (co)variances for the MPE effect if present | //gmpe// are (co)variances for the MPE effect if present | ||
+ | |||
+ | |||
+ | ==== User-defined UPG code ==== | ||
+ | |||
+ | The program accepts the following keywords in '' | ||
+ | |||
+ | UPG_TYPE | ||
+ | group | ||
+ | | ||
+ | or | ||
+ | | ||
+ | UPG_TYPE | ||
+ | group_unisex | ||
+ | |||
+ | With this option, the program looks at a particular column in the pedigree file as a group code and saves it. If an animal has a missing parent, the program assigns an UPG code according to the group code. If you want to assign separate UPGs by the parent' | ||
+ | |||
+ | The column in the pedigree file is specified with the 6th item in '' | ||
+ | |||
+ | FILE_POS | ||
+ | 1 2 3 0 0 5 | ||
+ | |||
+ | The program now accept 3 items, 5 items, or 6 items in '' | ||
+ | |||
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- the default size of character fields | - the default size of character fields | ||
< | < | ||
- | OPTION | + | OPTION |
</ | </ | ||
where //nn// is the new size. | where //nn// is the new size. | ||
Line 300: | Line 340: | ||
</ | </ | ||
catenates //b c// ... into //a//.\\ | catenates //b c// ... into //a//.\\ | ||
- | Keywords | + | Keyword |
There may be many combined fields. | There may be many combined fields. | ||
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if animal has genotype 10+number of know parents | if animal has genotype 10+number of know parents | ||
7) number of records | 7) number of records | ||
- | 8) number of progenies | + | 8) number of progeny |
- | 9) number of progenies | + | 9) number of progeny |
10) original animal id | 10) original animal id | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani