readme.renumf90
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readme.renumf90 [2012/05/29 11:38] – ignacio | readme.renumf90 [2012/05/29 11:42] – ignacio | ||
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effect for all traits; positions can be different for each trait for fixed | effect for all traits; positions can be different for each trait for fixed | ||
effects; for random effects, only one position + 0 (misising) efefct are | effects; for random effects, only one position + 0 (misising) efefct are | ||
- | possible. | + | possible. |
- | + | ||
* type is ' | * type is ' | ||
- | |||
* form is ' | * form is ' | ||
Line 143: | Line 141: | ||
</ | </ | ||
- | < | ||
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. | ||
- | + | ||
+ | < | ||
GEN_INT | GEN_INT | ||
min avg max | min avg max | ||
+ | </ | ||
+ | optional; specifies minimum, average and maximum generation interval; | ||
+ | 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. | ||
- | optional; specifies minimum, average and maximum generation interval; | + | < |
- | | + | |
- | | + | |
- | | + | |
- | + | ||
REC_SEX | REC_SEX | ||
i | i | ||
+ | </ | ||
+ | optional; if only one sex has records, specifies which parent it is; used for | ||
+ | pedigree checks. | ||
- | optional; if only one sex has records, specifies which parent it is; used for | + | < |
- | | + | |
- | + | ||
UPG_TYPE | UPG_TYPE | ||
t | t | ||
- | + | </ | |
- | | + | 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, |
- | + | < | |
RANDOM_REGRESSION | RANDOM_REGRESSION | ||
r_type | r_type | ||
+ | </ | ||
+ | Specifies that random regressions should be applied to the animal and | ||
+ | corresponding effects (mat, pe and mpe), this keyword also could be | ||
+ | applied to set covariables for fixed effects; r_type is ' | ||
+ | random regressions are in the data, or " | ||
+ | to be generated from a single data variable; not yet implemented | ||
- | Specifies that random regressions should be applied to the animal and | + | < |
- | | + | |
- | | + | |
- | | + | |
- | to be generated from a single data variable; not yet implemented | + | |
- | + | ||
RR_POSITION | RR_POSITION | ||
r1 .. rq | r1 .. rq | ||
- | for random regressions, | + | </ |
- | | + | for random regressions, |
- | | + | r_type=' |
- | | + | covariable if r_type=' |
+ | </ | ||
+ | |||
+ | < | ||
(CO)VARIANCES | (CO)VARIANCES | ||
g | g | ||
+ | </ | ||
- | g are (co)variances for the animal effect; the dimensions of g should | + | //g// are (co)variances for the animal effect; the dimensions of g should |
- | | + | account for the maternal effect if present |
- | | + | |
+ | < | ||
(CO)VARIANCES_PE | (CO)VARIANCES_PE | ||
gpe | gpe | ||
+ | </ | ||
+ | //gpe// are (co)variances for the PE effect if present | ||
- | gpe are (co)variances for the PE effect if present | + | < |
(CO)VARIANCES_MPE | (CO)VARIANCES_MPE | ||
gmpe | gmpe | ||
- | + | </ | |
- | | + | //gmpe// are (co)variances for the MPE effect if present |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani