readme.renumf90
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
readme.renumf90 [2022/03/17 18:59] – andres | readme.renumf90 [2023/03/02 01:08] – [Options] andres | ||
---|---|---|---|
Line 21: | Line 21: | ||
* missing animals have code 0; 00 may be treated as a known animal | * missing animals have code 0; 00 may be treated as a known animal | ||
+ | \\ | ||
+ | **Hint**: type '' | ||
=====Structure of parameter file====== | =====Structure of parameter file====== | ||
Line 67: | Line 68: | ||
< | < | ||
WEIGHT(S) | WEIGHT(S) | ||
- | w | + | w1 [w2 w3...wn] |
</ | </ | ||
- | w is | + | w1 [w2 w3...wn] are |
< | < | ||
Line 85: | Line 86: | ||
positions can be different for each trait for fixed effects; | positions can be different for each trait for fixed effects; | ||
- | for random effects, only one position + 0 (misising) efefct are | + | for random effects, only one position + 0 (missing) efefct are |
possible. | possible. | ||
* type is ' | * type is ' | ||
- | * form is ' | + | * for crossclassified effects: |
+ | * for covariables: | ||
< | < | ||
Line 182: | Line 184: | ||
the default is 3 | the default is 3 | ||
- | all pedigrees are loaded if p=0. To consider all ancestors | + | all pedigrees are loaded if p=0. This is the fastest as it reads the pedigree file only once. However, if you want to extract the informative animals (genotyped and phenotyped animals |
Line 226: | Line 228: | ||
</ | </ | ||
optional\\ | optional\\ | ||
- | use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file | + | use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file. Inbreeding calculation is a default in RENUMF90 ≥ v1.157, even if this keyword is not used. |
// | // | ||
* ' | * ' | ||
* ' | * ' | ||
+ | * 'self x' - Calculates inbreeding with selfing, where x is the column in the pedigree file with the number of selfing generation | ||
+ | * ' | ||
< | < | ||
Line 342: | Line 346: | ||
</ | </ | ||
where //nn// is the number of fields. | where //nn// is the number of fields. | ||
+ | |||
+ | < | ||
+ | OPTION no_basic_statistics | ||
+ | </ | ||
+ | avoids the computation of basic statistics (min, max, correlations...) which take a certain time for very large data file. | ||
+ | |||
+ | < | ||
+ | OPTION inbreeding_method n | ||
+ | </ | ||
+ | |||
+ | allows choosing a method for inbreeding calculation. The inbreeding coefficients are used later (in the other programs) to set up the coefficients for the A-inverse. Existing options are: | ||
+ | |||
+ | |||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani