readme.renumf90
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readme.renumf90 [2023/03/02 01:08] – [Options] andres | readme.renumf90 [2023/06/05 17:05] – [Options] andres | ||
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// | // | ||
* ' | * ' | ||
- | * ' | + | * ' |
* 'self x' - Calculates inbreeding with selfing, where x is the column in the pedigree file with the number of selfing generation | * 'self x' - Calculates inbreeding with selfing, where x is the column in the pedigree file with the number of selfing generation | ||
* ' | * ' | ||
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//r_type// could be: | //r_type// could be: | ||
* ' | * ' | ||
- | * " | + | * " |
< | < | ||
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* //r1-rq// specifies positions of covariables if r_type=' | * //r1-rq// specifies positions of covariables if r_type=' | ||
- | * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type=' | + | * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type=' |
< | < | ||
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where //nn// is the new size. | where //nn// is the new size. | ||
- | - the maximun | + | - the maximum |
< | < | ||
OPTION max_field_readline nn | OPTION max_field_readline nn | ||
</ | </ | ||
where //nn// is the number of fields. | where //nn// is the number of fields. | ||
+ | |||
+ | < | ||
+ | OPTION missing x | ||
+ | </ | ||
+ | |||
+ | allows indicating that missing value is the number x (e.g. 999) for instance if 0 is a valid record. | ||
< | < | ||
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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: | 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: | ||
- | + | * 7: Recursive tabular with self breeding generations . This method is for populations with selfing, i.e. wheat. | |
+ | * 6: Hybrid parallel computing which is basically a parallel (OMP) version of Meuwissen and Luo (1992) | ||
+ | * 5: method of Tier (1990) | ||
+ | * 4: recursive tabular method | ||
+ | * 3: Modified Colleau by Sargolzaei et al. (2005) | ||
+ | * 2: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004) | ||
+ | * 1: Meuwissen and Luo (1992) | ||
+ | the default is method 6, and speed-ups are made using method 6 but this requires using several threads (e.g. using '' | ||
The end of the parameter file for '' | The end of the parameter file for '' | ||
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2) parent 1 number or unknown parent group number for parent 1 | 2) parent 1 number or unknown parent group number for parent 1 | ||
3) parent 2 number or unknown parent group number for parent 2 | 3) parent 2 number or unknown parent group number for parent 2 | ||
- | 4) 3 minus number of known parents | + | 4) 3 minus number of known parents |
5) known or estimated year of birth (0 if not provided) | 5) known or estimated year of birth (0 if not provided) | ||
6) number of known parents (parents might be eliminated if not contributing; | 6) number of known parents (parents might be eliminated if not contributing; |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani