readme.renumf90
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readme.renumf90 [2022/09/13 19:43] – dani | readme.renumf90 [2024/05/22 18:47] – [Options] dani | ||
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=======RENUMF90====== | =======RENUMF90====== | ||
A renumbering program for the '' | A renumbering program for the '' | ||
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< | < | ||
WEIGHT(S) | WEIGHT(S) | ||
- | w | + | w1 [w2 w3...wn] |
</ | </ | ||
- | w is | + | w1 [w2 w3...wn] are |
< | < | ||
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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 |
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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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=====Options===== | =====Options===== | ||
- | The following options can added at the end of the parameter file to redefine | + | The following options can be added at the end of the parameter file to redefine |
parameters used to read the input file: | parameters used to read the input file: | ||
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where //nn// is the new size. | where //nn// is the new size. | ||
- | - the size of th record length (default = 800) | + | - the size of the record length (default = 800) |
< | < | ||
OPTION max_string_readline nn | OPTION max_string_readline nn | ||
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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 | ||
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where //nn// is the number of fields. | where //nn// is the number of fields. | ||
+ | < | ||
+ | OPTION missing x | ||
+ | </ | ||
+ | |||
+ | allows indicating that the missing value is the number x (e.g., 999), for instance, if 0 is a valid record. This is only to represent the missing value in the data. If there are covariables in the data, 0 is treated as a value, not missing information. Missing pedigree is always 0 and cannot be changed to another value. | ||
+ | |||
+ | < | ||
+ | OPTION missing_in_weights | ||
+ | </ | ||
+ | |||
+ | in addition, this indicates that if a weight for the trait is 0, then the value of the trait is converted to " | ||
+ | |||
+ | < | ||
+ | OPTION no_basic_statistics | ||
+ | </ | ||
+ | avoids the computation of basic statistics (min, max, correlations, | ||
+ | |||
+ | < | ||
+ | OPTION inbreeding_method m | ||
+ | </ | ||
+ | |||
+ | 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. Acceptable values for m are: | ||
+ | | ||
+ | 1: Meuwissen and Luo (1992) | ||
+ | 2: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004) | ||
+ | 3: Modified Colleau by Sargolzaei et al. (2005) | ||
+ | 4: recursive tabular method | ||
+ | 5: method of Tier (1990) | ||
+ | 6: Hybrid parallel computing, which is basically a parallel (OMP) version of Meuwissen and Luo (1992) | ||
+ | 7: Recursive tabular with self-breeding generations. For populations with selfing, i.e., wheat | ||
+ | |||
+ | The default is method 1. Large 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 '' | ||
- | All of these lines are passed to parameter file renf90.par to be used by application programs. | + | All of these lines are passed to the parameter file renf90.par to be used by application programs. |
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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