readme.renumf90
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| readme.renumf90 [2024/05/15 18:37] – [Options] dani | readme.renumf90 [2024/05/22 18:53] (current) – [Options] dani | ||
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| - | |||
| =======RENUMF90====== | =======RENUMF90====== | ||
| A renumbering program for the '' | A renumbering program for the '' | ||
| Line 253: | Line 252: | ||
| //r_type// could be: | //r_type// could be: | ||
| * ' | * ' | ||
| - | * " | + | * " |
| < | < | ||
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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: | ||
| Line 335: | Line 334: | ||
| 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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| 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. | 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 remove_all_missing | ||
| + | </ | ||
| + | |||
| + | removes lines in the data where phenotypes are missing. Keeping those lines may cause unexpected behavior in some programs. | ||
| < | < | ||
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| OPTION no_basic_statistics | OPTION no_basic_statistics | ||
| </ | </ | ||
| - | avoids the computation of basic statistics (min, max, correlations...) which take a certain time for very large data file. | + | avoids the computation of basic statistics (min, max, correlations, ...), which take a certain time for very large data file. |
| < | < | ||
| - | OPTION inbreeding_method | + | OPTION inbreeding_method |
| </ | </ | ||
| - | 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. | + | 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. |
| | | ||
| - | | + | 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. |
| - | | + | |
| The default is method 1. Large speed-ups are made using method 6, but this requires using several threads (e.g., using '' | The default is method 1. Large speed-ups are made using method 6, but this requires using several threads (e.g., using '' | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani