readme.renumf90
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readme.renumf90 [2016/10/13 21:58] – [Fields in the parameter file] ignacio | readme.renumf90 [2020/04/21 07:05] – yutaka | ||
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</ | </ | ||
The data file is f1 | The data file is f1 | ||
+ | |||
+ | < | ||
+ | SKIP_HEADER | ||
+ | n | ||
+ | </ | ||
+ | This is optional. It skips the first n lines as header in the data file. | ||
< | < | ||
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// | // | ||
+ | |||
+ | < | ||
+ | SKIP_HEADER | ||
+ | n | ||
+ | </ | ||
+ | This is optional. It skips the first n lines as header in the pedigree file. | ||
< | < | ||
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* if t is ' | * if t is ' | ||
+ | |||
+ | * There are the other values for t: ' | ||
+ | |||
< | < | ||
INBREEDING | INBREEDING | ||
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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 | ||
- | * if inb_type | + | |
- | * if inb_type is ' | + | //inb_type// could be: |
+ | * ' | ||
+ | * ' | ||
+ | |||
+ | < | ||
+ | FIXED_REGRESSION | ||
+ | r_type | ||
+ | </ | ||
+ | It is the same as '' | ||
< | < | ||
RANDOM_REGRESSION | RANDOM_REGRESSION | ||
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</ | </ | ||
//gmpe// are (co)variances for the MPE effect if present | //gmpe// are (co)variances for the MPE effect if present | ||
+ | |||
+ | |||
+ | ==== User-defined UPG code ==== | ||
+ | |||
+ | See [[undoc: | ||
+ | |||
+ | The program accepts one of the following keywords in '' | ||
+ | With one of these options, the program looks at a particular column in the pedigree file as a group code and use it for assigning the UPG code. If an animal has a missing parent, the program assigns a UPG code based on the group code. | ||
+ | |||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | |||
+ | For '' | ||
+ | |||
+ | FILE_POS | ||
+ | 1 2 3 0 0 5 | ||
+ | |||
+ | For '' | ||
+ | |||
+ | FILE_POS | ||
+ | 1 2 3 0 0 5 6 | ||
+ | |||
+ | The program now accept 3, 5, 6, or 7 items in '' | ||
+ | |||
=====Extra comments===== | =====Extra comments===== | ||
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parameters used to read the input file: | parameters used to read the input file: | ||
- | - the default size of character fields | + | - the default size of character fields |
< | < | ||
OPTION alpha_size nn | OPTION alpha_size nn | ||
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where //nn// is the new size. | where //nn// is the new size. | ||
- | - the size of th record length | + | - the size of th record length |
< | < | ||
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 number of fields | + | - the maximun number of fields |
< | < | ||
OPTION max_field_readline nn | OPTION max_field_readline nn | ||
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if animal has genotype 10+number of know parents | if animal has genotype 10+number of know parents | ||
7) number of records | 7) number of records | ||
- | 8) number of progenies | + | 8) number of progeny |
- | 9) number of progenies | + | 9) number of progeny |
10) original animal id | 10) original animal id | ||
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani