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readme.renumf90 [2016/11/04 21:17] – [Additive Pedigree File] shogoreadme.renumf90 [2018/06/05 23:50] – [Options] dani
Line 47: Line 47:
 </file> </file>
 The data file is f1 The data file is f1
 +
 +<file>
 +SKIP_HEADER
 +n
 +</file>
 +This is optional. It skips the first n lines as header in the data file.
  
 <file> <file>
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  //fped// specifies the pedigree file  //fped// specifies the pedigree file
 +
 +<file>
 +SKIP_HEADER
 +n
 +</file>
 +This is optional. It skips the first n lines as header in the pedigree file.
  
 <file> <file>
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   * 'pedigree' - the program computes inbreeding coefficients with Meuwissen and Luo (1992) using the pedigree to be saved in renaddxx.ped; calculated inbreeding coefficients will be saved in a file "renf90.inb" with the original ID   * 'pedigree' - the program computes inbreeding coefficients with Meuwissen and Luo (1992) using the pedigree to be saved in renaddxx.ped; calculated inbreeding coefficients will be saved in a file "renf90.inb" with the original ID
   * 'file' - the program reads inbreeding coefficients from an external file. You should put the filename after 'file' e.g. 'file inbreeding.txt'. The file has at least 2 columns: original_ID and inbreeding value (from 0.0 to 1.0). The program just skips unnecessary IDs   * 'file' - the program reads inbreeding coefficients from an external file. You should put the filename after 'file' e.g. 'file inbreeding.txt'. The file has at least 2 columns: original_ID and inbreeding value (from 0.0 to 1.0). The program just skips unnecessary IDs
 +
 +<file>
 +FIXED_REGRESSION 
 +r_type
 +</file>
 +It is the same as ''RANDOM_REGRESSION'' (see the explanation below) but it is effective only for fixed effects.
  
 <file> <file>
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 </file>  </file> 
 //gmpe// are (co)variances for the MPE effect if present //gmpe// are (co)variances for the MPE effect if present
 +
 +
 +==== User-defined UPG code ====
 +
 +The program accepts the following keywords in ''UPG_TYPE''.
 +
 +    UPG_TYPE
 +    group
 +    
 +    or
 +    
 +    UPG_TYPE
 +    group_unisex
 +
 +With this option, the program looks at a particular column in the pedigree file as a group code and saves it. If an animal has a missing parent, the program assigns an UPG code according to the group code. If you want to assign separate UPGs by the parent's sex (sire or dam), use ''group''. The ''group_unisex'' doesn't consider the sex of parents.
 +
 +The column in the pedigree file is specified with the 6th item in ''FILE_POS''. The following example tells the program the 5th column in the pedigree file as the group code. The group code will be treated as characters.
 +
 +    FILE_POS
 +    1 2 3 0 0 5
 +
 +The program now accept 3 items, 5 items, or 6 items in ''FILE_POS''.
 +
 +
 +
 =====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 (default = 20)
 <file> <file>
 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 (default = 800) 
 <file> <file>
 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 (default = 100) 
 <file> <file>
 OPTION max_field_readline nn OPTION max_field_readline nn
readme.renumf90.txt · Last modified: 2024/05/15 18:44 by dani
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