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readme.renumf90 [2016/10/13 22:02] – [Fields in the parameter file] ignacioreadme.renumf90 [2022/05/05 19:02] – [Summary] dani
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   * missing animals have code 0; 00 may be treated as a known animal   * missing animals have code 0; 00 may be treated as a known animal
  
 +\\ 
 +**Hint**: type ''renumf90 %%--%%show-template''  to have a template parameter file.
 =====Structure of parameter file====== =====Structure of parameter file======
  
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 =====Fields in the parameter file===== =====Fields in the parameter file=====
  
-# Parameter file for program renf90; it is translated to parameter +# Parameter file for renumf90. It is translated into a parameter file for the BLUPF90 family of programs.
-# file for BLUPF90 family of programs.+
  
 Lines with # are treated as comments Lines with # are treated as comments
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 </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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 the default is 3 the default is 3
  
-all pedigrees are loaded if p=0.+all pedigrees are loaded if p=0. To consider all ancestors to be traced back from genotyped and phenotyped animals, put a large number like 100. With p=0, RENUMF90 tries to include all animals found in the raw pedigree file even if the animals in the pedigree are not related to the animals with phenotype or genotype. Thus, p=0 is not recommended. 
  
 <file> <file>
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   * if t is 'internal',  allocation is by a user-written function custom_upg(year_of_birth,sex,ID, parent_code); not yet implemented.   * if t is 'internal',  allocation is by a user-written function custom_upg(year_of_birth,sex,ID, parent_code); not yet implemented.
 +
 +  * There are the other values for t: 'group', 'group_unisex', and 'group_sex'. See below for details.
 +
 <file> <file>
 INBREEDING INBREEDING
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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 ====
 +
 +See [[undoc:renumf90|a separate documentation]] for details.
 +
 +The program accepts one of the following keywords in ''UPG_TYPE'': ''group'', ''group_unisex'', and ''group_sex''.
 +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.
 +
 +  * ''group_unisex'': The program assigns a UPG code to the unknown parent regardless of the parent's sex.
 +  * ''group'': The program assigns a separate UPG code to the unknown sire and dam.
 +  * ''group_sex'': The user can specify a sex-specific UPG in the original pedigree file.
 +
 +For ''group_unisex'' and ''group'', 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
 +
 +For ''group_sex'', you need two additional columns in the pedigree file: one is for an unknown sire, and the other is for an unknown dam. For example, assume the 5th column is for unknown sire, and the 6th column is for unknown dam, the ''FILE_POS'' entry has 7 items.
 +
 +    FILE_POS
 +    1 2 3 0 0 5 6
 +
 +The program now accept 3, 5, 6, or 7 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
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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 (before elimination due to other effects) as parent 1 +   8) number of progeny (before elimination due to other effects) as parent 1 
-   9) number of progenies (before elimination due to other effects) as parent 2  +   9) number of progeny (before elimination due to other effects) as parent 2  
   10) original animal id                                               10) original animal id                                            
  
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani
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