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readme.renumf90 [2012/05/29 12:28] – [Options] ignacioreadme.renumf90 [2012/05/29 12:38] – [Fields in the parameter file] ignacio
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 =======RENUMF90====== =======RENUMF90======
-renumbering program for the BLUPF90 family now works with SNP info\\+A renumbering program for the ''BLUPF90'' family now works with SNP info\\
 Ignacy Misztal and Ignacio Aguilar, University of Georgia\\ Ignacy Misztal and Ignacio Aguilar, University of Georgia\\
 August 27, 2001 - Mar 17, 2011 August 27, 2001 - Mar 17, 2011
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 Lines with # are treated as comments Lines with # are treated as comments
              
-<file> +<file>
 DATAFILE DATAFILE
 f1 f1
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 The data file is f1 The data file is f1
  
-<file> +<file>
 TRAITS TRAITS
 t1 t2 .. tn t1 t2 .. tn
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 e1.. en type form e1.. en type form
 </file> </file>
-this line defines one group of effects; e1 .. en are positions of this effect for all traits;\\  +this line defines one group of effects; e1 .. en are positions of this effect for all traits; 
-positions can be different for each trait for fixed effects;\\ + 
 +positions can be different for each trait for fixed effects; 
 for random effects, only one position + 0 (misising) efefct are for random effects, only one position + 0 (misising) efefct are
 possible.  possible. 
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 d1 .. dn form d1 .. dn form
 </file> </file>
-optional for covariables only, specifies nesting;\\+optional for covariables only, specifies nesting; 
 form is as above form is as above
      
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 the RANDOM keyword occurs only if the current effect is random; the RANDOM keyword occurs only if the current effect is random;
-rtype is 'diagonal', 'sire' or 'animal'+rtype is: 
 +  * 'diagonal' 
 +  * 'sire' 
 +  * 'animal'
  
 <file> <file>
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 o1 o2.. oq o1 o2.. oq
 </file> </file>
-causes extra effects appended to the animal effect;\\ +causes extra effects appended to the animal effect; 
-current options include+ 
 +current options include:
   * 'pe' for permanent environment   * 'pe' for permanent environment
   * 'mat' for maternal   * 'mat' for maternal
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 </file> </file>
  
-for animal and sire model only, fped specifies the pedigree file+for animal and sire model only 
 + 
 + //fped// specifies the pedigree file
  
 <file> <file>
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 </file> </file>
  
-for animal effect only;\\+for animal effect only; 
 specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\ specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\
-missing alt_dam or yob can be replaced by 0\\ +missing alt_dam or yob can be replaced by 0 
-if this line is not given, defaults are 1 2 3 0 0.\\ + 
-If maternal effect is specified, the maternal effect is due to position of d if alt_dam field is 0, or otherwise is due to alt_dam;\\ If alt_dam field is not zero, it should include ID of real or recipient dam.+if this line is not given, defaults are 1 2 3 0 0. 
 + 
 +If maternal effect is specified, the maternal effect is due to position of d if alt_dam field is 0, or otherwise is due to alt_dam; 
 + 
 +If alt_dam field is not zero, it should include ID of real or recipient dam.
        
 <file> <file>
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 optional;\\ optional;\\
-//fsnp// specifies files with ID and SNP information;\\+//fsnp// specifies files with ID and SNP information; 
 if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will
-include the genomic information;\\ +include the genomic information; 
-file fsnp should start with ID with the same format as fped and SNP info needs to start from a fixed column and + 
-include digits 0, 1, 2 and 5;\\+file //fsnp// should start with ID with the same format as fped and SNP info needs to start from a fixed column and 
 +include digits 0, 1, 2 and 5; 
 + 
 ID and SNP info need to be separated by at leats one space; see info for program [[readme.pregsf90|PreGSf90]]  ID and SNP info need to be separated by at leats one space; see info for program [[readme.pregsf90|PreGSf90]] 
  
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 </file> </file>
  
-optional\\ +optional 
-for animal effect only;\\ + 
-p specifies the depth of pedigree search;\\ +for animal effect only; 
-the default is 3; all pedigrees are loaded if p=0.+ 
 +//p// specifies the depth of pedigree search; 
 + 
 +the default is 3 
 + 
 +all pedigrees are loaded if p=0.
  
 <file> <file>
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 min avg max min avg max
 </file> </file>
-optional\\ +optional 
-specifies minimum, average and maximum generation interval;\\+ 
 +specifies minimum, average and maximum generation interval 
 applicable only if year of birth present; minimum and maximum used for applicable only if year of birth present; minimum and maximum used for
-pedigree checks;\\+pedigree checks 
 average used to predict year of birth of parent with missing average used to predict year of birth of parent with missing
 pedigree. pedigree.
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 </file> </file>
 optional\\ optional\\
-if only one sex has records, specifies which parent it is;\\+if only one sex has records, specifies which parent it is 
 used for pedigree checks. used for pedigree checks.
  
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 </file> </file>
 Specifies that random regressions should be applied to the animal and Specifies that random regressions should be applied to the animal and
-corresponding effects (mat, pe and mpe),\\ +corresponding effects (mat, pe and mpe) 
-this keyword also could be applied to set covariables for fixed effects;\\ + 
-r_type is 'data' if covariables for random regressions are in the data, or "legendre' if legendre plynomials are +this keyword also could be applied to set covariables for fixed effects; 
-to be generated from a single data variable; not yet implemented+ 
 +//r_type// could be: 
 +  * 'data' if covariables for random regressions are in the data 
 +  * "legendre' if legendre plynomials are to be generated from a single data variable; not yet implemented
  
 <file> <file>
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 r1 .. rq r1 .. rq
 </file> </file>
-for random regressions, r1-rq specifies positions of covariables if +for random regressions, 
-r_type='data', or r1 is order of legendre polynomial and r2 is position of + 
-covariable if r_type='legendre'; not yet implemented +  * //r1-rq// specifies positions of covariables if r_type='data' 
-</file>+  * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type='legendre'; not yet implemented
  
 <file> <file>
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 </file> </file>
  
-//g// are (co)variances for the animal effect;\\ +//g// are (co)variances for the animal effect 
-the dimensions of g should account for the maternal effect if present+ 
 +the dimensions of g should account for random correlated effect if present (maternal or random regression)
  
 <file> <file>
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 =====Extra comments===== =====Extra comments=====
  
-Sections starting from EFFECTS can be repeated any number of types.\\+Sections starting from EFFECTS can be repeated any number of types. 
 If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0  If (Co)variances for any effect are missing, they are substituted with matrices containing 1.0 
 on diagonals and 0.1 on off-diagonals.  on diagonals and 0.1 on off-diagonals. 
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  - the default size of character fields  - the default size of character fields
 <file> <file>
- OPTION alpha size nn+OPTION alpha size nn
 </file> </file>
 where //nn// is the new size. where //nn// is the new size.
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  - the size of th record length   - the size of th record length 
 <file> <file>
- OPTION max_string_readline nn+OPTION max_string_readline nn
 </file> </file>
 where //nn// is the new size. where //nn// is the new size.
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  - the maximun number of fields    - the maximun number of fields  
 <file> <file>
-        OPTION max_field_readline nn+OPTION max_field_readline nn
 </file> </file>
 where //nn// is the number of fields.  where //nn// is the number of fields. 
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    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    +   6) number of known parents (parents might be eliminated if not contributing; 
-      contributing; 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)  +   8) number of progenies (before elimination due to other effects) as parent 1 
-      as parent 1 +   9) number of progenies (before elimination due to other effects) as parent 2  
-   9) number of progenies (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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