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readme.renumf90 [2012/05/29 11:36] – ignacioreadme.renumf90 [2012/05/29 11:42] – ignacio
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 # file for BLUPF90 family of programs. # file for BLUPF90 family of programs.
  
-   Lines with # are treated as comments+Lines with # are treated as comments
              
 <file>    <file>   
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 f1 f1
 </file> </file>
-   The data file is f1+The data file is f1
  
 <file>    <file>   
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 t1 t2 .. tn t1 t2 .. tn
 </file> </file>
-   t1-tn are positions of traits in datafile; n defines the number of traits+t1-tn are positions of traits in datafile; n defines the number of traits
  
 <file> <file>
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 p1 p2 .. pm p1 p2 .. pm
 <file> <file>
-   fields p1-pn are passed to output without changes; can be empty+fields p1-pn are passed to output without changes; can be empty
        
 <file> <file>
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 w w
 </file> </file>
-   w is  position of weight if present; can be empty+w is  position of weight if present; can be empty
  
 <file>    <file>   
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 r r
 </file> </file>
-   r is matrix of residual (co)variances  of size n x n+r is matrix of residual (co)variances  of size n x n
  
 <file> <file>
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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  +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 +effect for all traits; positions can be different for each trait for fixed 
-   effects; for random effects, only one position + 0 (misising) efefct are +effects; for random effects, only one position + 0 (misising) efefct are 
-   possible. +possible.  
-    +  * type is 'cross' for crossclassified or 'cov' for covariables 
-   type is 'cross' for crossclassified or 'cov' for covariables +  * form is 'alpha' for alphanumeric or 'numer' for numeric
-    +
-   form is 'alpha' for alphanumeric or 'numer' for numeric+
  
 <file> <file>
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 d1 .. dn form d1 .. dn form
 </file> </file>
-   optional for covariables only, specifies nesting; form is as above+optional for covariables only, specifies nesting; form is as above
      
 <file> <file>
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 </file> </file>
  
-   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' or 'animal'
  
 <file>    <file>   
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 o1 o2.. oq o1 o2.. oq
 <file> <file>
-   causes extra effects appended to the animal effect; current options include +causes extra effects appended to the animal effect; current options include 
-   'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal  +'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal  
-   permanent environment +permanent environment 
  
 <file>       <file>      
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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; specifies positions in the pedigree file of animal +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; missing +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; if this line is not given, defaults are  +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 +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 +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 +alt_dam field is not zero, it should include ID of real or recipient 
-   dam.+dam.
        
 <file>    <file>   
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 </file> </file>
  
-   optional; fsnp specifies files with ID and SNP information; if present, the  +optional; fsnp specifies files with ID and SNP information; if present, the  
-   relationship matrix will be constructed as in Aguilar et al. (2010) and will +relationship matrix will be constructed as in Aguilar et al. (2010) and will 
-   include the genomic information; file fsnp should start with ID with the +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 +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 +include digits 0, 1, 2 and 5; ID and SNP info need to be separated by 
-   at leats one space; see info for program PreGSf90 +at leats one space; see info for program PreGSf90 
 <file>    <file>   
 PED_DEPTH PED_DEPTH
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 </file> </file>
  
-<file>    +optional for animal effect only; p specifies the depth of pedigree search;  
-   optional for animal effect only; p specifies the depth of pedigree search;  +the default is 3; all pedigrees are loaded if p=0. 
-   the default is 3; all pedigrees are loaded if p=0. + 
-   +<file>    
 GEN_INT GEN_INT
 min avg max min avg max
 +</file>
 +optional; specifies minimum, average and maximum generation interval;
 +applicable only if year of birth present; minimum and maximum used for
 +pedigree checks; average used to predict year of birth of parent with missing
 +pedigree.
  
-   optional; specifies minimum, average and maximum generation interval; +<file>    
-   applicable only if year of birth present; minimum and maximum used for +
-   pedigree checks; average used to predict year of birth of parent with missing +
-   pedigree. +
-   +
 REC_SEX REC_SEX
 i i
 +</file>
 +optional; if only one sex has records, specifies which parent it is; used for
 +pedigree checks.
  
-   optional; if only one sex has records, specifies which parent it is; used for +<file>    
-   pedigree checks. +
-   +
 UPG_TYPE UPG_TYPE
 t t
- +</file> 
-   optional;  +optional;  
-   if t is 'yob', the asignment is based on year of birth; the +if t is 'yob', the asignment is based on year of birth; the 
-   subsequent line should contain list of years to separate different UPG; +subsequent line should contain list of years to separate different UPG; 
        
-   if t is 'in_pedigrees', the value of a missing parent should be -x, where x is +if t is 'in_pedigrees', the value of a missing parent should be -x, where x is 
-   UPG number that this missing parent should be allocated to; in this option,  +UPG number that this missing parent should be allocated to; in this option,  
-   all known parents should have pedigree lines, i.e., each parent field should +all known parents should have pedigree lines, i.e., each parent field should 
-   contain either the ID of a real parent, or a negative UPG number.+contain either the ID of a real parent, or a negative UPG number.
        
-   if t is 'internal',  allocation is by a user-written function  +if t is 'internal',  allocation is by a user-written function  
-   custom_upg(year_of_birth,sex,ID, parent_code).+custom_upg(year_of_birth,sex,ID, parent_code).
  
-   +<file>    
 RANDOM_REGRESSION  RANDOM_REGRESSION 
 r_type r_type
 +</file>
 +Specifies that random regressions should be applied to the animal and
 +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
 +to be generated from a single data variable; not yet implemented
  
-   Specifies that random regressions should be applied to the animal and +<file>    
-   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 +
-   to be generated from a single data variable; not yet implemented +
-   +
 RR_POSITION RR_POSITION
 r1 .. rq r1 .. rq
-   for random regressions, r1-rq specifies positions of covariables if +</file> 
-   r_type='data', or r1 is order of legendre polynomial and r2 is position of +for random regressions, r1-rq specifies positions of covariables if 
-   covariable if r_type='legendre'; not yet implemented +r_type='data', or r1 is order of legendre polynomial and r2 is position of 
-   +covariable if r_type='legendre'; not yet implemented 
 +</file> 
 + 
 +<file>    
 (CO)VARIANCES (CO)VARIANCES
 g g
 +</file>
  
-   g are (co)variances for the animal effect; the dimensions of g should  +//g// are (co)variances for the animal effect; the dimensions of g should  
-   account for the maternal effect if present +account for the maternal effect if present 
-   + 
 +<file>    
 (CO)VARIANCES_PE (CO)VARIANCES_PE
 gpe gpe
 +</file>
 +//gpe// are (co)variances for the PE effect if present
  
-   gpe are (co)variances for the PE effect if present +<file> 
 (CO)VARIANCES_MPE (CO)VARIANCES_MPE
 gmpe gmpe
- +</file>  
-   gmpe are (co)variances for the MPE effect if present+//gmpe// are (co)variances for the MPE effect if present
  
  
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani
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