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readme.renumf90 [2012/05/29 11:36] – ignacioreadme.renumf90 [2012/05/29 12:07] – [Structure of parameter file] ignacio
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 The parameter file contains keywords in capital followed by specifications The parameter file contains keywords in capital followed by specifications
-of a given effect/data item. The keywords need to be typed exactly. Specific+of a given effect/data item.\\ The keywords need to be typed exactly.\\ Specific
 keywords need to occur sequentially, as shown below.  keywords need to occur sequentially, as shown below. 
  
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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>
 FIELDS_PASSED TO OUTPUT FIELDS_PASSED TO OUTPUT
 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>   
 OPTIONAL OPTIONAL
 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 
  
 +----
  
 Sections starting from EFFECTS can be repeated any number of types. Sections starting from EFFECTS can be repeated any number of types.
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 skipped. Keywords out of order may not be recognized. skipped. Keywords out of order may not be recognized.
  
 +=====OPTIONS=====
 The following options can added at the end of the parameter file to redefine The following options can added at the end of the parameter file to redefine
 parameter used to read the input file: parameter used to read the input file:
  
  - the default size of character fields  - the default size of character fields
 +<file>
  OPTION alpha size nn  OPTION alpha size nn
 +</file>
    where nn is the new size.    where nn is the new size.
  
  - the size of th record length   - the size of th record length 
 +<file>
  OPTION max_string_readline nn  OPTION max_string_readline nn
 +</file>
    where nn is the new size.    where nn is the new size.
  
  - the maximun number of fields    - the maximun number of fields  
 +<file>
         OPTION max_field_readline nn         OPTION max_field_readline nn
 +</file>
    where nn is the number of fields.     where nn is the number of fields. 
  
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-Combining fields or interactions +=====Combining fields or interactions======
-================================+
 Several fields in the data file can be combined into one using a COMBINE keyword.  Several fields in the data file can be combined into one using a COMBINE keyword. 
- COMBINE a b c ....+<file> 
 +COMBINE a b c .... 
 +</file>
 catenates b c ... into c. Keywords COMBINE need to be on top of the parameter catenates b c ... into c. Keywords COMBINE need to be on top of the parameter
 file, but possibly after comments. There may be many combined fields.  file, but possibly after comments. There may be many combined fields. 
 For example: For example:
- COMBINE 7 2 3 4+</file> 
 +COMBINE 7 2 3 4 
 +</file>
 combines content of fields 2 3 4 into field 7; the data file is not changed, combines content of fields 2 3 4 into field 7; the data file is not changed,
 only the program treats field 7 as fields 2 3 4 put together (without spaces).  only the program treats field 7 as fields 2 3 4 put together (without spaces). 
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-Additive Pedigree File +=====Additive Pedigree File======
-======================+
  
 The additive pedigree file(s) renadd* has the following structure: The additive pedigree file(s) renadd* has the following structure:
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-Extensions +=====Extensions=======
-==========+
  
 The program is being modified to support inbreeding, dominance, random The program is being modified to support inbreeding, dominance, random
Line 285: Line 302:
  
  
-Example +=====Example======
-========+
  
-data file - data.test + 
----------------------+**__data file__** - ''data.test'' 
 + 
 +<file>
 1 aa 34.5 11 12 zz 1 aa 34.5 11 12 zz
 3 bb 21.333 22 23 xx 3 bb 21.333 22 23 xx
Line 296: Line 314:
 3 aa  30 55 56 yy 3 aa  30 55 56 yy
 5 bb 1234567.890 66 67 zz 5 bb 1234567.890 66 67 zz
 +</file>
  
-pedigree file - test.ped + 
-------------------------+**__pedigree file__** - ''test.ped'' 
 +<file>
 qq 0 0 qq 0 0
 aa 0 0 aa 0 0
Line 304: Line 324:
 cc qq 0 cc qq 0
 dd 0 aa dd 0 aa
 +</file>
  
-parameter file - testpar1 + 
--------------------------+**__parameter file__** - ''testpar1'' 
 +<file>
 # Parameter file for program renf90; it is translated to parameter # Parameter file for program renf90; it is translated to parameter
 # file for BLUPF90 family f programs. # file for BLUPF90 family f programs.
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 RANDOM RANDOM
 diagonal diagonal
 +</file>
  
- +**__printout__** \\ 
-printout (temporary; the amount of details may change) +\\ 
-------------------------------------------------------+(temporary; the amount of details may change) 
 +<file>
  RENUMF90 version 1.93  RENUMF90 version 1.93
  name of parameter file? testpar1                                  name of parameter file? testpar1                                
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  Wrote parameter file "renf90.par"  Wrote parameter file "renf90.par"
  Wrote renumbered data "renf90.dat"  Wrote renumbered data "renf90.dat"
 +</file>
  
- +**__new parameter file__** - ''renf90.par'' 
-new parameter file - renf90.par +<file>
--------------------------------+
 # BLUPF90 parameter file created by RENF90 # BLUPF90 parameter file created by RENF90
 DATAFILE DATAFILE
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    1.000      0.1000        1.000      0.1000    
   0.1000       1.000   0.1000       1.000
 +</file>
  
  
  
-data file - renf90.dat +**__data file__** - ''renf90.dat'' 
-----------------------+<file>
  34.5 11 1 3 5 12 1 3 aa 1  34.5 11 1 3 5 12 1 3 aa 1
  21.333 22 2 1 3 23 2 1 bb 3  21.333 22 2 1 3 23 2 1 bb 3
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  30 55 2 3 5 56 2 2 aa 3  30 55 2 3 5 56 2 2 aa 3
  1234567.890 66 3 1 3 67 3 3 bb 5  1234567.890 66 3 1 3 67 3 3 bb 5
 +</file>
    
- Pedigree file (same format as from renum) - renadd02.ped + 
- --------------------------------------------------------+**__Pedigree file__** - ''renadd02.ped'' 
 +<file>
  1 6 3 1 0 2 2 0 0 bb  1 6 3 1 0 2 2 0 0 bb
  6 0 0 1 0 0 0 2 0 qq  6 0 0 1 0 0 0 2 0 qq
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  3 0 5 1 0 1 2 0 2 aa  3 0 5 1 0 1 2 0 2 aa
  4 6 7 1 0 2 1 0 0 cc  4 6 7 1 0 2 1 0 0 cc
 +</file>
  
-renumbering tables - renf90.tables +**''renumbering tables''** - ''renf90.tables'' 
-----------------------------------+<file>
  Effect group 1 of column 1 with 4 levels  Effect group 1 of column 1 with 4 levels
  Value    #    consecutive number  Value    #    consecutive number
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani
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