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--- readme.renumf90 [2012/05/29 12:09] – [Fields in the parameter file] ignacio
+++ readme.renumf90 [2013/12/09 18:14] – shogo
@@ Line 1: / Line 1: @@
 =======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\\
 August 27, 2001 - Mar 17, 2011
@@ Line 42: / Line 42: @@
 Lines with # are treated as comments
 <file>
 DATAFILE
 f1
@@ Line 48: / Line 48: @@
 The data file is f1
 <file>
 TRAITS
 t1 t2 .. tn
@@ Line 76: / Line 76: @@
 e1.. en type form
 </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;
-effect for all traits; positions can be different for each trait for fixed
-effects; for random effects, only one position + 0 (misising) efefct are
+positions can be different for each trait for fixed effects;
+for random effects, only one position + 0 (misising) efefct are
 possible.
   * type is 'cross' for crossclassified or 'cov' for covariables
@@ Line 87: / Line 89: @@
 d1 .. dn form
 </file>
-optional for covariables only, specifies nesting; form is as above
+optional for covariables only, specifies nesting;
+form is as above
 <file>
@@ Line 95: / Line 99: @@
 the RANDOM keyword occurs only if the current effect is random;
-rtype is 'diagonal', 'sire' or 'animal'
+rtype is:
+  * 'diagonal'
+  * 'sire'; not yet implemented
+  * 'animal'
 <file>
@@ Line 101: / Line 108: @@
 o1 o2.. oq
 </file>
-causes extra effects appended to the animal effect; current options include
+causes extra effects appended to the animal effect;
-'pe' for permanent environment, 'mat' for maternal, and 'mped' for maternal
-permanent environment
+current options include:
+  * 'pe' for permanent environment
+  * 'mat' for maternal
+  * 'mpe' for maternal permanent environment; only if 'mat' is used
 <file>
@@ Line 110: / Line 120: @@
 </file>
-for animal and sire model only, fped specifies the pedigree file
+for animal and sire model only
+ //fped// specifies the pedigree file
 <file>
@@ Line 117: / Line 129: @@
 </file>
-for animal effect only; specifies positions in the pedigree file of animal
+for animal effect only;
-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
+specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\
-2 3 0 0. If maternal effect is specified, the maternal effect is due to
+missing alt_dam or yob can be replaced by 0
-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
+if this line is not given, defaults are 1 2 3 0 0.
-dam.
+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>
@@ Line 130: / Line 145: @@
 </file>
-optional; fsnp specifies files with ID and SNP information; if present, the
+optional;\\
-relationship matrix will be constructed as in Aguilar et al. (2010) and will
+//fsnp// specifies files with ID and SNP 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
+if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will
-include digits 0, 1, 2 and 5; ID and SNP info need to be separated by
+include the genomic information;
-at leats one space; see info for program PreGSf90
+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]]
 <file>
@@ Line 142: / Line 162: @@
 </file>
-optional for animal effect only; p specifies the depth of pedigree search;
+optional
-the default is 3; all pedigrees are loaded if p=0.
+for animal effect only;
+//p// specifies the depth of pedigree search;
+the default is 3
+all pedigrees are loaded if p=0.
 <file>
@@ Line 149: / Line 176: @@
 min avg max
 </file>
-optional; specifies minimum, average and maximum generation interval;
+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 checks
+average used to predict year of birth of parent with missing
 pedigree.
@@ Line 158: / Line 190: @@
 i
 </file>
-optional; if only one sex has records, specifies which parent it is; used for
+optional\\
-pedigree checks.
+if only one sex has records, specifies which parent it is
+used for pedigree checks.
 <file>
@@ Line 165: / Line 199: @@
 t
 </file>
-optional;
+optional\\
-if t is 'yob', the asignment is based on year of birth; the
+  * if t is 'yob', the assignment 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, 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.
-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
-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); not yet implemented.
-custom_upg(year_of_birth,sex,ID, parent_code).
 <file>
@@ Line 182: / Line 211: @@
 </file>
 Specifies that random regressions should be applied to the animal and
-corresponding effects (mat, pe and mpe), this keyword also could be
+corresponding random effects (mat, pe and mpe) or the diagonal random effect.
-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>
@@ Line 191: / Line 223: @@
 r1 .. rq
 </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>
@@ Line 201: / Line 233: @@
 </file>
-//g// are (co)variances for the animal effect; the dimensions of g should
+//g// are (co)variances for the animal effect
-account for the maternal effect if present
+the dimensions of g should account for random correlated effect if present (maternal or random regression)
 <file>
@@ Line 217: / Line 250: @@
-----
+=====Extra comments=====
 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
 on diagonals and 0.1 on off-diagonals.
@@ Line 228: / Line 262: @@
 The sequence of keywords should be as above although optional fields can be
-skipped. Keywords out of order may not be recognized.
+skipped.
+Keywords out of order may not be recognized.
-=====OPTIONS=====
+=====Options=====
 The following options can added at the end of the parameter file to redefine
-parameter used to read the input file:
+parameters used to read the input file:
  - 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
 <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
 <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.
-The end of the parameter file for RENUMF90 can contain many lines beginning with OPTION.
+The end of the parameter file for ''RENUMF90'' can contain many lines beginning with OPTION.
-All of these lines are passed to parameter file renf90.par to be used by
-application programs.
+All of these lines are passed to parameter file renf90.par to be used by application programs.
 =====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.
 <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 //a//.\\
-file, but possibly after comments. There may be many combined fields.
+Keywords COMBINE need to be on top of the parameter file, but possibly after comments.
+There may be many combined fields.
 For example:
-</file>
+<file>
 COMBINE 7 2 3 4
 </file>
-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).
+combines content of fields 2 3 4 into field 7;
-The combined fields can be treated as "numeric", if they are composed of numbers
-and if their total length is <9. Otherwise, they need to be used as "alpha".
+the data file is not changed, only the program treats field 7 as fields 2 3 4 put together (without spaces).
-Please note that the maximum size of the combined variable is limited by the
-largest size of the "alpha" field.
+The combined fields can be treated as "numeric", if they are composed of numbers and if their total length is <9. Otherwise, they need to be used as "alpha".\\
+Please note that the maximum size of the combined variable is limited by the largest size of the "alpha" field.
@@ Line 286: / Line 327: @@
 ) 3 minus number of known parents
 ) known or estimated year of birth (0 if not provided)
-) number of known parents (parents might be eliminated if not
+) 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
 ) number of records
-) number of progenies (before elimination due to other effects)
+) number of progenies (before elimination due to other effects) as parent 1
-      as parent 1
+) number of progenies (before elimination due to other effects) as parent 2
-) number of progenies (before elimination due to other effects)
-      as parent 2
 ) original animal id
@@ Line 331: / Line 370: @@
 <file>
 # Parameter file for program renf90; it is translated to parameter
-# file for BLUPF90 family f programs.
+# file for BLUPF90 family programs.
 DATAFILE
 data.test