Differences

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--- readme.renumf90 [2012/05/29 12:09] – [Fields in the parameter file] ignacio
+++ readme.renumf90 [2012/05/29 12:24] – [OPTIONS] ignacio
@@ 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
+positions can be different for each trait for fixed effects;\\
-effects; for random effects, only one position + 0 (misising) efefct are
+for random effects, only one position + 0 (misising) efefct are
 possible.
   * type is 'cross' for crossclassified or 'cov' for covariables
@@ Line 87: / Line 87: @@
 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 101: / Line 102: @@
 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
+current options include
-permanent environment
+  * 'pe' for permanent environment
+  * 'mat' for maternal
+  * 'mpe' for maternal permanent environment
 <file>
@@ Line 117: / Line 120: @@
 </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
+specifies positions in the pedigree file of animal an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob\\
-alt_dam or yob can be replaced by 0; if this line is not given, defaults are
+missing alt_dam or yob can be replaced by 0\\
-2 3 0 0. If maternal effect is specified, the maternal effect is due to
+if this line is not given, defaults are 1 2 3 0 0.\\
-position of d if alt_dam field is 0, or otherwise is due to alt_dam; If
+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.
-alt_dam field is not zero, it should include ID of real or recipient
-dam.
 <file>
@@ Line 130: / Line 131: @@
 </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
+if present, the relationship matrix will be constructed as in Aguilar et al. (2010) and will
-same format as fped and SNP info needs to start from a fixed column and
+include the genomic information;\\
-include digits 0, 1, 2 and 5; ID and SNP info need to be separated by
+file fsnp should start with ID with the same format as fped and SNP info needs to start from a fixed column and
-at leats one space; see info for program PreGSf90
+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 144: @@
 </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.
@@ Line 149: / Line 153: @@
 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 164: @@
 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 172: @@
 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).
-custom_upg(year_of_birth,sex,ID, parent_code).
 <file>
@@ Line 182: / Line 184: @@
 </file>
 Specifies that random regressions should be applied to the animal and
-corresponding effects (mat, pe and mpe), this keyword also could be
+corresponding effects (mat, pe and mpe),\\
-applied to set covariables for fixed effects; r_type is 'data' if covariables for
+this keyword also could be applied to set covariables for fixed effects;\\
-random regressions are in the data, or "legendre' if legendre plynomials are
+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
@@ Line 201: / Line 203: @@
 </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 the maternal effect if present
 <file>
@@ Line 217: / Line 219: @@
-----
+=====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
 on diagonals and 0.1 on off-diagonals.
@@ Line 228: / Line 230: @@
 The sequence of keywords should be as above although optional fields can be
-skipped. Keywords out of order may not be recognized.
+skipped.
-=====OPTIONS=====
+Keywords out of order may not be recognized.
+=====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
@@ Line 238: / Line 242: @@
 	OPTION alpha size nn
 </file>
-   where nn is the new size.
+where //nn// is the new size.
  - the size of th record length
@@ Line 244: / Line 248: @@
 	OPTION max_string_readline nn
 </file>
-   where nn is the new size.
+where //nn// is the new size.
  - the maximun number of fields
@@ Line 250: / Line 254: @@
         OPTION max_field_readline nn
 </file>
-   where nn is the number of fields.
+where //nn// is the number of fields.