Differences

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--- readme.renumf90 [2012/05/29 12:14] – [Fields in the parameter file] ignacio
+++ readme.renumf90 [2012/05/29 12:20] – [Fields in the parameter file] ignacio
@@ Line 144: / 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 151: / 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 160: / 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 167: / 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 184: / 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 203: / 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 221: / Line 221: @@
 ----
-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 230: / 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.
+Keywords out of order may not be recognized.
 =====OPTIONS=====