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--- readme.renumf90 [2012/05/29 11:39] – ignacio
+++ readme.renumf90 [2012/05/29 11:42] – ignacio
@@ Line 141: / Line 141: @@
 </file>
-<file>
 optional for animal effect only; p specifies the depth of pedigree search;
 the default is 3; all pedigrees are loaded if p=0.
+<file>
 GEN_INT
 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
 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
 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
 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
 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
 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
 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
 gmpe
+</file>
-   gmpe are (co)variances for the MPE effect if present
+//gmpe// are (co)variances for the MPE effect if present