Differences

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--- readme.renumf90 [2012/11/18 21:30] – ignacio
+++ readme.renumf90 [2016/11/04 21:17] – [Additive Pedigree File] shogo
@@ Line 131: / Line 131: @@
 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\\
+specifies positions in the pedigree file of animal (an), sire (s), dam (d), alternate dam (alt_dam) , and year of birth (yob)
 missing alt_dam or yob can be replaced by 0
@@ Line 204: / Line 205: @@
   * 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.
-  * if t is 'internal',  allocation is by a user-written function custom_upg(year_of_birth,sex,ID, parent_code).
+  * if t is 'internal',  allocation is by a user-written function custom_upg(year_of_birth,sex,ID, parent_code); not yet implemented.
+<file>
+INBREEDING
+inb_type
+</file>
+optional\\
+use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file
+//inb_type// could be:
+  * 'pedigree' - the program computes inbreeding coefficients with Meuwissen and Luo (1992) using the pedigree to be saved in renaddxx.ped; calculated inbreeding coefficients will be saved in a file "renf90.inb" with the original ID
+  * 'file' - the program reads inbreeding coefficients from an external file. You should put the filename after 'file' e.g. 'file inbreeding.txt'. The file has at least 2 columns: original_ID and inbreeding value (from 0.0 to 1.0). The program just skips unnecessary IDs
 <file>
@@ Line 211: / Line 222: @@
 </file>
 Specifies that random regressions should be applied to the animal and
-corresponding effects (mat, pe and mpe)
+corresponding random effects (mat, pe and mpe) or the diagonal random effect.
 this keyword also could be applied to set covariables for fixed effects;
@@ Line 248: / Line 259: @@
 </file>
 //gmpe// are (co)variances for the MPE effect if present
 =====Extra comments=====
@@ Line 272: / Line 281: @@
  - the default size of character fields
 <file>
-OPTION alpha size nn
+OPTION alpha_size nn
 </file>
 where //nn// is the new size.
@@ Line 300: / Line 309: @@
 </file>
 catenates //b c// ... into //a//.\\
-Keywords COMBINE need to be on top of the parameter file, but possibly after comments.
+Keyword COMBINE needs to be on top of the parameter file, but possibly after comments.
 There may be many combined fields.
@@ Line 330: / Line 339: @@
       if animal has genotype 10+number of know parents
 ) number of records
-) number of progenies (before elimination due to other effects) as parent 1
+) number of progeny (before elimination due to other effects) as parent 1
-) number of progenies (before elimination due to other effects) as parent 2
+) number of progeny (before elimination due to other effects) as parent 2
 ) original animal id