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--- readme.renumf90 [2012/11/18 21:49] – [Fields in the parameter file] ignacio
+++ readme.renumf90 [2018/05/18 23:36] – yutaka
@@ 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 205: / Line 206: @@
   * 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>
+FIXED_REGRESSION
+r_type
+</file>
+It is the same as ''RANDOM_REGRESSION'' (see the explanation below) but it is effective only for fixed effects.
 <file>
@@ Line 248: / Line 265: @@
 </file>
 //gmpe// are (co)variances for the MPE effect if present
+==== User-defined UPG code ====
+The program accepts the following keywords in ''UPG_TYPE''.
+    UPG_TYPE
+    group
+    or
+    UPG_TYPE
+    group_unisex
+With this option, the program looks at a particular column in the pedigree file as a group code and saves it. If an animal has a missing parent, the program assigns an UPG code according to the group code. If you want to assign separate UPGs by the parent's sex (sire or dam), use ''group''. The ''group_unisex'' doesn't consider the sex of parents.
+The column in the pedigree file is specified with the 6th item in ''FILE_POS''. The following example tells the program the 5th column in the pedigree file as the group code. The group code will be treated as characters.
+    FILE_POS
+2 3 0 0 5
+The program now accept 3 items, 5 items, or 6 items in ''FILE_POS''.
@@ Line 272: / Line 312: @@
  - 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 340: @@
 </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 370: @@
       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