Differences

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--- readme.renumf90 [2018/05/30 17:51] – yutaka
+++ readme.renumf90 [2022/01/22 20:26] – [Fields in the parameter file] dani
@@ Line 37: / Line 37: @@
 =====Fields in the parameter file=====
-# Parameter file for program renf90; it is translated to parameter
+# Parameter file for renumf90. It is translated into a parameter file for the BLUPF90 family of programs.
-# file for BLUPF90 family of programs.
 Lines with # are treated as comments
@@ Line 218: / Line 217: @@
   * if t is 'internal',  allocation is by a user-written function custom_upg(year_of_birth,sex,ID, parent_code); not yet implemented.
+  * There are the other values for t: 'group', 'group_unisex', and 'group_sex'. See below for details.
 <file>
 INBREEDING
@@ Line 281: / Line 283: @@
 ==== User-defined UPG code ====
-The program accepts the following keywords in ''UPG_TYPE''.
+See [[undoc:renumf90|a separate documentation]] for details.
-    UPG_TYPE
+The program accepts one of the following keywords in ''UPG_TYPE'': ''group'', ''group_unisex'', and ''group_sex''.
-    group
+With one of these options, the program looks at a particular column in the pedigree file as a group code and use it for assigning the UPG code. If an animal has a missing parent, the program assigns a UPG code based on the group code.
-    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.
+  * ''group_unisex'': The program assigns a UPG code to the unknown parent regardless of the parent's sex.
+  * ''group'': The program assigns a separate UPG code to the unknown sire and dam.
+  * ''group_sex'': The user can specify a sex-specific UPG in the original pedigree file.
-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.
+For ''group_unisex'' and ''group'', 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''.
+For ''group_sex'', you need two additional columns in the pedigree file: one is for an unknown sire, and the other is for an unknown dam. For example, assume the 5th column is for unknown sire, and the 6th column is for unknown dam, the ''FILE_POS'' entry has 7 items.
+    FILE_POS
+2 3 0 0 5 6
+The program now accept 3, 5, 6, or 7 items in ''FILE_POS''.
 =====Extra comments=====
@@ Line 322: / Line 324: @@
 parameters used to read the input file:
- - the default size of character fields
+ - the default size of character fields (default = 20)
 <file>
 OPTION alpha_size nn
@@ Line 328: / Line 330: @@
 where //nn// is the new size.
- - the size of th record length
+ - the size of th record length (default = 800)
 <file>
 OPTION max_string_readline nn
@@ Line 334: / Line 336: @@
 where //nn// is the new size.
- - the maximun number of fields
+ - the maximun number of fields (default = 100)
 <file>
 OPTION max_field_readline nn