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--- readme.renumf90 [2020/04/21 05:13] – yutaka
+++ readme.renumf90 [2022/08/08 17:56] – andres
@@ Line 21: / Line 21: @@
   * missing animals have code 0; 00 may be treated as a known animal
+\\
+**Hint**: type ''renumf90 %%--%%show-template''  to have a template parameter file.
 =====Structure of parameter file======
@@ Line 37: / Line 38: @@
 =====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 86: / Line 86: @@
 positions can be different for each trait for fixed effects;
-for random effects, only one position + 0 (misising) efefct are
+for random effects, only one position + 0 (missing) efefct are
 possible.
   * type is 'cross' for crossclassified or 'cov' for covariables
-  * form is 'alpha' for alphanumeric or 'numer' for numeric
+  * for crossclassified effects: form is 'alpha' for alphanumeric or 'numer' for numeric
+  * for covariables: neither 'alpha' nor 'numer' are needed; don't put anything after 'cov'
 <file>
@@ Line 183: / Line 184: @@
 the default is 3
-all pedigrees are loaded if p=0.
+all pedigrees are loaded if p=0. To consider all ancestors to be traced back from genotyped and phenotyped animals, put a large number like 100. With p=0, RENUMF90 tries to include all animals found in the raw pedigree file even if the animals in the pedigree are not related to the animals with phenotype or genotype. Thus, p=0 is not recommended.
 <file>
@@ Line 283: / Line 285: @@
 ==== User-defined UPG code ====
+See [[undoc:renumf90|a separate documentation]] for details.
 The program accepts one of the following keywords in ''UPG_TYPE'': ''group'', ''group_unisex'', and ''group_sex''.
-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 an UPG code based on the group code.
+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.
-* ''group_unisex'': The program assign an UPG code to the unknown parent regardless of the parent's sex.
+  * ''group_unisex'': The program assigns a UPG code to the unknown parent regardless of the parent's sex.
-* ''group'': The program assign a separate UPG code to the unknown sire and dam.
+  * ''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.
+  * ''group_sex'': The user can specify a sex-specific UPG in the original pedigree file.
 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.
@@ Line 296: / Line 300: @@
 2 3 0 0 5
-For ''group_sex'', you need two additional columns in the pedigree file: one is for unknown sire and the other is for 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.
+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
@@ Line 302: / Line 306: @@
 The program now accept 3, 5, 6, or 7 items in ''FILE_POS''.
 =====Extra comments=====