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--- readme.renumf90 [2020/04/21 06:03] – yutaka
+++ readme.renumf90 [2022/09/13 19:43] – dani
@@ 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 226: / Line 228: @@
 </file>
 optional\\
-use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file
+use of inbreeding coefficients to compute inb/upg code in the 4th column of the output pedigree file. Inbreeding calculation is a default in RENUMF90 ≥ v1.157, even if this keyword is not used.
 //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
+  * 'self x' - Calculates inbreeding with selfing, where x is the column in the pedigree file with the number of selfing generation
+  * 'no-inbreeding' - turn inbreeding calculation off in RENUMF90 ≥ v1.157
 <file>
@@ Line 283: / Line 287: @@
 ==== 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''.