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--- readme.renumf90 [2022/09/13 19:43] – dani
+++ readme.renumf90 [2023/03/02 01:08] – [Options] andres
@@ Line 68: / Line 68: @@
 <file>
 WEIGHT(S)
-w
+w1 [w2 w3...wn]
 </file>
-w is  position of weight if present; can be empty
+w1 [w2 w3...wn] are  position of weight(s) if present; can be empty (which means weight of 1 or no weight). Either there is a single weight, the same for all traits, or one weight per trait in which case ''ntrait'' positions are needed in this line. See [[readme.blupf90plus#weights|blupf90+ section on WEIGHTS]]  for details.
 <file>
@@ Line 184: / Line 184: @@
 the default is 3
-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.
+all pedigrees are loaded if p=0. This is the fastest as it reads the pedigree file only once. However, if you want to extract the informative animals (genotyped and phenotyped animals + their ancestors traced back) 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 unless your pedigree file is already prepared and consists in the informative animals or the animals of interest.
@@ Line 346: / Line 346: @@
 </file>
 where //nn// is the number of fields.
+<file>
+OPTION no_basic_statistics
+</file>
+avoids the computation of basic statistics (min, max, correlations...) which take a certain time for very large data file.
+<file>
+OPTION inbreeding_method n
+</file>
+allows choosing a method for inbreeding calculation. The inbreeding coefficients are used later (in the other programs) to set up the coefficients for the A-inverse. Existing options are: