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--- readme.renumf90 [2023/01/25 12:46] – [Fields in the parameter file] andres
+++ readme.renumf90 [2024/05/15 18:37] – [Options] dani
@@ 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 232: / Line 232: @@
 //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' - the program reads inbreeding coefficients from an external file. You should put the filename after 'file' e.g. 'file inbreeding.txt'. For instance a file "renf90.inb" (see above) from a previous run can be used. 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
@@ Line 253: / Line 253: @@
 //r_type// could be:
   * 'data' if covariables for random regressions are in the data
-  * "legendre' if legendre plynomials are to be generated from a single data variable; not yet implemented
+  * "legendre' if legendre plynomials are to be generated from a single data variable; fully implemented now
 <file>
@@ Line 262: / Line 262: @@
   * //r1-rq// specifies positions of covariables if r_type='data'
-  * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type='legendre'; not yet implemented
+  * //r1// is order of legendre polynomial and //r2// is position of covariable if r_type='legendre'
 <file>
@@ Line 341: / Line 341: @@
 where //nn// is the new size.
- - the maximun number of fields (default = 100)
+ - the maximum number of fields (default = 100)
 <file>
 OPTION max_field_readline nn
@@ Line 347: / Line 347: @@
 where //nn// is the number of fields.
+<file>
+OPTION missing x
+</file>
+allows indicating that the missing value is the number x (e.g., 999), for instance, if 0 is a valid record. This is only to represent the missing value in the data. If there are covariables in the data, 0 is treated as a value, not missing information. Missing pedigree is always 0 and cannot be changed to another value.
+<file>
+OPTION missing_in_weights
+</file>
+in addition, this indicates that if a weight for the trait is 0, then the value of the trait is converted to "missing" in the output file ''renf90.dat'', i.e. 0 by default or another value is set if  ''OPTION missing '' is used.
+<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 1
+</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:
+  * 1: Meuwissen and Luo (1992)
+  * 2: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004)
+  * 3: Modified Colleau by Sargolzaei et al. (2005)
+  * 4: recursive tabular method
+  * 5: method of Tier (1990)
+  * 6: Hybrid parallel computing, which is basically a parallel (OMP) version of Meuwissen and Luo (1992)
+  * 7: Recursive tabular with self-breeding generations. This method is for populations with selfing, i.e., wheat
+  *
+The default is method 1. Large speed-ups are made using method 6, but this requires using several threads (e.g., using ''OMP_NUM_THREADS=4'')
 The end of the parameter file for ''RENUMF90'' can contain many lines beginning with OPTION.
-All of these lines are passed to parameter file renf90.par to be used by application programs.
+All of these lines are passed to the parameter file renf90.par to be used by application programs.
@@ Line 384: / Line 416: @@
 ) parent 1 number or unknown parent group number for parent 1
 ) parent 2 number or unknown parent group number for parent 2
-) 3 minus number of known parents
+) 3 minus number of known parents or inbreeding code if inbreeding is used (inbreeding is default now)
 ) known or estimated year of birth (0 if not provided)
 ) number of known parents (parents might be eliminated if not contributing;