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--- readme.renumf90 [2023/03/02 01:18] – andres
+++ readme.renumf90 [2024/05/15 18:44] – [Options] dani
@@ 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 348: / Line 348: @@
 <file>
-OPTION no_basic_statistics
+OPTION missing x
 </file>
-avoids the computation of basic statistics (min, max, correlations...) which take a certain time for very large data 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 inbreeding_method n
+OPTION missing_in_weights
 </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:
+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 m
+</file>
-  * 7: Recursive tabular with self breeding generations . This method is for populations with selfing, i.e. wheat.
+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. Acceptable values for m are:
-  * 6: Hybrid parallel computing which is basically a parallel (OMP) version of Meuwissen and Luo (1992)
-  * 5: method of Tier (1990)
+: Meuwissen and Luo (1992)
-  * 4: recursive tabular method
+: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004)
-  * 3: Modified Colleau by Sargolzaei et al. (2005)
+: Modified Colleau by Sargolzaei et al. (2005)
-  * 2: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004)
+: recursive tabular method
-  * 1: Meuwissen and Luo (1992)
+: method of Tier (1990)
+: Hybrid parallel computing, which is basically a parallel (OMP) version of Meuwissen and Luo (1992)
+: Recursive tabular with self-breeding generations. For populations with selfing, i.e., wheat
-the default is method 1, and speed-ups are made using method 6 but this requires using several threads (e.g. using ''OMP_NUM_THREADS=4'')
+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 404: / 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;