Differences

This shows you the differences between two versions of the page.

--- readme.renumf90 [2023/03/08 08:53] – [Additive Pedigree File] dani
+++ readme.renumf90 [2024/05/22 18:27] – dani
@@ Line 1: / Line 1: @@
 =======RENUMF90======
 A renumbering program for the ''BLUPF90'' family now works with SNP info\\
@@ Line 253: / Line 252: @@
 //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; fully implemented now
+  * "legendre' if legendre polynomials are to be generated from a single data variable; fully implemented now
 <file>
@@ Line 348: / Line 347: @@
 <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.
-  * 7: Recursive tabular with self breeding generations . This method is for populations with selfing, i.e. wheat.
+<file>
-  * 6: Hybrid parallel computing which is basically a parallel (OMP) version of Meuwissen and Luo (1992)
+OPTION no_basic_statistics
-  * 5: method of Tier (1990)
+</file>
-  * 4: recursive tabular method
+avoids the computation of basic statistics (min, max, correlations, ...), which take a certain time for very large data file.
-  * 3: Modified Colleau by Sargolzaei et al. (2005)
-  * 2: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004)
+<file>
-  * 1: Meuwissen and Luo (1992)
+OPTION inbreeding_method m
+</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. Acceptable values for m are:
+: Meuwissen and Luo (1992)
+: Modified Meuwissen & Luo by Sargolzaei & Iwaisaki (2004)
+: Modified Colleau by Sargolzaei et al. (2005)
+: recursive tabular method
+: 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.