Differences

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--- readme.thrgibbs1 [2014/07/09 15:07] – shogo
+++ readme.thrgibbs1 [2017/10/26 08:45] – [Options] shogo
@@ Line 24: / Line 24: @@
 OPTION fixed_var all 1 2 3
 </file>
-Store all samples for solutions in "all_solutions" and posterior means and SD for 1, 2, and 3 effects in "final_solutions".
+Store all samples for solutions in "all_solutions" and posterior means and SD for 1, 2, and 3 effects in "final_solutions", assuming that (co)variances in the parameter file are known.
 <file>
 OPTION fixed_var mean
 </file>
-Only posterior means and SD for solutions are calculated for all effects in "final_solutions".
+Only posterior means and SD for solutions are calculated for all effects in "final_solutions", assuming that (co)variances in the parameter file are known.
 <file>
 OPTION fixed_var mean 1 2 3
-Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions".
+Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions", assuming that (co)variances in the parameter file are known.
 </file>
 <file>
@@ Line 44: / Line 44: @@
 OPTION solution mean
 </file>
-Only posterior means and SD for solutions are calculated for all effects in "final_solutions".
+Only posterior means and SD for solutions are calculated for all effects in "final_solutions" while sampling (co)variances.
 <file>
 OPTION solution mean 1 2 3
 </file>
-Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions".
+Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions" while sampling (co)variances.
 <file>
 OPTION cont 10000
 </file>
-"10000" is the number of samples run previously. The user can restart the program from the last run.
+"10000" is the number of samples run previously. The user can restart the program from the last run. This option requires "binary_final_solutions", "gibbs_samples", and "fort.99" files.
+When using "OPTION cont", all output files will be replaced by new ones. Before running with this option, all files should be backed up.
 <file>
 OPTION prior 5 2 -1 5
@@ Line 70: / Line 71: @@
 Set the fixed thresholds. No need to set 0 for binary traits.
 <file>
-OPTION residual 1.
+OPTION residual 1
 </file>
-Set the residual variance = 1.
+Set the residual variance = 1 (no need for binary traits).
 <file>
-OPTION censored 1 0.
+OPTION pos_def x.x
 </file>
-Negative values of the last category in the data set indicate censored records. "1 0" determines that the first categorical trait is censored but the second uncensored.
+Specify checking pos-def for fixed effects where x.x is a tolerance (default=1d-08).
+<file>
+OPTION censored 1 0
+</file>
+Negative values for the categorical trait in the data set indicate censored records. "1 0" determines that the first categorical trait is censored and the second uncensored.
 <file>
 OPTION SNP_file snp
 </file>
 Specify the SNP file name to use genotype data.