Differences

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

--- readme.thrgibbs1 [2018/04/12 20:26] – [Options] shogo
+++ readme.thrgibbs1 [2024/03/25 18:22] (current) – external edit 127.0.0.1
@@ Line 20: / Line 20: @@
 OPTION fixed_var all
 </file>
 Store all samples for solutions in "all_solutions" and posterior means and SD for all effects in "final_solutions", assuming that (co)variances in the parameter file are known.
 <file>
 OPTION fixed_var all 1 2 3
@@ Line 37: / Line 37: @@
 </file>
 Caution: this option will create a huge output solution file when you run many rounds and/or use a large model.
-Store all samples for solutions in "all_solutions" and posterior means and SD for all effects. The file "all_solutions" could be very large.
+Store all samples for solutions in "all_solutions" and posterior means and SD for all effects. The file "all_solutions" could be very large. This option uses (co)variances from each round to get solutions.
 <file>
 OPTION solution all 1 2 3
 </file>
 Caution: this option will create a huge output solution file when you run many rounds and/or use a large model.
-Store all samples for solutions in "all_solutions" and posterior means and SD for 1, 2, and 3 effects. The file "all_solutions" could be very large.
+Store all samples for solutions in "all_solutions" and posterior means and SD for 1, 2, and 3 effects. The file "all_solutions" could be very large. This option uses (co)variances from each round to get solutions.
 <file>
 OPTION solution mean
 </file>
-Only posterior means and SD for solutions are calculated for all effects in "final_solutions" while sampling (co)variances.
+Only posterior means and SD for solutions are calculated for all effects in "final_solutions" while sampling (co)variances. This option is not recommended to use unless the burn-in is known. This option uses (co)variances from each round to get solutions.
 <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" while sampling (co)variances.
+Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in "final_solutions" while sampling (co)variances. This option is not recommended to use unless the burn-in is known. This option uses (co)variances from each round to get solutions.
+<file>
+OPTION save_halfway_samples 5000
+</file>
+The program saves every "5000" samples to restart or recover the job right after the last saved samples. It is useful when the program accidentally stopped.
 <file>
 OPTION cont 10000
 </file>
-"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.
+"10000" is the number of samples run previously. The user can restart the program from the last run. This option requires "last_solutions", "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>
@@ Line 75: / Line 79: @@
 OPTION residual 1
 </file>
-Set the residual variance = 1 (no need for binary traits).
+The residual variance can be set to 1 but not necessary for categorical traits more than 2 categories. For binary traits, the residual variance is automatically set to 1, so no need to use this option.
 <file>
 OPTION pos_def x.x
@@ Line 88: / Line 92: @@
 </file>
 Specify the SNP file name to use genotype data.
 ==== Save intermediate results for "cold start" ====