This branch adds two stopping criteria that can be used in addition to the -c <iter-count> option in larch-usher executable:
-S option will exit when there ceases to be a change in optimal parsimony scores between iterations. This option defines the quantity current_window_size, which is the number of iterations since the last parsimony improvement. This quantity is incremented every iteration. It also introduces one called previous_window_size, which is the number of steps between the previous parsimony improvement. When the current window size meets 2*previous_window_size without improving parsimony, the program exits. Note that this option will override the -c option.
-T <time> specifies(in minutes) a hard time limit at which to exit. Note that this hard time limit is compared to the running total time at the end of each sample-optimize-merge loop, and so it will not guarantee that the program exits on time, but that it exits as soon as it registers the time limit as having been met. This flag can be used in combination with -S and -c options.
Also a small bug in the way that batching callbacks treat rejected moves is fixed.
This branch adds two stopping criteria that can be used in addition to the
-c <iter-count>option inlarch-usherexecutable:-Soption will exit when there ceases to be a change in optimal parsimony scores between iterations. This option defines the quantitycurrent_window_size, which is the number of iterations since the last parsimony improvement. This quantity is incremented every iteration. It also introduces one calledprevious_window_size, which is the number of steps between the previous parsimony improvement. When the current window size meets 2*previous_window_sizewithout improving parsimony, the program exits. Note that this option will override the-coption.-T <time>specifies(in minutes) a hard time limit at which to exit. Note that this hard time limit is compared to the running total time at the end of each sample-optimize-merge loop, and so it will not guarantee that the program exits on time, but that it exits as soon as it registers the time limit as having been met. This flag can be used in combination with-Sand-coptions.Also a small bug in the way that batching callbacks treat rejected moves is fixed.