added comments
added calls to parallel and doParallel libraries
added sim 3125 output
added specification of inputs and outputs for running sims_only_workflow_local.r
removed all hard-coded paths and replaced with relative pathswithin the repo; also binary indication of local vs cluster analysis (local=1, local = 0)
if raw simulation output data are not zipped, will read in appropriate raw files
removed specification of Rlib.loc, specified code folder path for sourced scripts, specified raw_sim_output folder path for output.unzip call, removed as.data.frame while reading in sim matrix
removed specification of Rlib.loc, specified code folder path for sourced scripts, specified raw_sim_output folder path for output.unzip call, removed as.data.frame while reading in sim matrix
created variable num.clusters for parallel processing
removed pre.equil.time, trop.orig.extreme, and temp.orig.extreme which were used in previous analyses at fixed pre-equilibrial time point
now deletes temporary files of extinct populations
undid the code deleting temporary files, which should have been done to senc_sim_fun.r
now deletes temporary files of extinct populations
cleaned up comments
deleted code that simply was a visual recheck of a calculation; e.g., x = operation(y) ; x; deleted the 'x;'
adding and cleaning comments
cleaning up formatting, spaces, ;s, etc