output file name now only depends on value of root.only and not on which timeslices were run; either _all_subclades or _rootclade_only
deleted summary plot code block
deleted all Blomberg's K code; modified summary_output file name
got rid of semicolons
converted code to an analysis function; changed default values of which.time.slices and time.sequence to NA instead of -999
removed calling of libraries and sourcing of functions, reading of sim.matrix; added comments; moved creation of new summary columns for sim.matrix to inside function
script in which user specifies parameters for simulation analysis which then calls analysis_workflow_Olympus.r
moved removal of sim output files to the end of the function
added stopCluster(cl) to end of function; changed output folder for stats file to analysis_output
wrapped stopCluster inside on.exit()
changed raw_sim_output to more generic output_dir
moved all references to local==1 or local==0 to analyzing_sims.r, deleted print(warnings())
put analysis function inside a foreach loop for local multi-core analysis; analysis on cluster still needs revising and fixing
added comments listing the simulation IDs that were used in the paper
added warning if no sim output exists, and assignment in that case of sim.results = NULL
summary stats for energy gradient simulation #3325, used as example in Figure 3
removed Allen==1, tidied up paths, specified sims for the 4 scenarios, wrote a function to rbind all the stat files for replicates of a particular scenario, modified name of output pdf
fixed compiled.stats function and added comments