SiteStats and WindowStats R files

This folder contains files containing locus-based statistics ("SiteStats") and window-based statistics (WindowStats) for each chromosome. These files can be produced by the R script (in this package), and they can also be used by that script (whether the script saves and/or loads SiteStats and WindowStats files can be adjusted in that script using the setting for "calculate_or_load_stats" and the related settings below that). Producing these files can take days of processing time; I have included them here so you can produce most of the figures in the paper, by running the R script below the heading "GENOME-WIDE plots". That script will call the appropriate files (as long as you have designated a path/folder structure that matches the R script). Files are included for both the "45-sample" analysis and the "nine_taxa.one_per_taxon" analysis.