R code to reproduce the figures is in pub_figures.Rmd.
Be sure to load the R data file into your R environment, which contains the necessary metadata and SSR data (in genind/genclone format) in the genclones_from_SSRs.Rd file.
Metadata and other important data structures for figures can be loaded from sample_info_all.Rd.
To create raincloud plots, some functions will be loaded from the scripts folder.