June 2022 Small GEA simulation

README Simulations correspond to those originally run in Lotterhos and Whitlock, 2015 (https://doi.org/10.1111/mec.13100). RDA was run as in Forester et al. 2017 (DOI: 10.1111/mec.14584), and loci that has locus scores +-3SD were considered significant. Files: meta.7z contains meta.test.csv, which contains the original simulation metadata from Lotterhos and Whitlock 2015 as provided in the SummaryFiles directory, with two additional columns appended: SNP (which can be ignored), Pval (which is the p-value for a multiple CMR knockoffs test), RDA (which signifies whether a locus was significant in redundancy analysis/RDA) and causal (which was used to calculate model performance). Inds.csv indicates the simulations from Lotterhos and Whitlock 2015 used in this short test. Analysis.R provides code to recreate the figure GEA.pdf, given the meta.test.csv file. FastRDAscores.R provides a quick function to calculate locus scores/species scores for a univariate RDA. Note that values are scaled, and are equivalent to scaling locus scores from RDA, but outlier tests should be unaffected.