June 2022 Small GEA simulation

README <br> 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. <br> Files: <br> 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). <br> Inds.csv indicates the simulations from Lotterhos and Whitlock 2015 used in this short test. <br> Analysis.R provides code to recreate the figure GEA.pdf, given the meta.test.csv file. <br> 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. <br>