nickjeff13 / rda-landscape-genomics Goto Github PK

This repository provides code and explanation associated with a review of the different applications of RDA in the field of landscape genomics written by Thibaut Capblancq & Brenna Forester (2021). Redundancy Analysis: A Swiss army knife for landscape genomics. Methods in Ecology and Evolution 12(12): 2298-2309. (https://doi.org/10.1111/2041-210X.13722)

1. "RDA_landscape_genomics.html" is a tutorial of the various RDA-based approaches reviewed in the study

2. "RDA_landscape_genomics.Rmd" is the Rmd script used to produce the html tutorial and which can be used to find the raw code used to produce all the results of the study

3. The "src" directory contains various functions used in the script RDA_landscape_genomics.R

4. The "Data" directory contains the list of outliers identified in Mahony et al. (2020) and a table with values of the different Climate NA variables for the Vancouver common garden site in 2012, 2013, 2014 and 2015. The other data needed to run the code and reproduce the results of the study can be downloaded directly from Climate NA (http://climatena.ca) for the different climate rasters and from dryad (https://datadryad.org/stash/dataset/doi:10.5061/dryad.56j8vq8) for the genotype datasets published in Mahony et al. (2020) and their associated metadata.

5. "ClimateNA_formatting.R" is a script used to re-project Climate NA bioclimate rasters into WGS84 coordinate system

Reminder: To access the html and R files, click the "Code" button at the upper right and select "Download ZIP".