Documents describing the LEA:
E. Frichot, O. François. (2015). LEA: an R package for Landscape and Ecological Association studies. Methods in Ecology and Evolution, 6(8), 925-929.
C. Gain, O. François. (2021). LEA 3: Factor models in population genetics and ecological genomics with R. Molecular Ecology Resources, 21(8), 2738-2748.
Reference manual with tutorials and examples: LEA: an R package for Landscape and Ecological Association studies (latest release from GitHub).
Tutorial on how to display ancestry coefficients (Q matrix) in geographic maps: Analyzing population genomic data with tess3r .
Tutorial on visualizing geographic predictions of genetic offset measures . Check the Web version .
References for methods implemented in LEA:
E. Frichot, S.D. Schoville, G. Bouchard, O. François. (2013). Testing for associations between loci and environmental gradients using latent factor mixed models. Molecular Biology and Evolution , 30(7), 1687-1699. Link to MBE.
K. Caye, B. Jumentier, J. Lepeule, O. François. (2019). LFMM 2: fast and accurate inference of gene-environment associations in genome-wide studies , 36(4), 852-860. Link to MBE.
E. Frichot, F. Mathieu, T. Trouillon, G. Bouchard, O. François. Fast and efficient estimation of individual ancestry coefficients. (2014). Genetics 196 (4), 973-983. Link to Genetics.
