Dear Colleagues, We wish to alert you to a new article, introducing phylogenetically aligned component analysis, currently in early release form:
Collyer, M.L. and D.C Adams. 2020 (in press). Phylogenetically aligned component analysis. Methods in Ecology and Evolution. If you do not have access to MEE, we have a link to the accepted article and supporting information here <https://www.researchgate.net/publication/344900621_Phylogenetically_Aligned_Component_Analysis>. (Or paste https://www.researchgate.net/publication/344900621_Phylogenetically_Aligned_Component_Analysis <https://www.researchgate.net/publication/344900621_Phylogenetically_Aligned_Component_Analysis> in your web browser.) Phylogenetically aligned component analysis (PACA) is an ordination method similar to phylogenetic PCA, but rather than finding eigenvectors that are evolutionarily independent, it finds vectors that are most associated with phylogenetic signal. PACA provides a tool for visualizing phylogenetic signal in multivariate data and can assist for discerning between weak phylogenetic signal and strong phylogenetic signal concentrated in only a portion of the data dimensions. In conjunction with PCA, and phylogenetic PCA, it can assist in isolating the phylogenetic signal in multivariate data that might be obscured by other signals (e.g., allometric, ecological). We make PACA available to GM users in the RRPP and geomorph R packages, with RRPP::ordinate and geomorph::gm.prcomp functions. These functions allow users to align data to either principal or phylogenetically aligned vectors, project ancestral states and phylogenetic tree edges into a plot, and evaluate the amount of covariance between data and phylogeny, by vector. Additionally, the physignal function in geomorph provides $PACA output, along with the amount of cumulative phylogenetic signal, by vector, which can inform if phylogenetic signal is especially strong in certain data dimensions. We recommend installing the latest versions of RRPP and geomorph via Github; i.e., devtools::install_github(“mlcollyer/RRPP”, build_vignettes = TRUE) devtools::install_github(“geomorphR/geomorph”, ref = “Stable”, build_vignettes = TRUE) Happy computing! Mike Collyer and Dean Adams [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
