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 principal component analysis (PCA), but aligns data to maximum phylogenetic signal rather than maximum variance. In conjunction with PCA (or phylogenetic PCA), PACA provides a tool for visualizing phylogenetic signal in multivariate data, even if other signals (e.g., allometry, ontogenetic, ecological) might obscure phylogenetic signal in PCA. 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, optionally transform data by phylogenetic covariances, 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 -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/AC2158F3-4CD2-4416-BEE0-ABECD864CE41%40gmail.com.
