Community phylogenetic ordination — ps

Perform an ordination that reduces a spatial phylogenetic data set into k dimensions, using one of several alternative ordination algorithms.

Usage

ps_ordinate(ps, method = c("nmds", "cmds", "pca"), k = 3, spatial = TRUE)

ps: A phylospatial object with a non-null dissim component, generated by ps_add_dissim.
method: Ordination method, either "pca" (principal component analysis implemented via stats::prcomp()), "cmds" (classical MDS, implemented via stats::cmdscale()), or "nmds" (the default, nonmetric MDS, implemented via vegan::metaMDS(); this is slower but often preferred).
k: Positive integer giving the desired number of output dimensions; default is 3.
spatial: Logical indicating whether a spatial object (inherited from ps) should be returned. Default is TRUE.

A matrix or spatial object with k variables.

ps <- ps_add_dissim(ps_simulate(50, 5, 5))
ord <- ps_ordinate(ps, method = "cmds", k = 4)
terra::plot(ord)