ps_ordinate: Community phylogenetic ordination

In phylospatial: Spatial Phylogenetic Analysis

Community phylogenetic ordination

Description

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)

Arguments

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.

Value

A matrix or spatial object with k variables.

See Also

For visualization using ordination onto RGB color space, see ps_rgb().

Examples

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

phylospatial documentation built on April 12, 2025, 1:35 a.m.