README.md
In phylospatial: Spatial Phylogenetic Analysis

phylospatial

phylospatial is an R package for spatial phylogenetic diversity analysis—accounting for evolutionary relationships among taxa when describing biodiversity patterns. The package provides functions for building and analyzing phylospatial data:

phylospatial() constructs a spatial phylogenetic data set from community data and a tree.
ps_diversity() calculates a range of phylogenetic diversity and endemism metrics.
ps_rand() computes significance values for diversity metrics using null model randomizations.
ps_dissim() calculates a pairwise community phylogenetic beta diversity matrix.
ps_ordinate() performs a community ordination to reduce the dimensionality of the data set.
ps_regions() clusters sites into phylogenetically similar biogeographic regions.
ps_prioritize() performs a spatial optimization to identify conservation priorities.

A key feature of phylospatial is full support for quantitative community data, including occurrence probabilities (e.g., from species distribution models) and abundances, in addition to binary presence-absence data. This avoids information loss from thresholding continuous data, and enables new analyses not available in other spatial phylogenetic R packages.

vignette("phylospatial-data") gives details about constructing phylospatial datasets with different types of data.
vignette("alpha-diversity") demonstrates calculation of alpha phylogenetic diversity and endemism measures, including statistical hypothesis testing using randomization-based null models.
vignette("beta-diversity") shows how to calculate phylogenetic beta diversity measures including nestedness and turnover, as well as phylogenetic ordination and regionalization to visualize phylogenetic community structure.
vignette("prioritization") explains how to perform a phylogenetic conservation prioritization.

# you can install the package from CRAN:
install.packages("phylospatial")

# or the development version from GitHub:
remotes::install_github("matthewkling/phylospatial")

library(phylospatial)
ps <- moss() # load example data
div <- ps_diversity(ps) # calculate diversity metrics
terra::plot(div)

To cite phylospatial in publications, please use:

Kling, M. (2025). phylospatial: an R package for spatial phylogenetic analysis with quantitative community data. Methods in Ecology and Evolution 16:1075–1083. DOI 10.1111/2041-210x.70056