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:
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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.
Vignettes
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vignette("phylospatial-data")gives details about constructingphylospatialdatasets 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.
Installation
# you can install the package from CRAN:
install.packages("phylospatial")
# or the development version from GitHub:
remotes::install_github("matthewkling/phylospatial")Quick start
library(phylospatial)
ps <- moss() # load example data
div <- ps_diversity(ps) # calculate diversity metrics
terra::plot(div)