README.md
In phylospatial: Spatial Phylogenetic Analysis

phylospatial

phylospatial is an R package for spatial phylogenetic diversity analysis. The field of spatial phylogenetics focuses on accounting for evolutionary relationships among taxa when describing biodiversity patterns, an approach that has a number of advantages over species-based accounting. This package provides a set of functions to build and analyze 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 difference between phylospatial and other spatial phylogenetic R libraries is that all functions in this package work not only with binary presence-absence data but also with quantitative community data types including occurrence probabilities or abundances. In particular, support for occurrence probabilities, such as from species distribution models, has not been implemented in other phylogenetic diversity tools and was a central motivation for the creation of this package. Probability, abundance, and binary data are incorporated in distinct ways in all computations throughout the package, avoiding the need to discard information by thresholding continuous data.

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")