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")