# Spatial Phylogenetic Analysis

## Documentation for package ‘phylospatial’ version 1.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

benefit | Calculate taxon conservation benefit
clade_dist | Pairwise distances among clades or nodes
moss | Load California moss spatial phylogenetic data
phylospatial | Create a spatial phylogenetic object
plot.phylospatial | Plot a 'phylospatial' object
plot_lambda | Plot alternative lambda values
ps_add_dissim | Add community dissimilarity data to a 'phylospatial' object
ps_canape | Categorical Analysis of Neo- and Paleo-Endemism (CANAPE)
ps_canaper | Binary randomization tests including CANAPE
ps_dissim | Quantitative phylogenetic dissimilarity
ps_diversity | Calculate spatial phylogenetic diversity and endemism metrics
ps_expand | Expand occupied-only results to full spatial extent
ps_geodist | Geographic distance between sites
ps_get_comm | Get 'phylospatial' community data
ps_grid | Convert occurrence point data to a gridded community data set
ps_ordinate | Community phylogenetic ordination
ps_prioritize | Phylogenetic conservation prioritization
ps_quantize | Stratified randomization of a phylospatial object
ps_rand | Null model randomization analysis of alpha diversity metrics
ps_regions | Cluster analysis to identify phylogenetic regions
ps_regions_eval | Evaluate region numbers
ps_rgb | Map phylospatial data onto RGB color bands
ps_simulate | Simulate a toy spatial phylogenetic data set
ps_suggest_n_iter | Suggest number of iterations for null model convergence
ps_trace | Trace diagnostics for null model mixing
quantize | Stratified randomization of community matrix
to_spatial | Convert a site-by-variable matrix into a SpatRaster or sf object