Package: phylospatial 1.5.0.9000

phylospatial: Spatial Phylogenetic Analysis

Analyze spatial phylogenetic diversity patterns. Use your data on an evolutionary tree and geographic distributions of the terminal taxa to compute diversity and endemism metrics, test significance with null model randomization, analyze community turnover and biotic regionalization, and perform spatial conservation prioritizations. All functions support quantitative community data in addition to binary data.

Authors:Matthew Kling [aut, cre, cph]

phylospatial_1.5.0.9000.tar.gz
phylospatial_1.5.0.9000.zip(r-4.7-any)phylospatial_1.5.0.9000.zip(r-4.6-any)phylospatial_1.5.0.9000.zip(r-4.5-any)
phylospatial_1.5.0.9000.tgz(r-4.6-any)phylospatial_1.5.0.9000.tgz(r-4.5-any)
phylospatial_1.5.0.9000.tar.gz(r-4.7-any)phylospatial_1.5.0.9000.tar.gz(r-4.6-any)
phylospatial_1.5.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
phylospatial/json (API)

# Install 'phylospatial' in R:
install.packages('phylospatial', repos = c('https://matthewkling.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/matthewkling/phylospatial/issues

Pkgdown/docs site:https://matthewkling.github.io

On CRAN:

Conda:

6.30 score 10 stars 10 scripts 518 downloads 32 exports 22 dependencies

Last updated from:dcbe67fa16. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK284
source / vignettesOK313
linux-releaseOK298
macos-releaseOK203
macos-oldrelOK198
windows-develOK148
windows-releaseOK207
windows-oldrelOK205
wasm-releaseOK184

Exports:benefitclade_distdelta_treemossphylospatialplot_lambdaps_add_dissimps_canapeps_canaperps_dissimps_diversityps_expandps_geodistps_get_commps_gridps_ordinateps_performanceps_prioritizeps_prioritizrps_quantizeps_randps_regionsps_regions_evalps_rgbps_simulateps_suggest_n_iterps_tracequantizerescale_treeslice_treeto_spatialuniform_tree

Dependencies:apeclassclassIntclusterDBIdigeste1071KernSmoothlatticeMASSMatrixmgcvnlmepermuteproxyRcpps2sfterraunitsveganwk

Conservation prioritization
Introduction | Greedy stepwise prioritization via ps_prioritize() | Performance curves | Probabilistic prioritization | Conservation benefit functions | Optimization with ps_prioritizr()
Rendered fromprioritization.Rmdusingknitr::rmarkdown

Last update: 2026-10-08
Started: 2024-12-13

Spatial phylogentic data
Introduction | A minimal example | Structure of a phylospatial object | Phylogeny | Community matrix | Spatial data | Starting from occurrence points | A realistic example | Non-phylogenetic data | Tree scaling | Affine rescaling | Differential transforms
Rendered fromphylospatial-data.Rmdusingknitr::rmarkdown

Last update: 2026-04-16
Started: 2024-12-13

Alpha phylogenetic diversity
Diversity measures | Null model randomization | Spatially constrained randomization | CANAPE
Rendered fromalpha-diversity.Rmdusingknitr::rmarkdown

Last update: 2026-04-10
Started: 2024-12-13

Phylogenetic beta diversity
Dissimilarity | Distance decay | Ordination | Regionalization
Rendered frombeta-diversity.Rmdusingknitr::rmarkdown

Last update: 2026-04-06
Started: 2024-12-13

Readme and manuals

Help Manual

Help pageTopics
Calculate taxon conservation benefitbenefit
Pairwise distances among clades or nodesclade_dist
Load California moss spatial phylogenetic datamoss
Create a spatial phylogenetic objectphylospatial
Plot alternative lambda valuesplot_lambda
Plot a 'phylospatial' objectplot.phylospatial
Add community dissimilarity data to a 'phylospatial' objectps_add_dissim
Categorical Analysis of Neo- and Paleo-Endemism (CANAPE)ps_canape
Binary randomization tests including CANAPEps_canaper
Quantitative phylogenetic dissimilarityps_dissim
Calculate spatial phylogenetic diversity and endemism metricsps_diversity
Expand occupied-only results to full spatial extentps_expand
Geographic distance between sitesps_geodist
Get 'phylospatial' community dataps_get_comm
Convert occurrence point data to a gridded community data setps_grid
Community phylogenetic ordinationps_ordinate
Performance curves for a conservation prioritizationplot.ps_performance ps_performance
Phylogenetic conservation prioritizationps_prioritize
Build a prioritizr conservation problemps_prioritizr
Stratified randomization of a phylospatial objectps_quantize
Null model randomization analysis of alpha diversity metricsps_rand
Cluster analysis to identify phylogenetic regionsps_regions
Evaluate region numbersps_regions_eval
Map phylospatial data onto RGB color bandsps_rgb
Simulate a toy spatial phylogenetic data setps_simulate
Suggest number of iterations for null model convergenceps_suggest_n_iter
Trace diagnostics for null model mixingps_trace
Stratified randomization of community matrixquantize
Convert a site-by-variable matrix into a SpatRaster or sf objectto_spatial
Scale branch lengths on a phylogenetic treedelta_tree rescale_tree slice_tree tree_scaling uniform_tree