phylospatial

1.4.0

Spatial Phylogenetic Analysis

0packages depend

6.9Kdownloads / year

90.4%test coverage

13/13checks pass

Overview

About

Maintained by Matthew KlingFirst published 2025-01-247 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phylospatial", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("matthewkling/phylospatial")

Development version from matthewkling/phylospatial. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phylospatial

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phylospatial

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phylospatial

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 7.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.27

90.4%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-04
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-31
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 295 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 54%
Documented parameters: 96%
Return-value docs: 100%
References docs: 21%

Downloads

6.9K

CRAN downloads in the past year

Rank #6,176 · ~19/day · ~573/mo

Releases R versions

Daily download trend is not available in this view yet.

36530 days

1.6K90 days

6.9K1 year

Compare downloads with other packages →

Also on159 r2u24 autocran

Repository

GitHub ↗ matthewkling/phylospatial

9Stars

1Forks

0Open issues

0Open PRs

6Releases

116Commits

1Contributors

116 commits · Last activity 2026-05-28 · 0% stars, 30d

Stars over time

2025-04-29 · 62026-07-07 · 9

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/matthewkling/phylospatial on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (6)

ape sfstatsterrautilsvegan

LinkingTo (0)

none

Suggests (14)

canaper furrr future testthat betapart knitr rmarkdown tmap magrittr hillR picante phytools nullcat parallelDist

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Matthew Kling

Author, Maintainer, Copyright holder

Authors (1)

Matthew Kling

Author, Maintainer, Copyright holder

Matthew Kling

Author, Maintainer, Copyright holder

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.4.0Latest
2026-04-16 · current release · diff ↗
1.3.0
2026-04-04 · diff ↗
1.2.1
2025-12-24 · diff ↗
1.2.0
2025-12-20 · diff ↗
unarchivedReturned to CRAN
2025-12-20
archivedRemoved from CRAN
2025-12-08
issues were not corrected in time
1.1.1
2025-05-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.0
2025-04-09 · diff ↗
1.0.0
2025-01-24
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-24
Total releases: 7 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Download size: 1.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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