R Observatory: Metrics for phylospatial version 1.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phylospatial

1.6.0Package record

Spatial Phylogenetic Analysis

0packages depend

6.6Kdownloads / year

87.3%test coverage

13/13flavors OK

Overview

About

Maintained by Matthew KlingCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.6.0

Sites no longer need to be equal-area. phylospatial() gains a site_weight argument controlling how much each site contributes to taxon range sizes, which underlie endemism metrics and prioritization. It can be NULL (the default, weighting all sites equally as before), "area" (weighting sites by their area), or one value per site supplied as a numeric vector, single-layer SpatRaster, or sf object (for example, site areas raised to a power between 0 and 1). Weights are rescaled to a mean of 1 across occupied sites and stored in ps$site_weight. Site weights are used by endemism metrics in ps_diversity(), ps_rand(), and ps_canape(); the endemism option of ps_dissim() and ps_regions(); and ps_prioritize(), ps_prioritizr(), and ps_performance(). ps_canaper() does not support them. See the "Site weights" section of ?phylospatial for guidance on choosing weights, and ?ps_rand for how they interact with null models.
phylospatial() now warns, rather than throwing an error, when sites vary in area by more than area_tol and no site_weight is given. The check now considers occupied sites only, and is skipped when site_weight is provided.
New function ps_area() returns the area (km²) of each site in a raster, sf polygon, or phylospatial object, or the length (km) of line features, for use in deriving site weights.
plot.phylospatial() gains a taxa argument for choosing which lineage ranges to plot when y = "comm", instead of a random sample.
moss() gains a data argument for loading companion layers on the same grid as the moss data set: "protection" (fraction of each cell in protected areas) and "popdens" (human population density), for use as init and cost in conservation prioritizations. Both are available in raster and polygon formats.
Fixed an error in ps_prioritize() and ps_prioritizr() when init or cost was supplied as an sf object, which the documentation already listed as supported.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 7.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-04
ERROR13 OK, 1 ERROR2026-03-31
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.0

READMEYes · 296 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 1.6.0Citation fileNoWebsiteYes · pkgdown

Help pages: 33 (2 internal)includes a package overview page
Examples that run: 53%16 run in a plain check (1 of them under a condition) · 14 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 97%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 21%

Vignettes (4)

How these are measured

Downloads

6.6K

CRAN downloads in the past year

Rank #6,043 · ~18/day · ~553/mo

Releases R versions

Daily download trend is not available in this view yet.

52630 days

1.4K90 days

6.6K1 year

Compare downloads with other packages →

Also on119 r2u4 autocran

How downloads are counted

Repository

matthewkling/phylospatial ↗Account: matthewkling

10Stars

1Forks

1Open issues

0Open PRs

7Releases

127Commits

1Commit identities

127 commits · Last activity 2026-10-22 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-14 · 72026-08-28 · 10

How these are measured

PracticesBeta

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

Checks run against github.com/matthewkling/phylospatial on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-14 · The repository has a site deploy workflow

pkgdown site last built 2026-10-14, before release 1.6.0 (2026-10-22)

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing phylospatial adds 14 packages (12 with compiled code, 21 MB of source tarballs). Heaviest: sf 9.3 MB, s2 2.8 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5

Imports (6)

ape sfstatsterrautilsvegan

LinkingTo (0)

none

Suggests (17)

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

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Matthew Kling

Releases (9)

Pick two releases to compare their code metrics.

1.6.0Latest
record
2026-10-22 · current release · diff ↗ ·
added 1 export
ps_area
1.5.0
record
2026-10-01 · diff ↗ ·
added 6 exports
delta_tree, ps_performance, ps_prioritizr, rescale_tree, slice_tree, uniform_tree
R
R 4.6.0 released · 2026-04-24
1.4.0
record
2026-04-16 · diff ↗ ·
added 3 exports
ps_grid, ps_suggest_n_iter, ps_trace
1.3.0
record
2026-04-03 · diff ↗ ·
added 2 exports
ps_expand, ps_geodist
1.2.1
record
2025-12-24 · diff ↗
unarchivedReturned to CRAN
2025-12-20
1.2.0
record
2025-12-20 · diff ↗ ·
added 1 export
ps_quantize
archivedRemoved from CRAN
2025-12-08
issues were not corrected in time
1.1.1
record
2025-05-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.0
record
2025-04-09 · diff ↗ ·
added 1 export
clade_dist
1.0.0
record
2025-01-24
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-24
Total releases: 9 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Download size: 2.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phylospatial")

Format

Kling, M. (2026). phylospatial: Spatial Phylogenetic Analysis (Version 1.6.0) [Computer software]. https://doi.org/10.32614/CRAN.package.phylospatial

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for phylospatial version 1.6.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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