R Observatory: Metrics for phyloregion version 1.0.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phyloregion

1.0.9Package record

Biogeographic Regionalization and Macroecology

1packages depend

7.1Kdownloads / year

5.6%test coverage

8/13flavors OK

Overview

About

Maintained by Barnabas H. DaruCRAN page ↗GitHub ↗Website ↗Issues ↗

Computational infrastructure for biogeography, community ecology, and biodiversity conservation (Daru et al. 2020) doi:10.1111/2041-210X.13478. It is based on the methods described in Daru et al. (2020) doi:10.1038/s41467-020-15921-6. The original conceptual work is described in Daru et al. (2017) doi:10.1016/j.tree.2017.08.013 on patterns and processes of biogeographical regionalization. Additionally, the package contains fast and efficient functions to compute more standard conservation measures such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and global endangerment, as well as compositional turnover (e.g., beta diversity).

Changes in 1.0.9

Prepared and updated package for CRAN.
Revised and updated plot_pie to plot_spatial_membership and now uses blended color visualization.
Automatically adjusts radius depending on the projection system (e.g., EPSG:4326 vs EPSG:6933).
Added new functions backg, randpoints, rast_quantile, rast_hotspot
Updated documentation and examples accordingly.

From NEWS.md in the release

Install

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

install.packages("phyloregion", 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("darunabas/phyloregion")

Development version from darunabas/phyloregion. 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-phyloregion

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-phyloregion

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-phyloregion

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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  phyloregion/R/phylo_beta.R (.Names: 1)
'.Names' should be changed to 'names'.

CRAN check page ↗

Slowest check: 7.8 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-07-16
OK13 OK2026-06-23
ERROR12 OK, 1 ERROR2026-06-20
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08

Show 4 earlier changesHide 4 earlier changes

WARNING12 OK, 1 WARNING2026-06-07
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

Documentation signals are not tracked yet for this package.

WebsiteYes · pkgdown

Vignettes (3)

How these are measured

Downloads

7.1K

CRAN downloads in the past year

Rank #5,065 · ~20/day · ~594/mo

phyloregion Releases R versions

Daily download trend is not available in this view yet.

65030 days

1.6K90 days

7.1K1 year

Compare downloads with other packages →

Also on87 r2u9 autocran1.2K conda_forge53 c2d4u

How downloads are counted

Repository

darunabas/phyloregion ↗Account: darunabas

20Stars

13Forks

9Open issues

1Open PRs

0Releases

528Commits

17Commit identities

528 commits · Last activity 2025-07-14 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 60%
Median days to close, 50 most recently updated closed issues: 172
Median days to close, 50 most recently updated closed PRs: 8

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/darunabas/phyloregion on 2026-10-11.

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 (3)

pkgdown

GitHub Pages site last deployed 2025-07-14 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing phyloregion adds 58 packages (34 with compiled code, 44 MB of source tarballs). Heaviest: sf 9.3 MB, igraph 4.8 MB, s2 2.8 MB.

Depends (1)

R >= 4.1.0

Imports (14)

ape phangornMatrixbetapartparallelmethodscolorspace igraph clustMixType maptpx terra vegan predicts smoothr

LinkingTo (0)

none

Suggests (8)

tinytest knitr rmarkdown mapprojsurvivalrJava phyloseq V8

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

canaper

How these are counted

Code & Tests

Datasets

People & History

People (6)

Author

Author

Contributor · added in 1.0.6

Albin Sandelin

Contributor

Xiaobei Zhao

Contributor

Releases (5)

R
R 4.6.0 released · 2026-04-24
1.0.9Latest
record
2025-07-15 · current release · diff ↗ ·
removed 1 export
plot_pie

added 9 exports
RPD, backg, choropleth, dirpath, plot_spatial_membership, randpoints, rast_hotspot, rast_quantile, tree_sampler
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.8
record
2023-08-15 · diff ↗ ·
removed 4 exports
choropleth, plot_structure, plot_swatch, raster2comm

added 5 exports
fitgom, functional_beta, plot.sparse, rast2comm, unifrac
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.6
record
2021-05-01 · diff ↗ ·
added 8 exports
PD_ses, arc_labels, counts, nodepie, phylobeta_ses, plot_pie, plot_structure, sdm
1.0.4
record
2020-07-19 · diff ↗ ·
removed 1 export
plot_evoldistinct

added 2 exports
indicators, plot.phyloregion
R
R 4.0.0 released · 2020-04-24
1.0.2
record
2020-03-30
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-30
Total releases: 5 / 6 yrs
License: AGPL-3 OSI
Download size: 1.5 MB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phyloregion")

Format

Daru, B. H., Karunarathne, P., Pataro, L., Sandelin, A., Schliep, K., & Zhao, X. (2025). phyloregion: Biogeographic Regionalization and Macroecology (Version 1.0.9) [Computer software]. https://doi.org/10.32614/CRAN.package.phyloregion

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 phyloregion version 1.0.9 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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