phyloregion

1.0.9

Biogeographic Regionalization and Macroecology

1packages depend

7.7Kdownloads / year

5.6%test coverage

9/13checks pass

Overview

About

Maintained by Barnabas H. DaruFirst published 2020-03-305 releasesCRAN page ↗GitHub ↗

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).

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.

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).

Health

CRAN checks

4NOTE9OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 10.3 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.00

5.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-23
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 4 earlier snapshots

WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
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 · 155 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 88%
Documented parameters: 100%
Return-value docs: 98%
References docs: 41%

Downloads

7.7K

CRAN downloads in the past year

Rank #6,686 · ~21/day · ~640/mo

Releases R versions

Daily download trend is not available in this view yet.

42730 days

1.4K90 days

7.7K1 year

Compare downloads with other packages →

Also on129 r2u3 autocran1.3K conda_forge20 c2d4u

Repository

GitHub ↗ darunabas/phyloregion

20Stars

13Forks

9Open issues

1Open PRs

0Releases

528Commits

17Contributors

528 commits · Last activity 2025-07-14 · +5.3% stars, 30d

Stars over time

2024-10-23 · 172026-07-07 · 20

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/darunabas/phyloregion on 2026-07-31.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

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

canaper

Code & Tests

People & History

People (6)

Maintainer (1)

Barnabas H. Daru

Author, Maintainer, Copyright holder

Authors (3)

Barnabas H. Daru

Author, Maintainer, Copyright holder

Piyal Karunarathne

Author

Klaus Schliep

Author

Contributors (3)

Luciano Pataro

Contributor · added in 1.0.6

Albin Sandelin

Contributor

Xiaobei Zhao

Contributor

Barnabas H. Daru

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.9Latest
2025-07-15 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.8
2023-08-15 · diff ↗
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
2021-05-01 · diff ↗
1.0.4
2020-07-19 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.2
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
Minimum R: ≥ 4.1.0
Bundled data: 673 KB / 1 file
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

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