R Observatory: Metrics for rdiversity version 2.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rdiversity

2.3.0Package record

Measurement and Partitioning of Similarity-Sensitive Biodiversity

0packages depend

3.2Kdownloads / year

86.0%test coverage

13/13flavors OK

Overview

About

Maintained by Richard ReeveCRAN page ↗GitHub ↗Issues ↗

Provides a framework for the measurement and partitioning of the (similarity-sensitive) biodiversity of a metacommunity and its constituent subcommunities. Richard Reeve, et al. (2016) doi:10.48550/arXiv.1404.6520.

Changes in 2.3.0

Fixed repartition() for non-phylogenetic metacommunities: it previously passed a bare similarity matrix to metacommunity(), which has not accepted matrices for a while
Added tests for gen2dist(), inddiv(), repartition() and the high-level diversity-measure wrappers
Corrected the gen2dist() documentation
Removed the vendored binary.R library; the taxonomic and genetic bit handling is now implemented directly in base R
**Breaking:** as.binary() (and its associated S3 methods) is no longer exported, as it was only ever an internal implementation detail
Removed unused stats/utils imports
Dropped the reshape2 dependency (superseded upstream); the melt() calls in inddiv()/subdiv()/metadiv() are replaced by a small internal base-R helper

Show all changes in 2.3.0Hide the rest of the changes in 2.3.0

Migrated continuous integration from Travis CI and AppVeyor to GitHub Actions
Added lint, pr-commands and R-hub v2 (rhub) workflows
Formatted the codebase with styler and added a .lintr configuration so the package passes lintr::lint_package() cleanly
Added a cran-comments.md template and tidied the repository (ignore rules, build artefacts).

From NEWS.md in the release

Install

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

install.packages("rdiversity", 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("boydorr/rdiversity")

Development version from boydorr/rdiversity. 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-rdiversity

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-rdiversity

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-rdiversity

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: 2.3 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.3.0

READMEYes · 150 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 2.3.0Citation fileYes · cites a publication

Help pages: 43includes a package overview page
Examples that run: 100%27 run in a plain check
Exported functions with examples: 74%
Documented parameters: 99%
Return-value docs: 97%
Help pages citing references: 60%

Vignettes (1)

rdiversity-examples

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #11,660 · ~9/day · ~270/mo

Releases R versions

Daily download trend is not available in this view yet.

30830 days

93590 days

3.2K1 year

Compare downloads with other packages →

Also on89 r2u3 autocran

How downloads are counted

Repository

boydorr/rdiversity ↗Organization: boydorr

11Stars

4Forks

0Open issues

0Open PRs

14Releases

1,387Commits

6Commit identities

rdiversity-measurementpartitioning-diversitybiodiversity

1,387 commits · Last activity 2026-07-16 · +10% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-01-23 · 82026-10-02 · 11

How these are measured

PracticesBeta

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

Checks run against github.com/boydorr/rdiversity 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 (2)

GitHub Pages site last deployed 2026-07-16 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

Show all practicesHide 2 practices

Research and citation (1)

Zenodo

Lint, format, editor (3)

lintrLint workflowRStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing rdiversity adds 1 package (1 with compiled code, 843 KB of source tarballs). Heaviest: stringdist 843 KB.

Depends (1)

R >= 3.5.0

Imports (4)

methodsstatsstringdistutils

LinkingTo (0)

none

Suggests (6)

ape testthat knitr markdown rmarkdown covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Richard Reeve

Maintainer since 2.2.0 (2022), Author, Thesis advisor

Sonia Mitchell

Author

Tom White

Contributor · added in 2.0

Previously maintained by Sonia Mitchell (1.0 to 2.0).

Listed in earlier versions (2)

Daniel Dörrhöfer

no longer listed · 2.2.0

Aaron Rudkin

no longer listed · 2.2.0

Releases (6)

Pick two releases to compare their code metrics.

2.3.0Latest
record
2026-07-15 · current release · diff ↗ ·
removed 1 export
as.binary
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-05-06
2.2.0
record
2022-05-06 · diff ↗ ·
added 1 export
as.binary
archivedRemoved from CRAN
2022-04-26
requires archived package 'binaryLogic'
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.0
record
2020-05-20 · diff ↗ ·
removed 22 exports
check_partition, check_phypartition, check_similarity, get_title, hs_parameters, inddiv, is.metacommunity, is.powermean, is.relativeentropy, metadiv, plot_diversity, powermean, qD, qDZ, qDZ_single, qD_single, relativeentropy, similarity_shimatani, smatrix, subdiv, tbar, zmatrix

added 5 exports
dist2sim, gen2dist, phy2branch, phy2dist, tax2dist
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.2.1
record
2018-06-19 · diff ↗
1.2
record
2018-06-12 · diff ↗ ·
added 1 export
check_phypartition
R
R 3.5.0 released · 2018-04-23

Show 2 earlier eventsHide 2 earlier events

1.0
record
2017-06-27
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-06-27
Total releases: 6 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Download size: 281 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("rdiversity")

The package provides a citation file, so citation() returns the authors' own entry.

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 rdiversity version 2.3.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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