R Observatory: Metrics for chemodiv version 0.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

chemodiv

0.3.1Package record

Analysing Chemodiversity of Phytochemical Data

0packages depend

4Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Hampus PetrénCRAN page ↗GitHub ↗Issues ↗

Quantify and visualise various measures of chemical diversity and dissimilarity, for phytochemical compounds and other sets of chemical composition data. Importantly, these measures can incorporate biosynthetic and/or structural properties of the chemical compounds, resulting in a more comprehensive quantification of diversity and dissimilarity. For details, see Petrén, Köllner and Junker (2023) doi:10.1111/nph.18685.

Changes in 0.3.1

Fixed error caused by NPCTable, due to internet resource being

temporarily unavailable. This was done by ensuring both NPCTable and compDis

properly "fail gracefully with an informative message if the resource

is not available or has changed".

Updated molNet to not use deprecated function.
Fixed roxygen documentation issue.
Made various minor updates to readme, documentation and vignette.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("chemodiv", 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("hpetren/chemodiv")

Development version from hpetren/chemodiv. 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-chemodiv

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

Health

CRAN checks

1ERROR12OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-x86_64

Packages required but not available: 'fmcsR', 'ChemmineR'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 2.8 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR9 OK, 5 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.1

READMEYes · 585 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.3.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 25 (1 internal)includes a package overview page
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 28%

Vignettes (1)

Analysing Phytochemical Diversity -- An introduction to *chemodiv* HTML

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #10,145 · ~11/day · ~336/mo

Releases R versions

Daily download trend is not available in this view yet.

37430 days

99190 days

4K1 year

Compare downloads with other packages →

Also on104 r2u

How downloads are counted

Repository

hpetren/chemodiv ↗Account: hpetren

10Stars

1Forks

0Open issues

0Open PRs

5Releases

189Commits

1Commit identities

License file reads as GPL-3.0 · 189 commits · Last activity 2025-06-21 · 0% stars, 30d · Default branch at 0.3.1.9000, ahead of CRAN 0.3.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 91
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-10-09 · 102026-07-07 · 10

How these are measured

PracticesBeta

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

Checks run against github.com/hpetren/chemodiv on 2026-10-18.

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 (1)

README.Rmd

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing chemodiv adds 120 packages (70 with compiled code, 97 MB of source tarballs). Heaviest: stringi 11 MB, ncbit 9.4 MB, ggplot2 6.0 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 2.10

Imports (18)

jsonlite httr vegan webchem fmcsR ChemmineR hillR ape GUniFrac tidygraph igraph ggraph ggplot2 gridExtra ggdendro tidyr rlang curl

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

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 (3)

Hampus Petrén

Author, Maintainer since 0.1.2 (2022)

Robert R. Junker

Author

Tobias G. Köllner

Author

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.1Latest
record
2025-06-18 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.3.0
record
2023-08-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.2.0
record
2023-01-12 · diff ↗
0.1.3
record
2022-08-26 · diff ↗
0.1.2
record
2022-06-02
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-02
Total releases: 5 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 51 KB / 13 files
Download size: 505 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("chemodiv")

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 chemodiv version 0.3.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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