R Observatory: Metrics for occumb version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

occumb

1.3.0

Site Occupancy Modeling for Environmental DNA Metabarcoding

0packages depend

4.8Kdownloads / year

71.7%test coverage

13/13checks pass

Overview

About

Maintained by Keiichi FukayaFirst published 2023-09-238 releasesCRAN page ↗GitHub ↗

Fits community site occupancy models to environmental DNA metabarcoding data collected using spatially-replicated survey design. Model fitting results can be used to evaluate and compare the effectiveness of species detection to find an efficient survey design. Reference: Fukaya et al. (2022) doi:10.1111/2041-210X.13732, Fukaya and Hasebe (2025) doi:10.1002/1438-390X.12219.

Install

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

install.packages("occumb", 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("fukayak/occumb")

Development version from fukayak/occumb. 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-occumb

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-occumb

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-occumb

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.41

71.7%

Coverage · measured lines

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 315 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 33%
Documented parameters: 96%
Return-value docs: 100%
References docs: 0%

Downloads

4.8K

CRAN downloads in the past year

Rank #8,389 · ~13/day · ~397/mo

Releases R versions

Daily download trend is not available in this view yet.

19030 days

1.1K90 days

4.8K1 year

Compare downloads with other packages →

Also on117 r2u

Repository

GitHub ↗ fukayak/occumb

3Stars

3Forks

0Open issues

0Open PRs

0Releases

535Commits

4Contributors

License GPL-3.0 · 535 commits · Last activity 2026-04-04 · 0% stars, 30d

Stars over time

2025-01-28 · 22026-07-07 · 3

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fukayak/occumb on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

lintr

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (2)

R >= 2.10jagsUI

Imports (6)

statsmethodsgraphicscheckmate crayon knitr

LinkingTo (0)

none

Suggests (10)

covr rmarkdown spelling testthat tibble vdiffr nimble codaparallelDoE.base

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Keiichi Fukaya

Author, Maintainer

Authors (2)

Keiichi Fukaya

Author, Maintainer

Mika Takahashi

Author · added in 1.2.0

Contributors (3)

Koji Makiyama

Contributor · added in 1.3.0

Kentaro Matsuura

Contributor · added in 1.3.0

Martyn Plummer

Contributor · added in 1.3.0

Copyright holders (1)

Ken Kellner

Copyright holder · added in 1.0.2

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.3.0Latest
2026-04-07 · current release · diff ↗
1.2.2
2026-01-09 · diff ↗
1.2.1
2025-07-16 · diff ↗
1.2.0
2025-05-24 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.0
2024-03-26 · diff ↗
1.0.3
2024-01-08 · diff ↗
1.0.2
2023-10-19 · diff ↗
1.0.1
2023-09-23
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-23
Total releases: 8 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 14 KB / 2 files
Download size: 864 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("occumb")

Format

Fukaya, K., Kellner, K., Makiyama, K., Matsuura, K., Plummer, M., & Takahashi, M. (2026). occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding (Version 1.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.occumb

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 occumb version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →