R Observatory: Metrics for occumb version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

occumb

1.3.0Package record

Site Occupancy Modeling for Environmental DNA Metabarcoding

0packages depend

5.1Kdownloads / year

71.7%test coverage

13/13flavors OK

Overview

About

Maintained by Keiichi FukayaCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.3.0

Add an option to select the NIMBLE engine in occumb() (thanks to hoxo-m).
Add a vignette comparing the performance of the JAGS and NIMBLE engines.
Fix a bug in eval_util_L() and eval_util_R() that could cause erroneous errors when species detection probabilities are low.
Some internal changes for package testing.

From NEWS.md in the release

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. 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-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). 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: 2.5 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.0

READMEYes · 315 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.3.0Citation fileNoWebsiteYes · pkgdown

Help pages: 16 (1 internal)
Examples that run: 33%2 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 75%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

Introduction to occumb HTML
Model specification in occumb() HTML
Options for MCMC engines in occumb() HTML

How these are measured

Downloads

5.1K

CRAN downloads in the past year

Rank #9,742 · ~14/day · ~425/mo

Releases R versions

Daily download trend is not available in this view yet.

39930 days

1K90 days

5.1K1 year

Compare downloads with other packages →

Also on92 r2u2 autocran

How downloads are counted

Repository

fukayak/occumb ↗Account: fukayak

3Stars

3Forks

0Open issues

0Open PRs

0Releases

535Commits

4Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-01-28 · 22026-07-07 · 3

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/fukayak/occumb 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 (3)

pkgdown

GitHub Pages site last deployed 2026-04-04 · The repository has a site deploy workflow

pkgdown site last built 2026-04-04, before release 1.3.0 (2026-04-06)

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

lintr

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing occumb adds 11 packages (5 with compiled code, 2.7 MB of source tarballs). Heaviest: jagsUI 1.4 MB, knitr 479 KB, checkmate 247 KB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Keiichi Fukaya

Author, Maintainer since 1.0.1 (2023)

Mika Takahashi

Author · added in 1.2.0

Koji Makiyama

Contributor · added in 1.3.0

option to use NIMBLE

Kentaro Matsuura

Contributor · added in 1.3.0

option to use NIMBLE

Martyn Plummer

Contributor · added in 1.3.0

fixes for JAGS 5.0.0 compatibility

Ken Kellner

Copyright holder · added in 1.0.2

summary method for occumbFit class, processing of NIMBLE results, and print method for nimbleSummary class

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.3.0Latest
record
2026-04-06 · current release · diff ↗
1.2.2
record
2026-01-09 · diff ↗
1.2.1
record
2025-07-16 · diff ↗
1.2.0
record
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
record
2024-03-26 · diff ↗
1.0.3
record
2024-01-08 · diff ↗
1.0.2
record
2023-10-19 · diff ↗
1.0.1
record
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 · relicensed from MIT + file LICENSE in 1.0.2
Minimum R: ≥ 2.10
Bundled data: 14 KB / 2 files
Download size: 864 KB

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-21. 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.

Report a problem with this page →