R Observatory: Metrics for eDNAjoint version 0.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

eDNAjoint

0.3.3Package record

Joint Modeling of Traditional and Environmental DNA Survey Data in a Bayesian Framework

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Abigail G. KellerCRAN page ↗GitHub ↗Website ↗Issues ↗

Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: https://ednajoint.netlify.app/). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and gear scaling coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.

Install

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

install.packages("eDNAjoint", 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("ropensci/eDNAjoint")

Development version from ropensci/eDNAjoint. 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-ednajoint

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-eDNAjoint

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-eDNAjoint

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: 18.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29
ERROR12 OK, 1 ERROR2026-07-27
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.3

READMEYes · 496 wordsVignettesNoNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 10includes a package overview page
Examples that run: 0%7 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 30%

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #11,865 · ~8/day · ~244/mo

Releases R versions

Daily download trend is not available in this view yet.

36630 days

91190 days

2.9K1 year

Compare downloads with other packages →

Also on385 r2u12 autocran

How downloads are counted

Repository

ropensci/ednajoint ↗Organization: ropensci

9Stars

3Forks

1Open issues

0Open PRs

0Releases

211Commits

2Commit identities

License file reads as GPL-3.0 · 211 commits · Last activity 2025-06-20 · 0% stars, 30d · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 152
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-15 · 82026-07-07 · 9

How these are measured

PracticesBeta

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

Checks run against github.com/ropensci/ednajoint on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Code of conductContributing guide

Docs source (1)

README.Rmd

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 2 practices

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing eDNAjoint adds 62 packages (31 with compiled code, 67 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1

Imports (13)

bayestestR dplyr ggplot2 lifecycle loomethodsRcpp (>= 0.12.0)RcppParallel rlist rstan rstantools tidyr scales

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.26.22)

Suggests (4)

bayesplot 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 (4)

Abigail G. Keller

Author, Maintainer since 0.2 (2024)

Ryan P. Kelly

Contributor

Chitra M. Saraswati

Reviewer

Saras M. Windecker

Reviewer

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.3Latest
record
2025-06-21 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.2
record
2025-03-17 · diff ↗
0.3.1
record
2025-01-25 · diff ↗
0.3
record
2025-01-17 · diff ↗ ·
removed 7 exports
detectionCalculate, detectionPlot, jointModel, jointSelect, jointSummarize, muCritical, traditionalModel

added 7 exports
detection_calculate, detection_plot, joint_model, joint_select, joint_summarize, mu_critical, traditional_model
0.2
record
2024-10-08
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-08
Total releases: 5 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1
Bundled data: 4.3 KB / 2 files
Download size: 2.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("eDNAjoint")

Format

Keller, A. G., Kelly, R. P., Saraswati, C. M., & Windecker, S. M. (2025). eDNAjoint: Joint Modeling of Traditional and Environmental DNA Survey Data in a Bayesian Framework (Version 0.3.3) [Computer software]. https://doi.org/10.32614/CRAN.package.eDNAjoint

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 eDNAjoint version 0.3.3 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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