eDNAjoint

0.3.3

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

0packages depend

3.1Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Abigail G. KellerFirst published 2024-10-085 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 15.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.37

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-29
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-27
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 496 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 30%

Downloads

3.1K

CRAN downloads in the past year

Rank #12,829 · ~8/day · ~257/mo

Releases R versions

Daily download trend is not available in this view yet.

37430 days

79490 days

3.1K1 year

Compare downloads with other packages →

Also on425 r2u3 autocran

Repository

GitHub ↗ ropensci/ednajoint

9Stars

3Forks

1Open issues

0Open PRs

0Releases

211Commits

2Contributors

License GPL-3.0 · 211 commits · Last activity 2025-06-20 · 0% stars, 30d

Stars over time

2025-04-11 · 72026-07-07 · 9

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/ropensci/ednajoint on 2026-07-31.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (4)

Maintainer (1)

Abigail G. Keller

Author, Maintainer

Authors (1)

Abigail G. Keller

Author, Maintainer

Contributors (1)

Ryan P. Kelly

Contributor

Reviewers (2)

Chitra M. Saraswati

Reviewer

Saras M. Windecker

Reviewer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.3.3Latest
2025-06-21 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.2
2025-03-17 · diff ↗
0.3.1
2025-01-25 · diff ↗
0.3
2025-01-17 · diff ↗
0.2
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
Installed size: not tracked yet
With dependencies: not tracked yet

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