R Observatory: Metrics for EcoDiet version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

EcoDiet

2.0.1Package record

Estimating a Diet Matrix from Biotracer and Stomach Content Data

0packages depend

3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Pierre-Yves HernvannCRAN page ↗GitHub ↗Issues ↗

Biotracers and stomach content analyses are combined in a Bayesian hierarchical model to estimate a probabilistic topology matrix (all trophic link probabilities) and a diet matrix (all diet proportions). The package relies on the JAGS software and the 'jagsUI' package to run a Markov chain Monte Carlo approximation of the different variables.

Install

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

install.packages("EcoDiet", 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("pyhernvann/EcoDiet")

Development version from pyhernvann/EcoDiet. 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-ecodiet

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-EcoDiet

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-EcoDiet

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: 4.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMEYes · 390 wordsVignettesYes · 3 · dynamicNEWSYes · 67% structuredCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 15 (1 internal)includes a package overview page
Examples that run: 50%4 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 57%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #13,950 · ~8/day · ~251/mo

Releases R versions

Daily download trend is not available in this view yet.

32930 days

82790 days

3K1 year

Compare downloads with other packages →

Also on83 r2u9 autocran

How downloads are counted

Repository

pyhernvann/ecodiet ↗Account: pyhernvann

5Stars

3Forks

2Open PRs

1Releases

385Commits

8Commit identities

385 commits · Last activity 2024-03-25 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 75%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 86

Stars over time

2023-08-08 · 32026-07-07 · 5

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/pyhernvann/ecodiet on 2026-10-11.

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing EcoDiet adds 41 packages (16 with compiled code, 39 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, patchwork 3.2 MB.

Depends (1)

R >= 3.5

Imports (6)

ggplot2 codastatsutils (>= 3.6)jagsUI ggmcmc

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown devtools 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 (7)

Pierre-Yves Hernvann

Maintainer since 1.0.0 (2020), Author

Author

Author

Author

Author

Author

Author

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.1Latest
record
2024-03-25 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
2.0.0
record
2023-01-07 · diff ↗ ·
added 1 export
diagnose_model
unarchivedReturned to CRAN
2022-10-06
1.0.1
record
2022-10-06 · diff ↗
archivedRemoved from CRAN
2022-10-03
check issues were not corrected despite reminders
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.0
record
2020-03-05
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-05
Total releases: 4 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5
Bundled data: 220 KB / 1 file
Download size: 1.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("EcoDiet")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1002/eap.2521.

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 EcoDiet version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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