R Observatory: Metrics for eDITH version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

eDITH

1.1.0Package record

Model Transport of Environmental DNA in River Networks

0packages depend

6.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Luca CarraroCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: University of Zurich

Runs the eDITH (environmental DNA Integrating Transport and Hydrology) model, which implements a mass balance of environmental DNA (eDNA) transport at a river network scale coupled with a species distribution model to obtain maps of species distribution. eDITH can work with both eDNA concentration (e.g., obtained via quantitative polymerase chain reaction) or metabarcoding (read count) data. Parameter estimation can be performed via Bayesian techniques (via the 'BayesianTools' package) or optimization algorithms. An interface to the 'DHARMa' package for posterior predictive checks is provided. See Carraro and Altermatt (2024) doi:10.1111/2041-210X.14317 for a package introduction; Carraro et al. (2018) doi:10.1073/pnas.1813843115 and Carraro et al. (2020) doi:10.1038/s41467-020-17337-8 for methodological details.

Changes in 1.1.0

Major changes

Functions run_eDITH_optim, run_eDITH_optim_joint have initial parameter set redefined.

Minor changes

Function eval_posterior_eDITH exports quantiles and mean of the model parameters.

From NEWS.md in the release

Install

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

install.packages("eDITH", 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("lucarraro/eDITH")

Development version from lucarraro/eDITH. 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-edith

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-eDITH

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 14.1 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 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.1.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 15includes a package overview page
Examples that run: 100%9 run in a plain check
Exported functions with examples: 100%
Documented parameters: 71%
Return-value docs: 100%
Help pages citing references: 7%

Vignettes (1)

An introduction to eDITH

How these are measured

Downloads

6.1K

CRAN downloads in the past year

Rank #7,725 · ~17/day · ~511/mo

Releases R versions

Daily download trend is not available in this view yet.

46630 days

1.1K90 days

6.1K1 year

Compare downloads with other packages →

Also on387 r2u

How downloads are counted

Repository

lucarraro/edith ↗Account: lucarraro

2Stars

0Forks

1Open issues

0Open PRs

1Releases

105Commits

2Commit identities

105 commits · Last activity 2025-09-15

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 4

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/lucarraro/edith on 2026-10-11.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-09-15 · The repository has a site deploy workflow

pkgdown site last built 2025-09-15

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing eDITH adds 160 packages (93 with compiled code, 178 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.6

Imports (8)

Rcpp OCNet rivnet BayesianTools LaplacesDemon DHARMa terra fields

LinkingTo (1)

Rcpp

Suggests (3)

knitr rmarkdown bookdown

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 (3)

Luca Carraro

Maintainer since 0.1.0 (2023), Author

Florian Altermatt

Author

University of Zurich

Copyright holder, Funder

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
record
2025-09-12 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
record
2024-05-24 · diff ↗ ·
added 4 exports
run_eDITH_optim_joint, run_eDITH_BT_joint, sampling_strategy_eDNA, sampling_strategy_direct
R
R 4.4.0 released · 2024-04-24
0.3.0
record
2024-03-28 · diff ↗
0.2.0
record
2024-01-16 · diff ↗ ·
added 1 export
run_eDITH_single
0.1.2
record
2023-10-24 · diff ↗
unarchivedReturned to CRAN
2023-10-15
0.1.1
record
2023-10-15 · diff ↗
archivedRemoved from CRAN
2023-09-16
requires archived package 'OCNet'
0.1.0
record
2023-09-14
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-14
Total releases: 7 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6
Bundled data: 1.3 MB / 6 files
Download size: 2.6 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("eDITH")

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

It points to 10.1111/2041-210x.14317.

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 eDITH version 1.1.0 [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.

Report a problem with this page →