R Observatory: Metrics for epizootic version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epizootic

2.0.0

Spatially Explicit Population Models of Disease Transmission in Wildlife

0packages depend

2.7Kdownloads / year

75.1%test coverage

13/13checks pass

Overview

About

Maintained by July PilowskyFirst published 2024-10-022 releasesCRAN page ↗GitHub ↗

This extension of the pattern-oriented modeling framework of the 'poems' package provides a collection of modules and functions customized for modeling disease transmission on a population scale in a spatiotemporally explicit manner. This includes seasonal time steps, dispersal functions that track disease state of dispersers, results objects that store disease states, and a population simulator that includes disease dynamics.

Install

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

install.packages("epizootic", 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("viralemergence/epizootic")

Development version from viralemergence/epizootic. 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-epizootic

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-epizootic

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-epizootic

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 13.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.60

75.1%

Coverage · measured lines

100%

Documentation · exports

11

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 255 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 82%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #14,142 · ~7/day · ~222/mo

Releases R versions

Daily download trend is not available in this view yet.

22730 days

74390 days

2.7K1 year

Compare downloads with other packages →

Also on426 r2u3 autocran

Repository

GitHub ↗ viralemergence/epizootic

4Stars

1Forks

0Open issues

0Open PRs

3Releases

97Commits

1Contributors

software

License GPL-3.0 · 97 commits · Last activity 2026-08-05

Stars over time

2025-02-28 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/viralemergence/epizootic on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

renv

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.3.0

Imports (11)

purrr dplyr tibble R6 (>= 2.5.1)cli raster qs2 poems doParallel foreach Rcpp

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

testthat geosphere knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

July Pilowsky

Author, Maintainer

Authors (1)

July Pilowsky

Author, Maintainer

Funders (1)

National Science Foundation Biology Integration Institute 2213854

Funder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.0.0Latest
2025-11-12 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.0
2024-10-02
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-10-02
Total releases: 2 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.3.0
Bundled data: 142 KB / 4 files
Download size: 786 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("epizootic")

Format

Pilowsky, J., & National Science Foundation Biology Integration Institute 2213854. (2025). epizootic: Spatially Explicit Population Models of Disease Transmission in Wildlife (Version 2.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.epizootic

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 epizootic version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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