R Observatory: Metrics for epiworldR version 0.14.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epiworldR

0.14.0.0

Fast Agent-Based Epi Models

2packages dependsuggested by 1

7.5Kdownloads / year

71.1%test coverage

13/13flavors OK

Overview

About

Maintained by George Vega YonCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Centers for Disease Control and Prevention

A flexible framework for Agent-Based Models (ABM), the 'epiworldR' package provides methods for prototyping disease outbreaks and transmission models using a 'C++' backend, making it very fast. It supports multiple epidemiological models, including the Susceptible-Infected-Susceptible (SIS), Susceptible-Infected-Removed (SIR), Susceptible-Exposed-Infected-Removed (SEIR), and others, involving arbitrary mitigation policies and multiple-disease models. Users can specify infectiousness/susceptibility rates as a function of agents' features, providing great complexity for the model dynamics. Furthermore, 'epiworldR' is ideal for simulation studies featuring large populations.

Changes in 0.14.0.0

The way seed is passed to run() and run_multiple() has been modified to ensure comparability with the C++ version. Now, a random seed number is drawn only if seed is not specified.

Internal changes

(epiworld#189) Addressing memory access issues that arise when calling run_multiple using OpenMP. The latest version reduces usage of points (including smart) to make the code more reliable. No penalties on its performance are expected.
Switch vignette building engine to quarto.

From NEWS.md in the release

Install

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

install.packages("epiworldR", 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("UofUEpiBio/epiworldR")

Development version from UofUEpiBio/epiworldR. 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-epiworldr

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-epiworldR

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-epiworldR

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: 7.0 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
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.14.0.0

READMEYes · 1,119 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 0.14.0.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Cites a JOSS paper

Help pages: 36 (1 internal)includes a package overview page
Examples that run: 97%33 run in a plain check · 1 hold no code
Exported functions with examples: 97%
Documented parameters: 93%
Return-value docs: 97%
Help pages citing references: 0%

Vignettes (6)

Advanced Modeling - Multiple Diseases, Tools, and Events HTML
Getting started with epiworldR HTML
Implementation details of epiworldR HTML
Likelihood Free Markhov Chain Monte Carlo (LFMCMC) HTML
Mixing models HTML
Run Multiple HTML

How these are measured

Downloads

7.5K

CRAN downloads in the past year

Rank #4,920 · ~21/day · ~625/mo

Releases R versions

Daily download trend is not available in this view yet.

71630 days

1.6K90 days

7.5K1 year

Compare downloads with other packages →

Also on558 r2u7 autocran

How downloads are counted

Repository

uofuepibio/epiworldr ↗Organization: UofUEpiBio

14Stars

3Forks

28Open issues

3Open PRs

13Releases

442Commits

8Commit identities

abmagent-based-modelingrpackrpkgsimulationcovid-19epidemicsepidemiology

442 commits · Last activity 2026-10-12 · 0% stars, 30d · Default branch at 0.19.0-0, ahead of CRAN 0.14.0.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-27 · 112026-07-13 · 14

How these are measured

PracticesBeta

16 development-tooling and community-health practices detected across 9 families in the upstream repository

Checks run against github.com/uofuepibio/epiworldr 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 (1)

Code of conduct

Docs source (4)

README.qmdpkgdown

GitHub Pages site last deployed 2026-10-09 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Show all practicesHide 5 practices

Reproducibility and dev environment (3)

data-raw/MakefileDev Container

Research and citation (2)

CITATION.cffJOSS paper

Automation and maintenance (1)

pre-commit

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-07-16
Seen in the repository: .github/copilot-instructions.md, .github/workflows/copilot-setup-steps.yml
Pull request: opened by its own account
Commits: 6 by its own account · at least 13 crediting it in the message
Claude Codefirst seen 2026-07-17
Seen in the repository: CLAUDE.md
Named in .Rbuildignore: CLAUDE.md
Pull request it wrote: opened by a project member
Commits: at least 21 crediting it in the message
Codexfirst seen 2026-08-15
Commits: at least 1 crediting it in the message

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: AGENTS.md

Review tools

Copilot code review
Commits: at least 2 accepting its review suggestions

Models named in its commits

Claude Opus 5.511 commits · Sep to Oct 2026
Claude Sonnet 5.54 commits · Oct 2026
Claude Opus 53 commits · Aug 2026
Claude Sonnet 52 commits · Sep 2026
Claude Fable 51 commit · Aug 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing epiworldR adds 1 package (0 with compiled code, 298 KB of source tarballs). Heaviest: cpp11 298 KB.

Depends (1)

R >= 4.1.0

Imports (3)

utilsparallelmethods

LinkingTo (1)

cpp11

Suggests (6)

quarto tinytest netplot igraph data.table DiagrammeR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Depends 1 · Imports 1 · LinkingTo 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

epiworldRShiny measles

Suggests, most downloaded first

epiworldRcalibrate

How these are counted

Code & Tests

People & History

People (7)

George Vega Yon

Author, Maintainer since 0.10.0.0 (2025)

Derek Meyer

Author

Andrew Pulsipher

Author · added in 0.6.0.0

Centers for Disease Control and Prevention

Funder

Award number 1U01CK000585; 75D30121F00003

Carinogurjao

Reviewer · added in 0.0-3

Susan Holmes

Reviewer · added in 0.0-3

JOSS reviewer

Abinash Satapathy

Reviewer · added in 0.0-3

JOSS reviewer

Previously maintained by Andrew Pulsipher (0.6.0.0 to 0.8.3.0) and George Vega Yon (0.3-2).

Releases (18)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.14.0.0Latest
record
2026-03-28 · current release · diff ↗
0.13.0.0
record
2026-03-12 · diff ↗
0.12.0.0
record
2026-02-21 · diff ↗
0.11.2.0
record
2026-02-03 · diff ↗
0.11.0.1
record
2026-01-14 · diff ↗
0.11.0.0
record
2025-12-22 · diff ↗ ·
removed 4 exports
ModelMeaslesMixing, ModelMeaslesMixingRiskQuarantine, ModelMeaslesQuarantine, ModelMeaslesSchool

added 6 exports
add_entities_from_dataframe, distribute_tool_to_entities, distribute_virus_to_entities, get_active_cases, get_hospitalizations, get_outbreak_size
0.10.0.0
record
2025-11-14 · diff ↗ ·
added 4 exports
ModelMeaslesMixing, ModelMeaslesMixingRiskQuarantine, ModelMeaslesSchool, ModelSEIRMixingQuarantine
0.8.3.0
record
2025-06-13 · diff ↗
0.8.2.0
record
2025-05-13 · diff ↗ ·
added 1 export
distribute_virus_to_set
0.8.1.0
record
2025-04-23 · diff ↗ ·
added 6 exports
ModelMeaslesQuarantine, draw_mermaid, draw_mermaid_from_data, draw_mermaid_from_file, draw_mermaid_from_files, draw_mermaid_from_matrix
R
R 4.5.0 released · 2025-04-11
0.6.1.0
record
2025-01-29 · diff ↗
0.6.0.0
record
2025-01-16 · diff ↗ ·
added 33 exports
LFMCMC, add_param, get_all_accepted_kernel_scores, get_all_accepted_params, get_all_accepted_stats, get_all_sample_acceptance, get_all_sample_drawn_prob, get_all_sample_kernel_scores, get_all_sample_params, get_all_sample_stats, get_current_accepted_params, get_current_accepted_stats, get_current_proposed_params, get_current_proposed_stats, get_initial_params, get_mean_params, get_mean_stats, get_n_params, get_n_samples, get_n_stats, get_observed_stats, rm_globalevent, run_lfmcmc, set_kernel_fun, set_observed_data, set_params_names, set_proposal_fun, set_simulation_fun, set_stats_names, set_summary_fun and 3 more
0.3-2
record
2024-10-08 · diff ↗ ·
added 20 exports
ModelSEIRMixing, ModelSIRMixing, add_entity, distribute_entity_randomly, distribute_entity_to_set, distribute_tool_randomly, distribute_tool_to_set, distribute_virus_randomly, distribute_virus_set, entity, entity_add_agent, entity_get_agents, get_entities, get_entity_name, get_entity_size, load_agents_entities_ties, rm_entity, set_distribution_entity, set_distribution_tool, set_distribution_virus
R
R 4.4.0 released · 2024-04-24

Show 8 earlier eventsHide 8 earlier events

0.1-0
record
2024-04-08 · diff ↗
unarchivedReturned to CRAN
2024-02-09
0.0-4
record
2024-02-09 · diff ↗ ·
removed 2 exports
add_global_action, get_agents_viruses

added 7 exports
add_globalevent, clone_model, globalevent_fun, globalevent_set_params, globalevent_tool, globalevent_tool_logit, initial_states
archivedRemoved from CRAN
2024-01-12
issues were not corrected despite reminders
0.0-3
record
2023-09-08 · diff ↗ ·
added 5 exports
ModelSEIRD, ModelSEIRDCONN, ModelSIRD, ModelSIRDCONN, ModelSISD
0.0-2
record
2023-06-22 · diff ↗ ·
removed 2 exports
get_hist_variant, get_n_variants

added 15 exports
add_tool_agent, add_virus_agent, change_state, get_agents_states, get_agents_tools, get_agents_viruses, get_hist_virus, get_n_viruses, get_today_total, globalaction_fun, has_tool, has_virus, set_incubation, set_incubation_fun, set_incubation_ptr
0.0-1
record
2023-06-09
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-06-09
Total releases: 18 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 3.0 MB

Appears in task views

Epidemiology Network Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("epiworldR")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

The repository also keeps a CITATION.cff.

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 epiworldR version 0.14.0.0 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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