R Observatory: Metrics for measles version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

measles

0.2.0

Measles Epidemiological Models

0packages depend

2.5Kdownloads / year

87.1%test coverage

13/13flavors OK

Overview

About

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

A specialized collection of measles epidemiological models built on the 'epiworldR' framework. This package is a spinoff from 'epiworldR' focusing specifically on measles transmission dynamics. It includes models for school settings with quarantine and isolation policies, mixing models with population groups, and risk-based quarantine strategies. The models use Agent-Based Models (ABM) with a fast 'C++' backend from the 'epiworld' library. Ideal for studying measles outbreaks, vaccination strategies, and intervention policies.

Changes in 0.2.0

User visible changes

The vaccination efficacy has been modified to reflect a probability (the original intent) instead of a rate. Previous versions were resulting in a higher than expected vaccinated individuals becoming infected (update from epiworldR 0.13.0.0).
Improved documentation regarding vaccination rates and probabilities across models.

Internal changes

This version uses the latest version of epiworld (0.14.0), which introduced several important changes. You can read more about the changes here (the corresponding epiworldR PR is here.).

From NEWS.md in the release

Install

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

install.packages("measles", 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/measles")

Development version from UofUEpiBio/measles. 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-measles

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-measles

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-measles

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-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-07
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE6 OK, 2 NOTE2026-04-01

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.0

READMEYes · 647 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.0Citation fileYes · cites a publication

Cites a JOSS paper

Help pages: 7 (1 internal)includes a package overview page
Examples that run: 100%5 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 14%

Vignettes (1)

Mixing model in Short Creek HTML

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #12,058 · ~7/day · ~209/mo

Releases R versions

Daily download trend is not available in this view yet.

32830 days

89090 days

2.5K1 year

Compare downloads with other packages →

Also on249 r2u4 autocran

How downloads are counted

Repository

uofuepibio/measles ↗Organization: UofUEpiBio

5Stars

1Forks

4Open issues

0Open PRs

3Releases

454Commits

8Commit identities

abmagent-based-modelingepidemiologyindividual-based-modellingmeaslesmeasles-mumps-rubella-vacciner-packager-programming

454 commits · Last activity 2026-10-09 · 0% stars, 30d · Default branch at 0.4.1-0, ahead of CRAN 0.2.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-02-10 · 12026-08-28 · 5

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/uofuepibio/measles 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 4 practices

Reproducibility and dev environment (3)

data-raw/MakefileDev Container

Research and citation (1)

CITATION.cff

Automation and maintenance (1)

pre-commit

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 2025-07-21
Seen in the repository: .github/workflows/copilot-setup-steps.yml
Pull request: opened by its own account
Commits: 15 by its own account · at least 11 crediting it in the message
Claude Codefirst seen 2026-07-17
Pull request it wrote: opened by a project member
Commits: at least 10 crediting it in the message
Codexfirst seen 2026-08-15
Commits: at least 2 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 5 accepting its review suggestions

Models named in its commits

Claude Opus 5.56 commits · Oct 2026
Claude Fable 51 commit · Jul 2026
Claude Opus 4.81 commit · Jul 2026
Claude Opus 51 commit · Aug 2026
Claude Sonnet 51 commit · Sep 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

6 external dependencies (excludes base and recommended)

Installing measles adds 2 packages (1 with compiled code, 3.3 MB of source tarballs). Heaviest: epiworldR 3.0 MB, cpp11 298 KB.

Depends (2)

R >= 4.1.0epiworldR

Imports (1)

utils

LinkingTo (2)

cpp11 epiworldR

Suggests (3)

tinytest data.table quarto

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 (5)

George Vega Yon

Author, Maintainer since 0.1.0 (2026)

Olivia Banks

Contributor

Damon Toth

Contributor

Jake Wagoner

Contributor

Centers for Disease Control and Prevention

Funder

Award number 1U01CK000585; 75D30121F00003

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-01
0.2.0Latest
record
2026-03-31 · current release · diff ↗
archivedRemoved from CRAN
2026-03-10
issues were not corrected despite reminders Use of misaligned addresses detected by M1-SAN tests
0.1.1
record
2026-02-21 · diff ↗
0.1.0
record
2026-02-12
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-12
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.5 KB / 2 files
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("measles")

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 measles version 0.2.0 [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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