R Observatory: Metrics for facilityepimath version 0.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

facilityepimath

0.2.3Package record

Analyze Mathematical Models of Healthcare Facility Transmission

0packages depend

2.3Kdownloads / year

83.5%test coverage

13/13flavors OK

Overview

About

Maintained by Damon TothCRAN page ↗GitHub ↗Issues ↗Declared funder: Centers for Disease Control and Prevention

Calculate useful quantities for a user-defined differential equation model of infectious disease transmission among individuals in a healthcare facility. Input rates of transition between states of individuals with and without the disease-causing organism, distributions of states at facility admission, relative infectivity of transmissible states, and the facility length of stay distribution. Calculate the model equilibrium and the basic facility reproduction number, as described in Toth et al. (2025) doi:10.1371/journal.pcbi.1013577.

Install

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

install.packages("facilityepimath", 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("EpiForeSITE/facilityepimath")

Development version from EpiForeSITE/facilityepimath. 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-facilityepimath

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-facilityepimath

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-facilityepimath

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: 2.1 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.3

READMEYes · 561 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.3Citation fileNo

Help pages: 7
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

facility-R0-and-equilibrium HTML

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #19,061 · ~6/day · ~195/mo

Releases R versions

Daily download trend is not available in this view yet.

35330 days

68190 days

2.3K1 year

Compare downloads with other packages →

Also on87 r2u4 autocran

How downloads are counted

Repository

epiforesite/facilityepimath ↗Organization: EpiForeSITE

1Stars

0Forks

1Open issues

0Open PRs

4Releases

151Commits

4Commit identities

151 commits · Last activity 2026-10-02 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-03-09 · 12026-07-07 · 1

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/epiforesite/facilityepimath 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

Docs source (4)

README.qmdpkgdown

GitHub Pages site last deployed 2026-10-02 · The repository has a site deploy workflow

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2025-11-04
Pull request: opened by its own account
Commits: 3 by its own account · at least 1 crediting it in the message

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

3 external dependencies (excludes base and recommended)

Installing facilityepimath adds no packages beyond those that come with R.

Depends (0)

none

Imports (1)

MASS

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown 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 (2)

Damon Toth

Centers for Disease Control and Prevention

Funder

Modeling Infectious Diseases in Healthcare Network award number U01CK000585 and Insight Net award number…

Releases (3)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-09-29
0.2.3Latest
record
2026-09-29 · current release · diff ↗
archivedRemoved from CRAN
2026-09-27
issues were not corrected in time
R
R 4.6.0 released · 2026-04-24
0.2.1
record
2025-11-07 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.0
record
2025-03-07
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-03-07
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 51 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("facilityepimath")

Format

Toth, D., & Centers for Disease Control and Prevention. (2026). facilityepimath: Analyze Mathematical Models of Healthcare Facility Transmission (Version 0.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.facilityepimath

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 facilityepimath version 0.2.3 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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