R Observatory: Metrics for covidprobability version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

covidprobability

0.1.0

Estimate the Unit-Wide Probability of COVID-19

0packages depend

2.5Kdownloads / year

100.0%test coverage

13/13checks pass

Overview

About

Maintained by Eric BrownFirst published 2021-02-111 releasesCRAN page ↗GitHub ↗

We propose a method to estimate the probability of an undetected case of COVID-19 in a defined setting, when a given number of people have been exposed, with a given pretest probability of having COVID-19 as a result of that exposure. Since we are interested in undetected COVID-19, we assume no person has developed symptoms (which would warrant further investigation) and that everyone was tested on a given day, and all tested negative.

Install

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

install.packages("covidprobability", 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("eebrown/covidprobability")

Development version from eebrown/covidprobability. 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-covidprobability

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-covidprobability

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-covidprobability

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

Health

CRAN checks

13OK

Slowest check: 1.1 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.63

100.0%

Coverage · measured lines

100%

Documentation · exports

2

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-06-08
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 130 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 25%

Downloads

2.5K

CRAN downloads in the past year

Rank #18,342 · ~7/day · ~211/mo

Releases R versions

Daily download trend is not available in this view yet.

13230 days

59690 days

2.5K1 year

Compare downloads with other packages →

Also on129 r2u24 autocran

Repository

GitHub ↗ eebrown/covidprobability

1Stars

0Forks

0Open issues

0Open PRs

1Releases

20Commits

1Contributors

License GPL-3.0 · 20 commits · Last activity 2021-02-12

Stars over time

2021-09-13 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/eebrown/covidprobability on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (2)

statsutils

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Eric Brown

Author, Maintainer

Authors (1)

Eric Brown

Author, Maintainer

Contributors (1)

Wei Wang

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2021-02-11
Total releases: 1 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 0.6 KB / 1 file
Download size: 325 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("covidprobability")

Format

Brown, E., & Wang, W. (2021). covidprobability: Estimate the Unit-Wide Probability of COVID-19 (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.covidprobability

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 covidprobability version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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