R Observatory: Metrics for epicontacts version 1.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epicontacts

1.1.4

Handling, Visualisation and Analysis of Epidemiological Contacts

6packages depend

9.6Kdownloads / year

89.3%test coverage

8/13checks pass

Overview

About

Maintained by Finlay CampbellFirst published 2017-04-276 releasesCRAN page ↗GitHub ↗

A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.

Install

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

install.packages("epicontacts", 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("reconhub/epicontacts")

Development version from reconhub/epicontacts. 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-epicontacts

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-epicontacts

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-epicontacts

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

Health

CRAN checks

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.47

89.3%

Coverage · measured lines

100%

Documentation · exports

6

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 58%
References docs: 5%

Downloads

9.6K

CRAN downloads in the past year

Rank #4,692 · ~26/day · ~798/mo

Releases R versions

Daily download trend is not available in this view yet.

42130 days

1.6K90 days

9.6K1 year

Compare downloads with other packages →

Also on155 r2u21 autocran48 c2d4u

Repository

GitHub ↗ reconhub/epicontacts

18Stars

19Forks

14Open issues

2Open PRs

0Releases

582Commits

12Contributors

r-packageoutbreakr

582 commits · Last activity 2025-04-17 · 0% stars, 30d

Stars over time

2025-03-29 · 162026-07-07 · 18

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/reconhub/epicontacts on 2026-08-16.

Continuous integration (3)

GitHub ActionsTravis CIAppVeyor

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (6)

grDevicesdplyr igraph visNetwork threejsmethods

LinkingTo (0)

none

Suggests (7)

outbreaks testthat covr shiny readr knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

0indirect

epiflows epichains linktree o2ools outbreaker2 simulist

Code & Tests

People & History

People (7)

Maintainer (1)

Finlay Campbell

Author, Maintainer

Authors (7)

Author, Maintainer

Author

Author

Author · added in 1.1.2

VP Nagraj

Author

Nistara Randhawa

Author

Bertrand Sudre

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.4Latest
2024-04-30 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.1.3
2023-03-28 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.2
2021-10-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.1.0
2017-11-21 · diff ↗
1.0.1
2017-05-16 · diff ↗
1.0.0
2017-04-27
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-04-27
Total releases: 6 / 9 yrs
License: GPL (>= 2) OSI
Download size: 1.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("epicontacts")

Format

Campbell, F., Crellen, T., Jombart, T., Kamvar, Z. N., Nagraj, V., Randhawa, N., & Sudre, B. (2024). epicontacts: Handling, Visualisation and Analysis of Epidemiological Contacts (Version 1.1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.epicontacts

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 epicontacts version 1.1.4 [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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