R Observatory: Metrics for epicontacts version 1.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

epicontacts

1.1.4Package record

Handling, Visualisation and Analysis of Epidemiological Contacts

1packages dependsuggested by 5

8.3Kdownloads / year

89.3%test coverage

8/13flavors OK

Overview

About

Maintained by Finlay CampbellCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.1.4

BUG FIXES

Fix thin option for plot.epicontacts
Deal with duplicated IDs

From NEWS.md in the release

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. 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-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). 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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  epicontacts/R/codeawesome.R (.Names: 1)
'.Names' should be changed to 'names'.

CRAN check page ↗

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-07-16
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.4

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 33% structured · mentions 1.1.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 19
Examples that run: 100%15 run in a plain check
Exported functions with examples: 92%
Documented parameters: 100%
Return-value docs: 58%
Help pages citing references: 5%

Vignettes (2)

How these are measured

Downloads

8.3K

CRAN downloads in the past year

Rank #4,707 · ~23/day · ~690/mo

Releases R versions

Daily download trend is not available in this view yet.

68230 days

1.8K90 days

8.3K1 year

Compare downloads with other packages →

Also on112 r2u3 autocran88 c2d4u

How downloads are counted

Repository

reconhub/epicontacts ↗Organization: reconhub

18Stars

19Forks

14Open issues

2Open PRs

0Releases

582Commits

12Commit identities

r-packageoutbreakr

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

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-03-29 · 162026-07-07 · 18

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/reconhub/epicontacts on 2026-10-22.

Continuous integration (3)

GitHub ActionsTravis CI (config file)AppVeyor

Docs source (3)

README.Rmd

GitHub Pages site last deployed 2025-04-17 · 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 v4 (2026-10-20)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing epicontacts adds 43 packages (23 with compiled code, 32 MB of source tarballs). Heaviest: bslib 5.6 MB, igraph 4.8 MB, visNetwork 4.1 MB.

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

1direct

0indirect

Imports 1

Suggested by 5

Depends, Imports or LinkingTo, most downloaded first

epiflows

Suggests, most downloaded first

outbreaker2 o2ools epichains simulist linktree

How these are counted

Code & Tests

People & History

People (7)

Finlay Campbell

Author, Maintainer since 1.1.2 (2021)

Thomas Crellen

Author

Thibaut Jombart

Author

Zhian N. Kamvar

Author · added in 1.1.2

VP Nagraj

Author

Nistara Randhawa

Author

Bertrand Sudre

Author

Previously maintained by VP Nagraj (1.0.0 to 1.1.0).

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.1.4Latest
record
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
record
2023-03-28 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.2
record
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
record
2017-11-21 · diff ↗ ·
removed 1 export
char2col

added 3 exports
codeawesome, edges_pal, fac2col
1.0.1
record
2017-05-16 · diff ↗
1.0.0
record
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

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' entry:

citation("epicontacts")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.12688/f1000research.14492.1.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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