linelist

2.0.1

Tagging and Validating Epidemiological Data

2packages depend

7.9Kdownloads / year

96.7%test coverage

13/13checks pass

Overview

About

Maintained by Chris HartgerinkFirst published 2022-05-138 releasesCRAN page ↗GitHub ↗

Provides tools to help storing and handling case line list data. The 'linelist' class adds a tagging system to classical 'data.frame' objects to identify key epidemiological data such as dates of symptom onset, epidemiological case definition, age, gender or disease outcome. Once tagged, these variables can be seamlessly used in downstream analyses, making data pipelines more robust and reliable.

Install

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

install.packages("linelist", 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("epiverse-trace/linelist")

Development version from epiverse-trace/linelist. 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-linelist

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-linelist

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-linelist

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

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.69

96.7%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 517 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

7.9K

CRAN downloads in the past year

Rank #5,271 · ~22/day · ~662/mo

Releases R versions

Daily download trend is not available in this view yet.

58030 days

1.7K90 days

7.9K1 year

Compare downloads with other packages →

Also on104 r2u40 autocran41 c2d4u

Repository

GitHub ↗ epiverse-trace/linelist

11Stars

5Forks

6Open issues

0Open PRs

8Releases

447Commits

9Contributors

dataoutbreaksrstructured-datadata-structuresepidemiologyr-packageepiverse

447 commits · Last activity 2026-06-06 · 0% stars, 30d

Stars over time

2025-07-17 · 102026-07-07 · 11

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/epiverse-trace/linelist on 2026-07-26.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Research and citation (1)

CITATION.cff

Show all practices

Automation and maintenance (1)

pre-commit

Lint, format, editor (2)

lintrRStudio project

Coverage (1)

Codecov

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (3)

checkmate rlang tidyselect

LinkingTo (0)

none

Suggests (8)

callr dplyr knitr outbreaks rmarkdown spelling testthat tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

cleanepi vaccineff

Code & Tests

People & History

People (4)

Maintainer (1)

Chris Hartgerink

Maintainer, Reviewer · added in 1.1.0

Authors (2)

Hugo Gruson

Author · added in 1.0.0

Thibaut Jombart

Author, ccp

Contributors (1)

Tim Taylor

Contributor · added in 1.0.0

Reviewers (1)

Chris Hartgerink

Maintainer, Reviewer · added in 1.1.0

Listed in earlier versions (1)

Pietro Monticone

no longer listed · 1.0.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.0.1Latest
2025-06-25 · current release · diff ↗
2.0.0
2025-04-23 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.1.4
2024-06-17 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.3
2024-04-21 · diff ↗
1.1.2
2024-04-19 · diff ↗
1.1.0
2024-02-28 · diff ↗
1.0.0
2023-10-19 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.0.1
2022-05-13
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-13
Total releases: 8 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 252 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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