R Observatory: Metrics for linelist version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

linelist

2.0.1Package record

Tagging and Validating Epidemiological Data

2packages depend

7.3Kdownloads / year

96.7%test coverage

13/13flavors OK

Overview

About

Maintained by Chris HartgerinkCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 2.0.1

Internal changes

Chris Hartgerink (@chartgerink) is now linelist maintainer.

From NEWS.md in the release

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. 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-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). 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: 2.0 min · r-oldrel-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 2.0.1

READMEYes · 517 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 2.0.1Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 16 (1 internal)includes a package overview page
Examples that run: 100%16 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (4)

An introduction to linelist HTML
Compatibility with dplyr HTML
Design Principles for linelist HTML
Software permissions and regulations HTML

How these are measured

Downloads

7.3K

CRAN downloads in the past year

Rank #4,931 · ~20/day · ~606/mo

Releases R versions

Daily download trend is not available in this view yet.

49930 days

1.7K90 days

7.3K1 year

Compare downloads with other packages →

Also on103 r2u6 autocran81 c2d4u

How downloads are counted

Repository

epiverse-trace/linelist ↗Organization: epiverse-trace

11Stars

5Forks

6Open issues

0Open PRs

8Releases

447Commits

9Commit identities

dataoutbreaksrstructured-datadata-structuresepidemiologyr-packageepiverse

447 commits · Last activity 2026-06-06 · 0% stars, 30d · Default branch at 2.0.1.9000, ahead of CRAN 2.0.1 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-17 · 102026-07-07 · 11

How these are measured

PracticesBeta

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

Checks run against github.com/epiverse-trace/linelist on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (3)

Code of conduct (inherited from epiverse-trace)Contributing guide (inherited from epiverse-trace)PR template (inherited from epiverse-trace)

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-07-07 · The repository has a site deploy workflow

pkgdown site last built 2025-06-25

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 5 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Automation and maintenance (1)

pre-commit

Lint, format, editor (3)

lintrLint workflowRStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing linelist adds 9 packages (7 with compiled code, 3.1 MB of source tarballs). Heaviest: vctrs 1.0 MB, rlang 766 KB, cli 629 KB.

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

Imports 2

Depends, Imports or LinkingTo, most downloaded first

cleanepi vaccineff

How these are counted

Code & Tests

People & History

People (4)

Chris Hartgerink

Maintainer since 2.0.1 (2025), Reviewer · added in 1.1.0

Hugo Gruson

Author · added in 1.0.0

Thibaut Jombart

Author, ccp

Tim Taylor

Contributor · added in 1.0.0

Previously maintained by Hugo Gruson (1.0.0 to 2.0.0) and Thibaut Jombart (0.0.1).

Listed in earlier versions (1)

Pietro Monticone

no longer listed · 1.0.0

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.0.1Latest
record
2025-06-25 · current release · diff ↗
2.0.0
record
2025-04-23 · diff ↗ ·
removed 1 export
select_tags
R
R 4.5.0 released · 2025-04-11
1.1.4
record
2024-06-17 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.3
record
2024-04-21 · diff ↗
1.1.2
record
2024-04-19 · diff ↗
1.1.0
record
2024-02-28 · diff ↗
1.0.0
record
2023-10-19 · diff ↗ ·
added 1 export
has_tag
R
R 4.3.0 released · 2023-04-21
0.0.1
record
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

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("linelist")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

The repository also keeps a CITATION.cff.

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 linelist version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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