R Observatory: Metrics for simulist version 0.7.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

simulist

0.7.0Package record

Simulate Disease Outbreak Line List and Contacts Data

0packages depend

4.1Kdownloads / year

99.0%test coverage

13/13flavors OK

Overview

About

Maintained by Joshua W. LambertCRAN page ↗GitHub ↗Website ↗Issues ↗

Tools to simulate realistic raw case data for an epidemic in the form of line lists and contacts using a branching process. Simulated outbreaks are parameterised with epidemiological parameters and can have age-structured populations, age-stratified hospitalisation and death risk and time-varying case fatality risk.

Changes in 0.7.0

This minor version release contains a range of minor updates and accompanies the _simulist_ publication in the Journal of Open Source Software (JOSS).

New features

The sampling of sex for line list and contacts data can now be weighted instead of assuming a uniform probability via prob_male in config (#255).
The reporting_delay argument in sim_linelist() and sim_outbreak() now supports <epiparameter> objects, matching the functionality of the other delay distribution arguments (#262).
A new line list events plot has been added to the vis-linelist.Rmd vignette (#278).

Breaking changes

None

Minor changes

Added dependabot (#258).
GitHub actions versions are updated (multiple PRs).
.lintr is updated to include more linters (#279) and the # nolint flag syntax is fixed (#263).

Bug fixes

Show all changes in 0.7.0Hide the rest of the changes in 0.7.0

None

Deprecated and defunct

None

From NEWS.md in the release

Install

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

install.packages("simulist", 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/simulist")

Development version from epiverse-trace/simulist. 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-simulist

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-simulist

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-simulist

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: 8.8 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.7.0

READMEYes · 1,566 wordsVignettesYes · 8 · dynamicNEWSYes · 100% structured · mentions 0.7.0Citation fileYes · computed when R runs itWebsiteYes · pkgdown

Help pages: 21 (14 internal)includes a package overview page
Examples that run: 100%7 run in a plain check
Exported functions with examples: 100%
Documented parameters: 73%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (8)

How these are measured

Downloads

4.1K

CRAN downloads in the past year

Rank #14,641 · ~11/day · ~339/mo

Releases R versions

Daily download trend is not available in this view yet.

27730 days

81090 days

4.1K1 year

Compare downloads with other packages →

Also on106 r2u4 autocran

How downloads are counted

Repository

epiverse-trace/simulist ↗Organization: epiverse-trace

11Stars

1Forks

7Open issues

1Open PRs

8Releases

968Commits

5Commit identities

epidemiologyepiverselinelistoutbreaksrr-package

968 commits · Last activity 2026-09-07 · 0% stars, 30d · Default branch at 0.7.1.9000, ahead of CRAN 0.7.0 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 96%
Median days to close, 50 most recently updated closed issues: 11
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-04-04 · 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/simulist 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 2026-09-07 · The repository has a site deploy workflow

pkgdown site last built 2026-03-02

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)

Dependabot

Lint, format, editor (3)

lintrLint workflowRStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing simulist adds 27 packages (13 with compiled code, 13 MB of source tarballs). Heaviest: data.table 5.7 MB, jsonlite 1.0 MB, vctrs 1.0 MB.

Depends (1)

R >= 4.2.0

Imports (7)

checkmate english epiparameter grates randomNames rlangstats

LinkingTo (0)

none

Suggests (9)

dplyr epicontacts ggplot2 incidence2 (>= 2.6.2)knitr rmarkdown spelling testthat tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (8)

Joshua W. Lambert

Carmen Tamayo Cuartero

Author · added in 0.6.0

Sebastian Funk

Contributor · added in 0.5.0

Hugo Gruson

Contributor, Reviewer

Pratik R. Gupte

Contributor, Reviewer

London School of Hygiene and Tropical Medicine, LSHTM

Copyright holder · added in 0.5.0

Chris Hartgerink

Reviewer

Adam Kucharski

Reviewer

Listed in earlier versions (1)

Carmen Tamayo

no longer listed · 0.4.0 to 0.5.0

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.7.0Latest
record
2026-02-06 · current release · diff ↗
0.6.0
record
2025-08-28 · diff ↗ ·
added 1 export
censor_linelist
R
R 4.5.0 released · 2025-04-11
0.5.0
record
2025-03-25 · diff ↗ ·
added 2 exports
messy_linelist, truncate_linelist
0.4.0
record
2025-01-10
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-10
Total releases: 4 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.2.0
Download size: 2.9 MB

Appears in task views

Epidemiology

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("simulist")

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 simulist version 0.7.0 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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