simulist

0.7.0

Simulate Disease Outbreak Line List and Contacts Data

0packages depend

4.6Kdownloads / year

99.0%test coverage

12/13checks pass

Overview

About

Maintained by Joshua W. LambertFirst published 2025-01-104 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 8.8 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 1.75

99.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,566 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 73%
Return-value docs: 100%
References docs: 0%

Downloads

4.6K

CRAN downloads in the past year

Rank #13,774 · ~13/day · ~381/mo

Releases R versions

Daily download trend is not available in this view yet.

26430 days

74890 days

4.6K1 year

Compare downloads with other packages →

Also on123 r2u1 autocran

Repository

GitHub ↗ epiverse-trace/simulist

11Stars

1Forks

7Open issues

4Open PRs

8Releases

962Commits

5Contributors

epidemiologyepiverselinelistoutbreaksrr-package

962 commits · Last activity 2026-07-01 · 0% stars, 30d

Stars over time

2025-04-04 · 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/simulist on 2026-07-31.

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)

Dependabot

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

15 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (8)

Maintainer (1)

Joshua W. Lambert

Author, Maintainer, Copyright holder

Authors (2)

Joshua W. Lambert

Author, Maintainer, Copyright holder

Carmen Tamayo Cuartero

Author · added in 0.6.0

Contributors (3)

Sebastian Funk

Contributor · added in 0.5.0

Hugo Gruson

Contributor, Reviewer

Pratik R. Gupte

Contributor, Reviewer

Joshua W. Lambert

Author, Maintainer, Copyright holder

London School of Hygiene and Tropical Medicine, LSHTM

Reviewers (4)

Hugo Gruson

Contributor, Reviewer

Pratik R. Gupte

Contributor, Reviewer

Chris Hartgerink

Reviewer

Adam Kucharski

Reviewer

Listed in earlier versions (1)

Carmen Tamayo

no longer listed · 0.4.0 to 0.5.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.7.0Latest
2026-02-06 · current release · diff ↗
0.6.0
2025-08-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.5.0
2025-03-25 · diff ↗
0.4.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Epidemiology

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