Package: simulist 0.7.1.9000

Joshua W. Lambert

simulist: Simulate Disease Outbreak Line List and Contacts Data

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.

Authors:Joshua W. Lambert [aut, cre, cph], Carmen Tamayo Cuartero [aut], Hugo Gruson [ctb, rev], Pratik R. Gupte [ctb, rev], Adam Kucharski [rev], Chris Hartgerink [rev], Sebastian Funk [ctb], London School of Hygiene and Tropical Medicine, LSHTM [cph]

simulist_0.7.1.9000.tar.gz
simulist_0.7.1.9000.zip(r-4.7)simulist_0.7.1.9000.zip(r-4.6)simulist_0.7.1.9000.zip(r-4.5)
simulist_0.7.1.9000.tgz(r-4.6-any)simulist_0.7.1.9000.tgz(r-4.5-any)
simulist_0.7.1.9000.tar.gz(r-4.7-any)simulist_0.7.1.9000.tar.gz(r-4.6-any)
simulist_0.7.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
simulist/json (API)

# Install 'simulist' in R:
install.packages('simulist', repos = c('https://epiverse-trace.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epiverse-trace/simulist/issues

Pkgdown/docs site:https://epiverse-trace.github.io

On CRAN:

Conda:

epidemiologyepiverselinelistoutbreaks

7.69 score 11 stars 46 scripts 192 downloads 7 exports 35 dependencies

Last updated from:469fbe4f66. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK178
source / vignettesOK197
linux-release-x86_64OK158
macos-release-arm64OK146
macos-oldrel-arm64OK85
windows-develOK148
windows-releaseOK95
windows-oldrelOK94
wasm-releaseOK123

Exports:censor_linelistcreate_configmessy_linelistsim_contactssim_linelistsim_outbreaktruncate_linelist

Dependencies:askpassbackportscachemcheckmateclicrayoncurldata.tabledistcretedistributionalenglishepiparameterepiparameterDBfastmapfastymdgenericsgluegrateshttr2jsonlitelifecyclemagrittrnumDerivopensslpillarpkgsearchR6randomNamesrappdirsrlangsystoOrdinalutf8vctrswithr

Age-stratified hospitalisation and death risks
Population-wide risks
Rendered fromage-strat-risks.Rmdusingknitr::rmarkdown

Last update: 2026-05-01
Started: 2024-01-08

Age-structured population
Uniform population age | Structured population age
Rendered fromage-struct-pop.Rmdusingknitr::rmarkdown

Last update: 2026-05-01
Started: 2023-11-01

Time-varying case fatality risk
Constant case fatality risk | Higher risk of case fatality | Continuous time-varying case fatality risk | Stepwise time-varying case fatality risk
Rendered fromtime-varying-cfr.Rmdusingknitr::rmarkdown

Last update: 2026-02-06
Started: 2024-04-25

Wrangling simulated outbreak data
Simulate an outbreak | Censoring dates | Under-reporting of cases and contacts | Tidyverse | Base R | Removing a line list column
Rendered fromwrangling-linelist.Rmdusingknitr::rmarkdown

Last update: 2026-02-06
Started: 2024-04-29

Visualising simulated data
Visualising incidence of onset, hospitalisation and death | Reshape line list data | Base R | Tidyverse | Visualising individual line list events through time | Demographic data | Visualising contact data | Subset contact network to transmission network | Visualising other line list information
Rendered fromvis-linelist.Rmdusingknitr::rmarkdown

Last update: 2026-02-05
Started: 2023-11-02

Reporting delays and right-truncation of line list data
Reporting delays | Truncation | Truncate to emulate different stages of outbreak
Rendered fromreporting-delays-truncation.Rmdusingknitr::rmarkdown

Last update: 2026-02-04
Started: 2025-02-07

Getting Started with {simulist}
Controlling outbreak size | Case type | Anonymous line list | Population age | Age-stratified hospitalisation and death risks | Simulate contacts table | Simulate both line list and contacts table | Using functions for distributions instead of <epiparameter> | Predefined functions | Anonymous functions | Simulating without hospitalisations and/or deaths
Rendered fromsimulist.Rmdusingknitr::rmarkdown

Last update: 2025-11-19
Started: 2023-10-19

Design Principles for {simulist}
Scope | Output | Package architecture | Design decisions | Dependencies | Contribute
Rendered fromdesign-principles.Rmdusingknitr::rmarkdown

Last update: 2025-04-15
Started: 2023-11-09