Package: simulist 0.4.0.9000

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 [aut], Hugo Gruson [ctb, rev], Pratik R. Gupte [ctb, rev], Adam Kucharski [rev], Chris Hartgerink [rev]

simulist_0.4.0.9000.tar.gz
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simulist.pdf |simulist.html✨
simulist/json (API)
NEWS

# 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 site:https://epiverse-trace.github.io

On CRAN:

Conda:

epidemiologyepiverselinelistoutbreaks

7.84 score 9 stars 27 scripts 176 downloads 6 exports 41 dependencies

Last updated 4 days agofrom:f584d89fdb. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 07 2025
R-4.5-winOKMar 07 2025
R-4.5-macOKMar 07 2025
R-4.5-linuxOKMar 07 2025
R-4.4-winOKMar 07 2025
R-4.4-macOKMar 07 2025
R-4.4-linuxOKMar 07 2025
R-4.3-winOKMar 07 2025
R-4.3-macOKMar 07 2025

Exports:create_configmessy_linelistsim_contactssim_linelistsim_outbreaktruncate_linelist

Dependencies:backportsbriocachemcallrcheckmateclicrayondata.tabledescdiffobjdigestdistcretedistributionalenglishepiparameterepiparameterDBevaluatefastmapfsgenericsgluejsonlitelifecyclemagrittrnumDerivpillarpkgbuildpkgloadpraiseprocessxpsR6randomNamesrlangrprojroottestthattoOrdinalutf8vctrswaldowithr

Age-stratified hospitalisation and death risks

Rendered fromage-strat-risks.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-01-21
Started: 2024-01-08

Age-structured population

Rendered fromage-struct-pop.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-02-26
Started: 2023-11-01

Design Principles for {simulist}

Rendered fromdesign-principles.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-02-26
Started: 2023-11-09

Getting Started with {simulist}

Rendered fromsimulist.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-02-26
Started: 2023-10-19

Reporting delays and right-truncation of line list data

Rendered fromreporting-delays-truncation.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-03-07
Started: 2025-02-07

Time-varying case fatality risk

Rendered fromtime-varying-cfr.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-01-21
Started: 2024-04-25

Visualising simulated data

Rendered fromvis-linelist.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-02-26
Started: 2023-11-02

Wrangling simulated outbreak data

Rendered fromwrangling-linelist.Rmdusingknitr::rmarkdownon Mar 07 2025.

Last update: 2025-02-19
Started: 2024-04-29