Package: simulist 0.3.0.9000

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]

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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'))

Peer review:

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

On CRAN:

epidemiologyepiverselinelistoutbreaks

6.44 score 5 stars 23 scripts 4 exports 38 dependencies

Last updated 1 months agofrom:d6c8ca7fcf. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winNOTENov 16 2024
R-4.5-linuxNOTENov 16 2024
R-4.4-winOKNov 16 2024
R-4.4-macOKNov 16 2024
R-4.3-winOKNov 16 2024
R-4.3-macOKNov 16 2024

Exports:create_configsim_contactssim_linelistsim_outbreak

Dependencies:backportsbriocallrcheckmateclicrayondata.tabledescdiffobjdigestdistcretedistributionalepiparameterevaluatefansifsgenericsgluejsonlitelifecyclemagrittrnumDerivpillarpkgbuildpkgloadpraiseprocessxpsR6randomNamesrlangrprojroottestthattoOrdinalutf8vctrswaldowithr

Age structured population

Rendered fromage-struct-pop.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2024-10-17
Started: 2023-11-01

Age-stratified hospitalisation and death risks

Rendered fromage-strat-risks.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2024-10-17
Started: 2024-01-08

Design Principles for {simulist}

Rendered fromdesign-principles.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2024-07-18
Started: 2023-11-09

Getting Started with {simulist}

Rendered fromsimulist.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2024-10-17
Started: 2023-10-19

Time-varying case fatality risk

Rendered fromtime-varying-cfr.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2024-10-17
Started: 2024-04-25

Visualising simulated data

Rendered fromvis-linelist.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2024-10-17
Started: 2023-11-02

Wrangling simulated outbreak data

Rendered fromwrangling-linelist.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2024-10-17
Started: 2024-04-29