Package: epidemics 0.4.0.9000

Rosalind Eggo

epidemics: Composable Epidemic Scenario Modelling

A library of compartmental epidemic models taken from the published literature, and classes to represent affected populations, public health response measures including non-pharmaceutical interventions on social contacts, non-pharmaceutical and pharmaceutical interventions that affect disease transmissibility, vaccination regimes, and disease seasonality, which can be combined to compose epidemic scenario models.

Authors:Pratik Gupte [aut, cph], Rosalind Eggo [aut, cph, cre], Edwin Van Leeuwen [aut, cph], Adam Kucharski [ctb, rev], Tim Taylor [ctb, rev], Banky Ahadzie [ctb], Hugo Gruson [rev], Joshua W. Lambert [rev], James M. Azam [rev], Alexis Robert [rev]

epidemics_0.4.0.9000.tar.gz
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epidemics_0.4.0.9000.tgz(r-4.4-x86_64)epidemics_0.4.0.9000.tgz(r-4.4-arm64)epidemics_0.4.0.9000.tgz(r-4.3-x86_64)epidemics_0.4.0.9000.tgz(r-4.3-arm64)
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epidemics_0.4.0.9000.tgz(r-4.4-emscripten)epidemics_0.4.0.9000.tgz(r-4.3-emscripten)
epidemics.pdf |epidemics.html
epidemics/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

decision-supportepidemic-modellingepidemic-simulationsepidemiologyepiverseinfectious-disease-dynamicsmodel-librarynon-pharmaceutical-interventionsrcpprcppeigenscenario-analysisvaccination

18 exports 8 stars 7.76 score 9 dependencies 54 scripts

Last updated 4 months agofrom:f706261bac. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 11 2024
R-4.5-win-x86_64WARNINGOct 11 2024
R-4.5-linux-x86_64WARNINGOct 11 2024
R-4.4-win-x86_64WARNINGOct 11 2024
R-4.4-mac-x86_64WARNINGOct 11 2024
R-4.4-mac-aarch64WARNINGOct 11 2024
R-4.3-win-x86_64WARNINGOct 11 2024
R-4.3-mac-x86_64WARNINGOct 11 2024
R-4.3-mac-aarch64WARNINGOct 11 2024

Exports:as.interventionas.vaccinationepidemic_peakepidemic_sizeinterventionis_contacts_interventionis_interventionis_populationis_rate_interventionis_vaccinationmodel_defaultmodel_diphtheriamodel_ebolamodel_vacamolenew_infectionsoutcomes_avertedpopulationvaccination

Dependencies:backportsBHcheckmateclidata.tableglueRcppRcppEigenwithr

Design principles for epidemics

Rendered fromdesign-principles.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-05-30
Started: 2024-03-11

Getting started with epidemic scenario modelling components

Rendered fromepidemics.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-04-23
Started: 2023-03-06

Getting started with modelling interventions targeting social contacts

Rendered frommodelling_interventions.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-04-23
Started: 2023-04-14

Guide to developing epidemics features

Rendered fromdeveloper-walkthrough.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-05-30
Started: 2024-05-30

Modelling a diphtheria outbreak in a humanitarian camp setting

Rendered frommodel_diphtheria.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-03-18
Started: 2024-03-14

Modelling intervention scenarios

Rendered frommodelling_scenarios.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-05-07
Started: 2024-03-14

Modelling interventions that change infection parameters

Rendered frommodelling_rate_interventions.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-05-07
Started: 2024-03-14

Modelling leaky vaccination and hospitalisation outcomes with Vacamole

Rendered frommodel_vacamole.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-04-23
Started: 2024-03-14

Modelling overlapping and sequential interventions targeting social contacts

Rendered frommodelling_multiple_interventions.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-03-14
Started: 2024-03-14

Modelling parameter uncertainty

Rendered frommodelling_param_uncertainty.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-05-07
Started: 2024-05-07

Modelling responses to a stochastic Ebola virus epidemic

Rendered frommodel_ebola.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-04-23
Started: 2024-03-14

Modelling the effect of a vaccination campaign

Rendered frommodelling_vaccination.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-05-24
Started: 2023-04-14

Modelling time-dependence and seasonality in transmission dynamics

Rendered frommodelling_time_dependence.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-04-23
Started: 2024-03-14

Reducing parameters required for final size estimation

Rendered fromfinalsize_comparison.Rmdusingknitr::rmarkdownon Oct 11 2024.

Last update: 2024-03-18
Started: 2023-10-25