Package: finalsize 0.2.1.9000

Rosalind Eggo

finalsize: Calculate the Final Size of an Epidemic

Calculate the final size of a susceptible-infectious-recovered epidemic in a population with demographic variation in contact patterns and susceptibility to disease, as discussed in Miller (2012) <doi:10.1007/s11538-012-9749-6>.

Authors:Pratik Gupte [aut, cph], Edwin Van Leeuwen [aut, cph], Adam Kucharski [aut, cph], Rosalind Eggo [ctb, cre], Hugo Gruson [ctb], Thibaut Jombart [ctb], Andree Valle-Campos [ctb], Joshua W. Lambert [rev]

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manual.pdf |manual.html✨
card.svg |card.png
finalsize/json (API)
NEWS

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

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

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • polymod_uk - Example POLYMOD social contact data for the U.K.

On CRAN:

Conda:

epidemic-modellingepidemiologyepiverseoutbreak-analysisrcppsdg-3cpp

7.53 score 15 stars 72 scripts 369 downloads 4 exports 4 dependencies

Last updated from:13278f6800. Checks:2 ERROR, 11 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR149
linux-devel-x86_64ERROR161
source / vignettesOK227
linux-release-arm64OK147
linux-release-x86_64OK152
macos-release-arm64OK128
macos-release-x86_64OK204
macos-oldrel-arm64OK112
macos-oldrel-x86_64OK169
windows-develOK138
windows-releaseOK133
windows-oldrelOK142
wasm-releaseOK160

Exports:final_sizelambda_to_r0r_effr0_to_lambda

Dependencies:backportscheckmateRcppRcppEigen

Calculating the final size of an epidemic

Rendered fromfinalsize.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2025-01-13
Started: 2022-11-29

Comparison with a compartmental model

Rendered fromcompare_sir_model.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2023-04-17
Started: 2023-04-17

Guide to constructing susceptibility matrices

Rendered fromsusceptibility_matrices.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2023-11-22
Started: 2023-02-17

Modelling heterogeneous social contacts

Rendered fromvarying_contacts.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2023-11-22
Started: 2023-02-06

Modelling heterogeneous susceptibility

Rendered fromvarying_susceptibility.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2024-04-09
Started: 2022-11-29

Modelling uncertainty in Râ‚€

Rendered fromuncertainty_params.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2024-06-12
Started: 2022-11-29

Projecting re-emergence risk after waning or new births

Rendered fromdemographic_turnover.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2024-06-12
Started: 2024-02-22

Ready reckoner for Reff

Rendered fromr_eff_reckoner.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2025-02-13
Started: 2025-02-13

Theoretical background

Adam Kucharski

Rendered fromtheoretical_background.Rmdusingknitr::rmarkdownon Jun 24 2026.

Last update: 2024-04-09
Started: 2024-04-08