Package: epitrix 0.4.0

Thibaut Jombart

epitrix: Small Helpers and Tricks for Epidemics Analysis

A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.

Authors:Thibaut Jombart [aut, cre], Anne Cori [aut], Zhian N. Kamvar [ctb], Dirk Schumacher [ctb], Flavio Finger [aut], Charlie Whittaker [ctb]

epitrix_0.4.0.tar.gz
epitrix_0.4.0.zip(r-4.5)epitrix_0.4.0.zip(r-4.4)epitrix_0.4.0.zip(r-4.3)
epitrix_0.4.0.tgz(r-4.5-any)epitrix_0.4.0.tgz(r-4.4-any)epitrix_0.4.0.tgz(r-4.3-any)
epitrix_0.4.0.tar.gz(r-4.5-noble)epitrix_0.4.0.tar.gz(r-4.4-noble)
epitrix_0.4.0.tgz(r-4.4-emscripten)epitrix_0.4.0.tgz(r-4.3-emscripten)
epitrix.pdf |epitrix.html✨
epitrix/json (API)
NEWS

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

Bug tracker:https://github.com/reconhub/epitrix/issues

Pkgdown site:https://www.repidemicsconsortium.org

On CRAN:

Conda:

epidemiology

8.58 score 11 stars 5 packages 231 scripts 564 downloads 2 mentions 14 exports 23 dependencies

Last updated 2 years agofrom:94cb02aa83. Checks:5 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 03 2025
R-4.5-winNOTEMar 03 2025
R-4.5-macNOTEMar 03 2025
R-4.5-linuxNOTEMar 03 2025
R-4.4-winOKMar 03 2025
R-4.4-macOKMar 03 2025
R-4.3-winOKMar 03 2025
R-4.3-macOKMar 03 2025

Exports:AR2R0clean_labelsempirical_incubation_distfit_disc_gammafit_gamma_incubation_distgamma_log_likelihoodgamma_mucv2shapescalegamma_shapescale2mucvhash_nameslm2R0_sampleR02ARR02herd_immunity_thresholdr2R0sim_linelist

Dependencies:clicpp11distcretedplyrfansigenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangsodiumstringistringrtibbletidyrtidyselectutf8vctrswithr

Example to estimate incubation period

Flavio Finger

Rendered fromestimate_incubation.Rmdusingknitr::rmarkdownon Mar 03 2025.

Last update: 2022-12-09
Started: 2019-02-12

Overview of the epitrix package

Thibaut Jombart

Rendered fromepitrix.Rmdusingknitr::rmarkdownon Mar 03 2025.

Last update: 2023-01-13
Started: 2017-05-17