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 562 downloads 2 mentions 14 exports 23 dependencies

Last updated 2 years agofrom:94cb02aa83. Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKApr 02 2025
R-4.5-winNOTEApr 02 2025
R-4.5-macNOTEApr 02 2025
R-4.5-linuxNOTEApr 02 2025
R-4.4-winOKApr 02 2025
R-4.4-macOKApr 02 2025
R-4.4-linuxOKApr 02 2025
R-4.3-winOKApr 02 2025
R-4.3-macOKApr 02 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 Apr 02 2025.

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

Overview of the epitrix package

Thibaut Jombart

Rendered fromepitrix.Rmdusingknitr::rmarkdownon Apr 02 2025.

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