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-4.7)epitrix_0.4.0.zip(r-4.6)epitrix_0.4.0.zip(r-4.5)
epitrix_0.4.0.tgz(r-4.6-any)epitrix_0.4.0.tgz(r-4.5-any)
epitrix_0.4.0.tar.gz(r-4.7-any)epitrix_0.4.0.tar.gz(r-4.6-any)
epitrix_0.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
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/docs site:https://www.repidemicsconsortium.org

On CRAN:

epidemiology

8.61 score 12 stars 5 packages 228 scripts 535 downloads 2 mentions 14 exports 22 dependencies

Last updated from:94cb02aa83. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	141
source / vignettes	OK	190
linux-release-x86_64	NOTE	155
macos-release-arm64	NOTE	125
macos-oldrel-arm64	NOTE	104
windows-devel	NOTE	196
windows-release	NOTE	103
windows-oldrel	NOTE	79
wasm-release	OK	127

Exports:AR2R0 clean_labels empirical_incubation_dist fit_disc_gamma fit_gamma_incubation_dist gamma_log_likelihood gamma_mucv2shapescale gamma_shapescale2mucv hash_names lm2R0_sample R02AR R02herd_immunity_threshold r2R0 sim_linelist

Dependencies:cli cpp11 distcrete dplyr generics glue lifecycle magrittr pillar pkgconfig purrr R6 rlang sodium stringi stringr tibble tidyr tidyselect utf8 vctrs withr

Example to estimate incubation period

Flavio Finger

Rendered fromestimate_incubation.Rmdusingknitr::rmarkdownon May 19 2026.

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

Overview of the epitrix package

Thibaut Jombart

Rendered fromepitrix.Rmdusingknitr::rmarkdownon May 19 2026.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Title Calculate basic reproduction number from attack rate	AR2R0
Standardise labels	clean_labels
Extract empirical incubation period distribution from linelist data	empirical_incubation_dist
Fit discretised distributions using ML	fit_discrete fit_disc_gamma
Fit discrite gamma distribution to incubation periods	fit_gamma_incubation_dist
Reparameterise Gamma distributions	gamma_log_likelihood gamma_mucv2shapescale gamma_shapescale2mucv
Anonymise data using scrypt	hash_names
Title Calculate attack rate from basic reproduction number	R02AR
Title Calculate herd immunity threshold from basic reproduction number	R02herd_immunity_threshold
Transform a growth rate into a reproduction number	lm2R0_sample r2R0
Simulate simple linelist data	sim_linelist