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
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epitrix_0.4.0.tgz(r-4.4-any)epitrix_0.4.0.tgz(r-4.3-any)
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epitrix.pdf |epitrix.html✨
epitrix/json (API)
NEWS

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

Peer review:

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

On CRAN:

epidemiology

8.47 score 11 stars 4 packages 226 scripts 672 downloads 2 mentions 14 exports 23 dependencies

Last updated 2 years agofrom:94cb02aa83. Checks:OK: 5 NOTE: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-winNOTEOct 10 2024
R-4.5-linuxNOTEOct 10 2024
R-4.4-winOKOct 10 2024
R-4.4-macOKOct 10 2024
R-4.3-winOKOct 10 2024
R-4.3-macOKOct 10 2024

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 Oct 10 2024.

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

Overview of the epitrix package

Thibaut Jombart

Rendered fromepitrix.Rmdusingknitr::rmarkdownon Oct 10 2024.

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