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 anonymise data, and fitting discretised Gamma distributions.


epitrix 0.2.2

  • Replace digest with sodium in Imports
  • Use sodium::scrypt() as a more cryptographically secure hashing algorithm for hash_names(). Thanks to @dirkschumacher for this addition. For details, see
  • Fix LICENSE file to show who the copyright holder is.

epitrix 0.2.1

  • update documentation for compatibility with incidence 1.4.1

epitrix 0.2.0

  • added function clean_labels which can be used to standardise labels in variables, removing non-ascii characters, standardising separators, and more; now used in hash_names

epitrix 0.1.2

  • added salting algorithm to hash_names (issue 1)

  • fixed bug happening when using tibble inputs in hash_names (issue 2)

epitrix 0.1.1

  • fit_disc_gamma now also returns the fitted discretised gamma distribution as a distcrete object

epitrix 0.1.0

First release of the package! This includes the following features:

  • fit_disc_gamma: fit discretised gamma distribution

  • gamma_log_likelihood: compute gamma log likelihood

  • gamma_mucv2shapescale/gamma_shapescale2mucv: convert between different parametrisation of gamma distributions.

  • hash_names: generate hashed ('anonymised') labels from individual data.

  • r2R0: compute R0 from r

  • lm2R0_sample: genrate samples of R0 from a log-linear regression

Reference manual

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0.2.2 by Thibaut Jombart, a year ago

Report a bug at

Browse source code at

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

Documentation:   PDF Manual  

MIT + file LICENSE license

Imports sodium, distcrete, stringi

Suggests testthat, roxygen2, outbreaks, incidence, knitr, rmarkdown

Imported by earlyR.

See at CRAN