Learn R Programming

epitrix (version 0.4.0)

Small Helpers and Tricks for Epidemics Analysis

Description

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.

Copy Link

Version

Install

install.packages('epitrix')

Monthly Downloads

593

Version

0.4.0

License

MIT + file LICENSE

Maintainer

Thibaut Jombart

Last Published

January 13th, 2023

Functions in epitrix (0.4.0)

sim_linelist

Simulate simple linelist data
AR2R0

Title Calculate basic reproduction number from attack rate
r2R0

Transform a growth rate into a reproduction number
R02AR

Title Calculate attack rate from basic reproduction number
R02herd_immunity_threshold

Title Calculate herd immunity threshold from basic reproduction number
empirical_incubation_dist

Extract empirical incubation period distribution from linelist data
hash_names

Anonymise data using scrypt
fit_disc_gamma

Fit discretised distributions using ML
gamma_shapescale2mucv

Reparameterise Gamma distributions
clean_labels

Standardise labels
fit_gamma_incubation_dist

Fit discrite gamma distribution to incubation periods