Small Helpers and Tricks for Epidemics Analysis
Title Calculate basic reproduction number from attack rate
Standardise labels
Extract empirical incubation period distribution from linelist data
Fit discretised distributions using ML
Fit discrite gamma distribution to incubation periods
Reparameterise Gamma distributions
Anonymise data using scrypt
Title Calculate attack rate from basic reproduction number
Title Calculate herd immunity threshold from basic reproduction number
Transform a growth rate into a reproduction number
Simulate simple linelist data
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.