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.
sodium::scrypt()as a more cryptographically secure hashing algorithm for
hash_names(). Thanks to @dirkschumacher for this addition. For details, see https://github.com/reconhub/epitrix/pull/7.
clean_labelswhich can be used to standardise labels in variables, removing non-ascii characters, standardising separators, and more; now used in
added salting algorithm to
hash_names (issue 1)
fixed bug happening when using
tibble inputs in
hash_names (issue 2)
fit_disc_gammanow also returns the fitted discretised gamma distribution as a
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_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