`AR2R0`

: calculate the R0 corresponding to a give attack rate`R02AR`

: calculate the attack rate corresponding to a give R0`R02herd_immunity_threshold`

: calculate the herd immunity threshold for a given R0`sim_linelist`

: simulates a simple linelist (with no epi model implied)`data.frame`

- removed the dependency on the
*linelist*package by RECON - updated testing infrastructure to testthat 3rd edition
- replaced appveyor and travis by github actions for continuous integration
- fixed LaTeX conversion issues due to non-latin symbols in the
example of
`clean_labels()`

`emperical_incubation_dist()`

will estimate the empirical incubation distribution if given a data frame with dates of onset and a range of exposure dates (@ffinger, #13)`fit_gamma_incubation_dist()`

wraps`empirical_incubation_dist()`

and`fit_disc_gamma()`

to fit a discretized gamma distribution to the empirical incubation distribution results (@ffinger, #13).

`clean_labels()`

gains the`protect`

argument to protect meaningful symbols in the data.`hash_names()`

now has the`hashfun`

option that allows users to specify either a “fast” or “secure” hashing function to use (@zkamvar, #21).

- “Estimating Incubation Period” shows the use of empirical incubation dist.

- functions from
`dplyr`

,`purrr`

,`rlang`

, and`tidyr`

are now imported.

`clean_labels()`

can now handle non-latin characters and gains the`trans_id`

argument, which allows the user to customise the transformations (see https://github.com/reconhub/epitrix/issues/19 for details).

- 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 https://github.com/reconhub/epitrix/pull/7. - Fix LICENSE file to show who the copyright holder is.

- update documentation for compatibility with incidence 1.4.1

- 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`

added salting algorithm to

`hash_names`

(issue 1)fixed bug happening when using

`tibble`

inputs in`hash_names`

(issue 2)

`fit_disc_gamma`

now also returns the fitted discretised gamma distribution as a`distcrete`

object

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