NEWS

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epitrix 0.4.0 (2023-01-13)

New Functions

• 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

Bug fixes

• 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()

epitrix 0.3.0

New Functions

• 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).

New Features

• 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).

New Vignettes

• "Estimating Incubation Period" shows the use of empirical incubation dist.

New Imports

• functions from dplyr, purrr, rlang, and tidyr are now imported.

Bug Fix

• 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).

epitrix 0.2.2 (2019-01-15)

• 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.

epitrix 0.2.1 (2018-08-28)

• update documentation for compatibility with incidence 1.4.1

epitrix 0.2.0 (2018-04-24)

• 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 (2018-03-01)

• added salting algorithm to hash_names (issue 1)

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

epitrix 0.1.1 (2018-01-24)

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

epitrix 0.1.0 (2017-11-26)

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