Changelog • bpmodels

bpmodels 0.3.2

chain_sim() now ensures that the parameters of the negative binomial offspring are not both zero else returns an informative error.

The following internal functions now have input validation: rborel(), dborel(), complementary_logprob(), and rnbinom_mean_disp().
Code coverage has been improved with more tests on the following functions: rborel(), dborel(), chain_sim(), rnbinom_mean_disp(), complementary_logprob(), rgen_length(), and rbinom_size().

The website has been updated to use bootstrap 5. This means it has a slightly new look.
Exported functions under “references” have been grouped into topics.

A new vignette has been added to compile a bibliography of papers that apply branching processes to infectious disease epidemiology.
The “quickstart” section of the README has been moved to the “Getting started” section of the website.
The README now only provides a quick description of the core functions in the package and users are referred to the website for a quick start.

The README no longer has a quickstart section as it has been moved to the website. This is to give the README a minimalistic look.

chain_sim() now throws a warning, instead of an error, when tree is set to FALSE with serial also specified. We assume that providing a serial interval means you want the tree of transmissions to be simulated, so chain_sim() internally sets tree = TRUE and throws a warning explaining what happened. This behaviour should not break any simulations with previous versions with bpmodels, but if it does, please submit an issue. To remove the warning, the user should explicitly set tree = TRUE when they specify serial.

chain_sim()’s help file has been updated with more details. In particular, we describe in detail how to specify the serial argument as a function. We have also added more examples.
A new vignette describing how to project COVID-19 incidence with chain_sim() has been added and can be accessed on the bpmodels website under “Articles”.
The README’s “quick start” section has been updated with what was previously the introduction vignette.