bpmodels v0.3.2

bpmodels 0.3.2

This is a maintenance update

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

bpmodels v0.3.1

Input validation

• The following internal functions now have input validation: rborel(), dborel(), complementary_logprob(), and rnbinom_mean_disp().

Unit tests

• 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().

bpmodels v0.3.0

Website

• 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.

Vignettes

• 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.

README

• 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.

bpmodels v0.2.1

Minor functionality change

• 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.

bpmodels 0.2.0

Documentation

• bpmodels now has a website.

• chain_sim()'s documentation (help file) has been improved with a lot more details.
  In particular, we clearly describe how to specify arguments such as serial and disambiguate
  the definitions of serial and generation intervals. The help file also now has 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.