simulist 0.4.0

A minor version release of simulist containing various minor improvements to the functions and documentation, as well as removing some triggers for warning users. There are also a few bug fixes and internal enhancements.

New features

External

• Defaults have been added to all sim_*() arguments that previously did not have one. Allowing functions to be run without specifying any arguments (e.g. linelist <- sim_linelist()) (#149).
• Documentation for sim_*() function arguments that accept either a function or an <epiparameter> object has been improved (#149).
• sim_*() functions no longer warn if the user has not specified *_risk arguments and have set onset_to_* arguments to NULL (#149).
• All vignettes now use rmarkdown::html_vignette for to correctly render the website and for maximum compatibility with {pkgdown} >= 2.1.0. This removes figure numbering and code folding (#153).

Internal

• .add_hospitalisation() has been vectorised following .add_outcome() in PR #101 (#150).

Breaking changes

• The function arguments infect_period and prob_infect have been renamed infectious_period and prob_infection (#143).
• sim_*() functions now use NULL instead of NA to turn off processes (e.g. onset_to_death = NULL for no deaths) (#148).

Bug fixes

• A new function, .sample_infect_period() is added that errors if the infectious period function generates a negative number (#142).
• sim_linelist() no longer errors when hosp_death_risk is NULL and onset_to_death is parameterised as a delay distribution (#144).
• .add_ct() generates the correct number of values and does not duplicate Ct values due to vector recycling (#158).
• Update {epiparameter} usage (#159).

Deprecated and defunct

• None