The third minor release of the superspreading package contains enhancements to several functions and a new vignette.
We are also pleased to welcome Dillon Adam (@dcadam) as a new package author for his contributions towards this version.
proportion_transmission() function has been expanded to incorporate a new method. The new method calculates the proportion of transmission from X% the most infectious individuals, corresponding to the Lloyd-Smith et al. (2005) calculation. The proportion_transmission() has a new method argument to toggle between the two calculations (@dcadam, #99).proportion_transmission() function (#101).bpmodels::chain_sim(), is added to the {superspreading} package (#103). @sbfnk is added as copyright holder and @jamesmbaazam as a contributor.probability_contain() is enhanced to enable to probability of containment within a certain amount of time since the outbreak started. This adds outbreak_time and generation_time arguments to probability_contain(). This addition is backwards compatible as by default the time is unlimited, outbreak_time = Inf, and no generation time is required.stochastic argument in probability_contain() has been renamed simulate to be consistent with other functions (#103).proportion_*() functions are now formatted to significant figures rather than rounding to prevent small values being rounded to zero (#102).rmarkdown::html_vignette instead of bookdown::html_vignette2 and as_is: true has been removed due to changes to {pkgdown} in v2.1.0. {bookdown} has been removed as a suggested package and code folding is removed from vignettes. KaTeX headers have been added to _pkgdown.yml for correct math rendering (#104 & #109).get_epidist_params() internal function has been renamed get_epiparameter_params() since {epiparameter} renamed the <epidist> class to <epiparameter> (#100).R and k) or provides an <epiparameter> object is now in .check_input_params() (#111).Second minor release of superspreading. This release enhances functions added in v0.1.0 and adds two new exported functions, and two new vignettes.
calc_network_R()) to estimate the reproduction number for heterogeneous networks and a vignette outlining use cases for the function from existing epidemiological literature is added (#71).probability_epidemic() and probability_extinct() now have individual-level and population-level control in a joint framework (#70).proportion_*() functions can now return proportion columns of the output <data.frame> as numeric when the new argument format_prop is set to FALSE (#72).ic_tbl()) to improve model comparison tables (#65).probability_*() functions now accept dynamic dots ({rlang} is added as a dependency) (#82).ind_control and pop_control arguments replace control and control_type arguments in probability_contain(); and the argument default for num_init_infect is removed (#70).epidist argument to offspring_dist to follow Epiverse style (affects several functions) (#64).proportion_transmission() has been renamed from sim to simulate (#81).optim() by default (#82).Initial release of superspreading, an R package to estimate individual-level variation in disease transmission and provide summary metrics for superspreading events.