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.