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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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.