Changelog
Source:NEWS.md
ringbp 0.1.2.9999
The outbreak simulation functions (
scenario_sim()
,outbreak_model()
,outbreak_setup()
andoutbreak_step()
) have been refactored to provide a more modular and functional interface. Newdelay_opts()
,event_prob_opts()
,intervention_opts()
,offspring_opts()
, andsim_opts()
helper functions are added.check_dist_func()
is added andcheck_outbreak_input()
removed. Theparameter_sweep()
function is removed and converted into a vignette ({purrr} is removed as a package dependency).prop_presymptomatic_to_alpha()
is renamed topresymptomatic_transmission_to_alpha()
. Addresses #65, #91 by @joshwlambert in #127 and reviewed by @pearsonca and @sbfnk.The
inf_fn()
function has been renamed toincubation_to_generation_time()
and thek
function argument (scenario_sim()
,outbreak_model()
,outbreak_step()
) has been renamedprop_presymptomatic
(inscenario_sim()
andoutbreak_model()
) oralpha
(inoutbreak_step()
). The internalprop_presymptomatic_to_alpha()
function has been added to do the conversion fromprop_presymptomatic
toalpha
. Addresses #119, #120 by @joshwlambert in #123 and reviewed by @pearsonca and @sbfnk.Added input checking, including new
check_outbreak_input()
function, removed unused argument defaults, consistently ordered arguments in functions, and moved function argument documentation to functions that use the argument. Addresses #89, #91, #93, #116 by @joshwlambert in #117 and reviewed by @pearsonca and @sbfnk.Function argument and variable names are consistently named and styled (snake case). Arguments that were abbreviated (e.g.
iso
) now use the full word, and arguments that had aliases (e.g.prop_ascertain
andcontrol_effectiveness
) now use a single name. By @joshwlambert in #112 and reviewed by @pearsonca and @sbfnk.Fixed a bug in the implementation of quarantine, where isolation could happen later than onset + delay, if this was earlier than the isolation time of the infector. By @sbfnk in #107 and reviewed by @pearsonca and @joshwlambert.
Changed internal sampling to vector draws in several locations; in some cases, this was an optimization, but in others it was a bug fix correcting the use of single draw where there should have been many. Also incorporates other vectorization changes to improve performance. Because of the bug fix, users should expect results to change. Addresses issues #90, #92, #94, in #98 by @pearsonca (now added as a contributor) with review by @sbfnk and @joshwlambert.
The minimum R version required by the {ringbp} package is now
>= 4.4.0
. This is due to the dependency on {Matrix}. A GitHub actions workflow for R CMD check has been added to check the package is valid on the minimum required R version. Addressed in #85 by @joshwlambert with review by @sbfnk.Parameterisation of delay distributions accepted by the model have been generalised in
scenario_sim()
andoutbreak_model()
.delay_shape
anddelay_scale
arguments have been replaced by theonset_to_isolation
argument, and anincubation_period
argument is added. Addresses issues #59 and #63 in #84 by @joshwlambert with review by @sbfnk and @pearsonca.Function examples are added and updated, and
\dontrun{}
is removed. Addresses issue #27 in #83 by @joshwlambert with review by @pearsonca.Use {roxyglobals} to manage global variables. Addresses issue #66 in #81 by @joshwlambert with review by @sbfnk.
Remove silent printing of returned
data.table
s fromoutbreak_model()
andscenario_sim()
by adding[]
toreturn()
. Addresses issue #64 in #80 by @joshwlambert with review from @sbfnk.Function documentation is updated, including function arguments, function outputs, inheriting arguments across functions and fixing out-of-date references. Addressed issue #58 and #67 in #78 by @joshwlambert with review by @sbfnk and @pearsonca and issue #79 in #82 by @joshwlambert with review by @sbfnk.
ringbp 0.1.1
Added unit tests. By @timcdlucas in #43 and reviewed by @sbfnk.
Added testing and checking infrastructure using github actions.
ringbp 0.1.0
- Initial release alongside paper on Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts.