Changelog • ringbp

ringbp 0.1.2.9999

The lower bound for the generation time returned by incubation_to_generation_time() is now greater or equal to the latent period (default 0) instead of 1. A latent_period argument has been added to delay_opts(). incubation_to_generation_time() gains two new arguments: exposure_time and latent_period to prevent a bug where an infectee’s exposure precedes an infector’s exposure time. When latent_period > 0, generation times are left‑truncated at latent_period; this can reduce the realised presymptomatic transmission proportion, for which a warning is issued and the realised value is reported after simulation. Addresses #124 by @joshwlambert in #142 and reviewed by @sbfnk and @pearsonca.
The outbreak simulation functions (scenario_sim(), outbreak_model(), outbreak_setup() and outbreak_step()) have been refactored to provide a more modular and functional interface. New delay_opts(), event_prob_opts(), intervention_opts(), offspring_opts(), and sim_opts() helper functions are added. check_dist_func() is added and check_outbreak_input() removed. The parameter_sweep() function is removed and converted into a vignette ({purrr} is removed as a package dependency). prop_presymptomatic_to_alpha() is renamed to presymptomatic_transmission_to_alpha(). Addresses #65, #91 by @joshwlambert in #127 and reviewed by @pearsonca and @sbfnk.
The inf_fn() function has been renamed to incubation_to_generation_time() and the k function argument (scenario_sim(), outbreak_model(), outbreak_step()) has been renamed prop_presymptomatic (in scenario_sim() and outbreak_model()) or alpha (in outbreak_step()). The internal prop_presymptomatic_to_alpha() function has been added to do the conversion from prop_presymptomatic to alpha. 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 and control_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() and outbreak_model(). delay_shape and delay_scale arguments have been replaced by the onset_to_isolation argument, and an incubation_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.tables from outbreak_model() and scenario_sim() by adding [] to return(). 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 0.1.2

Improved package infrastructure by remove the number of dependencies, removing deprecated function calls and reducing clutter in the repo. In #70, #71, #72 and #73 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.