Software Open Access
Sam Abbott; Joe Hickson; Sebastian Funk; Hamada S. Badr; Pietro Monticone; Peter Ellis; James Munday; Jamie Allen; Carl A. B. Pearson; Lloyd Chapman; Michael DeWitt; Nikos Bosse; Sophie Meakin
This release adds a range of new minor features, squashes bugs, enhances documentation, expands unit testing, implements some minor run-time optimisations, and removes some obsolete features.
Thanks to @Bisaloo, @hsbadr, @LloydChapman, @medewitt, and @sbfnk for contributing to this release.
Thanks to @sbfnk, @pearsonca, and @nicholasdavies for regression testing this release against
simulate_infectionsso that a
data.frameof R samples can be passed in instead of a vector of R values. By @seabbs.
estimate_infections. By @seabbs.
zero_thresholdto users allowing for control over when zeros or NAs in count data are treated as true zeros versus as reporting errors that require some smoothing. By @seabbs.
obs_opts()). This allows, for example, fitting to data with cases only reported every 3 days. By @seabbs.
plot_estimates()and higher level functions to choose which estimate type to plot. By @seabbs.
regional_summaryto allow plotting to be optional. Closes #250. By @seabbs in #317
obs_opts()). This allows, for example, fitting to data with cases only reported every 3 days.
targetlikelihood definition approach when required and in the use of
fminover using if statements. By @seabbs.
obs_optswith the default of a normal distribution with mean 0 and standard deviation of 1 truncated at 0 remaining unchanged. By @seabbs.
estimate_truncationmodel to deal with zeroes. By @sbfnk.
epinowcastby Adrian Lison and Sam Abbott. By @seabbs in #320.
contributing.mdto guide contributors and added
pre-commitsupport to check new contributions styling. By @seabbs.
ggplot2::theme_bw(). This allows the removal of
cowplotas a dependency as well making plots visible for users saving as pngs and using a dark theme. By @seabbs.
epinowand downstream functions remove leading zeros. Now this is optional with the new
filter_leading_zerosoption. Thanks to @LloydChapman in #285.
estimate_truncation(). By @seabbs in #315.
adjust_infection_to_report. By @seabbs in #316.
rstantoolsto manage compiler flags.
future::multiprocess()as the latter is being depreciated in the
futurepackage. By @seabbs and @sbfnk.
forecast_infections()have been deprecated and have been removed. These functions depend on
EpiSoonwhich itself is archived and near equivalent functionality is available within
EpiNow2and in other packages (@seabbs).
forecast_infections()(i.e in `epinow()) have been removed along with the arguments that supported them (@seabbs).
theme_map()have all been deprecated and have been removed. These functions were used to support reporting of reproduction number estimates and are considered out of scope for
EpiNow2. If finding useful contacting the
forecast_secondarywhich meant that a Poisson observation model used for estimation would lead to a error. By @seabbs.
use_rt = FALSEdid not properly cancel user settings. By @sbfnk.
estimate_truncationwhere phi was not initialised. By @sbfnk.
zero_thresholdwas being ignored and so no post-processing was happening. To maintain backwards compatibility the default has been changed to
Inf(i.e. no zero threshold). By @LloydChapman in #285.
ls_sd = 0by @hsbadr in https://github.com/epiforecasts/EpiNow2/pull/257
use_rt=FALSEby @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/274
estimate_truncationby @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/300
estimate_truncationby @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/301
Full Changelog: https://github.com/epiforecasts/EpiNow2/compare/1.3.3...v1.3.3