epiforecasts/EpiNow2: 1.3.3 CRAN Release

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 1.3.2. New features Added supported to simulate_infections so that a data.frame of R samples can be passed in instead of a vector of R values. By @seabbs. Added extraction of posterior samples to the summary method for estimate_infections. By @seabbs. Exposed zero_threshold to 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. Added support for varying the length of the day of the week effect (see obs_opts()). This allows, for example, fitting to data with cases only reported every 3 days. By @seabbs. Adds option to plot_estimates() and higher level functions to choose which estimate type to plot. By @seabbs. Adds support for fixed generation times (either mean only or fixed gamma distributed). By @sbfnk. Adds support for optionally using an inverse gamma prior for the lengthscale of the gaussian process. This scaled prior has been tested for both short and long simulations where the default prior may make the model unstable. The new prior is more stable for long simulations and adaptively change the distribution based on the simulation length (total number of days) without relying on the user inputs or the fixed defaults. It can be tested by setting ls_sd = 0 in gp_opts(). By @hsbadr. Updated the prior on the magnitude of the gaussian process to be 0.05 vs 0.1 leading to slightly more stable estimates. By @hsbadr. Added an argument (plot) to regional_summary to allow plotting to be optional. Closes #250. By @seabbs in #317 Model changes Added support for varying the length of the day of the week effect (see obs_opts()). This allows, for example, fitting to data with cases only reported every 3 days. Minor optimisations in the observation model by only using the target likelihood definition approach when required and in the use of fmax and fmin over using if statements. By @seabbs. Added support for users setting the overdispersion (parameterised as one over the square root of phi) of the reporting process. This is accessible via the phi argument of obs_opts with the default of a normal distribution with mean 0 and standard deviation of 1 truncated at 0 remaining unchanged. By @seabbs. Added additive noise term to the estimate_truncation model to deal with zeroes. By @sbfnk. Switched to using optimised versions of the discretised distributions supported for the reporting delay and the generation time. These are based on an implementation in epinowcast by Adrian Lison and Sam Abbott. By @seabbs in #320. Documentation Updates to all synthetic delays to reduce runtime of examples. By @seabbs. Additional statements to make it clear to users examples should be used for real world analysis. By @seabbs. Additional context in the README on package functionality. By @seabbs. Added some work in progress model definitions and a resource list for case studies using the package. By @seabbs. Package changes Added a contributing.md to guide contributors and added pre-commit support to check new contributions styling. By @seabbs. Better test skipping thanks to @Bisaloo. Switched from cowplot::theme_cowplot() to ggplot2::theme_bw(). This allows the removal of cowplot as a dependency as well making plots visible for users saving as pngs and using a dark theme. By @seabbs. By default epinow and downstream functions remove leading zeros. Now this is optional with the new filter_leading_zeros option. Thanks to @LloydChapman in #285. Basic tests have been added to cover estimate_secondary(), forecast_secondary(), and estimate_truncation(). By @seabbs in #315. Add basic snapshot tests for adjust_infection_to_report. By @seabbs in #316. Update to use rstantools to manage compiler flags. Update the Dockerfile to work better with vscode. Other changes Updated the classification of growth to use stable rather than unsure when Rt is approximately 1. By @seabbs. The default parallisation has been changed to future::multisession() from future::multiprocess() as the latter is being depreciated in the future package. By @seabbs and @sbfnk. Ensure the seeding time is at least the maximum generation time (@sbfnk). Deprecated features simulate_cases() and forecast_infections() have been deprecated and have been removed. These functions depend on EpiSoon which itself is archived and near equivalent functionality is available within EpiNow2 and in other packages (@seabbs). Functions supporting secondary forecasting using forecast_infections() (i.e in `epinow()) have been removed along with the arguments that supported them (@seabbs). global_map(), country_map(), and 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 EpiNow2 developers (@seabbs). Bug fixes Fixed a bug in the deconvolution Rt estimation method where the mean of the generation time was being used as the standard deviation. For the default package generation time these are close and so the impact will be limited but in cases where the standard deviation is << than the mean this should result in more accurate Rt estimates. By @seabbs. Fixed a bug where the number of threads used by the data.table package were set to one in the global environment. Now the number of threads used by data.table are set to whatever the used specified on exit. By @medewitt. Fixed a bug in simulate_infections and forecast_secondary which meant that a Poisson observation model used for estimation would lead to a error. By @seabbs. Fixed a bug where use_rt = FALSE did not properly cancel user settings. By @sbfnk. Fixed a bug in estimate_truncation where phi was not initialised. By @sbfnk. Fixed a bug where zero_threshold was 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. Pull requests sort table by hidden numeric columns by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/265 Read summary table in report template by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/266 fixed generation times or distributions by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/276 GP: lengthscale: Use inverse-gamma prior if ls_sd = 0 by @hsbadr in https://github.com/epiforecasts/EpiNow2/pull/257 Update README.Rmd by @pitmonticone in https://github.com/epiforecasts/EpiNow2/pull/263 Fix a typo in _regional-summary.Rmd by @pitmonticone in https://github.com/epiforecasts/EpiNow2/pull/278 change deprecated future::multiprocess -> multicore by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/289 ensure seeding_time is at least max_gt by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/275 ensure correct parameters if use_rt=FALSE by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/274 initialise phi in estimate_truncation by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/300 fix rt = NULL case by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/302 deal with zeroes in estimate_truncation by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/301 only call truncate if truncation is modelled by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/304 don't pass R to update_Rt by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/303 fix CRAN issues by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/309 fix estimate_secondary example by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/314 Add option for filtering leading zeros and correct zero_threshold by @LloydChapman in https://github.com/epiforecasts/EpiNow2/pull/285 Fixed a few typos by @pitmonticone in https://github.com/epiforecasts/EpiNow2/pull/306 Add estimate_secondarry and estimate_truncation simple tests by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/315 Add tests adjust to report by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/316 Add plot arg to regional_summary by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/319 Optimisations and updates for CRAN check by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/320 Add skeleton for documentation by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/321 Final changes for 1.3.3 by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/322 fix typo by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/323 update in progress message for docs by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/324 spell check by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/325 fix typo by @sbfnk in https://github.com/epiforecasts/EpiNow2/pull/326 revert dev version by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/327 update rendered README by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/328 Develop by @seabbs in https://github.com/epiforecasts/EpiNow2/pull/329 New Contributors @LloydChapman made their first contribution in https://github.com/epiforecasts/EpiNow2/pull/285 Full Changelog: https://github.com/epiforecasts/EpiNow2/compare/1.3.3...v1.3.