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@seabbs seabbs released this 06 Feb 11:55
· 1677 commits to main since this release
v1.3.4
ca17494

EpiNow2 1.3.4

This release focusses on bug fixes and package infrastructure updates along with a few quality of life improvements such as enabling the use of fixed delays and generation times.

Thanks to @seabbs, and @sbfnk and for SACEMA for hosting @seabbs whilst some of the development work on this release was being done.

Breaking changes

  • To streamline the interface with the definition of delay distributions trunc_opts() now takes a single argument (dist) which defines the truncation delay rather than a arbitrary list of arguments (which was previously used to define the distribution).
  • Updated the handling of generation times in the renewal equation to be left truncation adjusted for the zeroth day. This more better the approach taken to estimate generation times but may slightly impact estimates vs those produced using previous versions.
  • The range of the frac_obs parameter has restricted with an upper bound of 1 to reflect its name and description. This may impact a small number of edge case uses with the majority being models fit using estimate_secondary(). By @sbfnk in #340.

Features

  • Adds a new function simulate_secondary() for simulating secondary observations under the generative process model assumed by estimate_secondary. Unlike forecast_secondary() which uses a stan model to simulate secondary cases (which shares code with the estimate_secondary model) this new function is implemented entirely in R and is therefore useful to sense check any results from the stan implementation.
  • Adds support for fixed delays (mean only or fixed lognormal distributed) or truncations (fixed lognormal distributed), and for pre-computing these delays as well as generation times if they are fixed. By @sbfnk and @seabbs.
  • Support for gamma distributed delays and log-normal distributed generation times.

Package

  • Update the GitHub Action files to new versions.
  • Switched to using seq_along() rather than 1:length() in all package code.
  • Fixed a broken example in the documentation for regional_runtimes().
  • Add compatibility changes for the latest version of rstan and rstantools.
  • Remove legacy use of pkgnet for package dependency visualisation.
  • Restyled all code using styler.
  • Dropped dependency on RcppParallel.
  • Updated report_cases to work with the new delay_opts helper function.
  • Added test coverage for report_cases though note this function will likely be deprecated in future releases.
  • Switched to linewidth in plot_CrIs rather than size to avoid issues with ggplot2 3.4.0.
  • Set up validation against synthetic data to run as a CI check.
  • Added tests for internal stan convolution functions.
  • Update all get_ distribution functions to return the distribution as well as summary
    parameters.
  • Added support for model fitting benchmarking using touchstone.

Documentation

  • Slight edits to the model outline for estimate_infections().
  • Updated examples to make use of fixed distributions.

Bugs

  • Fixed a bug in simulate_infections() where passing a custom number of samples would cause the input vector of R values to be replicated in a column-wise fashion meaning that the intended R trajectory was not simulated.
  • Fixed a bug in the estimate_infections() deconvolution model where the generation time was not correctly being reversed.

Pull requests

Full Changelog: v1.3.3...v1.3.4

Contributors

sbfnk and seabbs
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