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@seabbs seabbs released this 19 Oct 21:59
v1.2.1
71165c3

This release introduces multiple breaking interface changes. Please see the README for examples of the new interface. It adds a range of quality of life improvements including updating the stan interface to support fitting each chain independently and offering variational inference as an alternative, experimental, fitting option. Notably it also adds support for nesting logging and a parallel enabled progress bar via the progressr package. Minor bugs have been fixed in the core model implementation focussing on stability and several already implemented features have been extended. Major model developments are planned for the next release of EpiNow2.

New features

  • Added support for either NUTs sampling (method = "exact") or Variational inference (method = "approximate").
  • Update the prior on the initial Rt estimate to be lognormal rather than gamma distributed. For users the interface remains unchanged but this parameterisation should be more numerically stable.
  • Added get_dist, get_generation_time, get_incubation_period based on ideas from @pearsonca. (This leads to breaking changes with the removal of covid_generation_times and covid_incubation_periods).
  • Added setup_logging to enable users to specify the level and location of logging (wrapping functionality from futile.logger). Also added setup_default_logging to give users sensible defaults and embedded this
    function in regional_epinow and epinow.
  • Added setup_future to making using nested futures easier (required when using future = TRUE).
  • Implemented progress bar support using progressr.
  • Added timeout and timing option to regional_epinow
  • Improved logging of warnings in regional_epinow
  • Enabled the user to specify the credible intervals desired with 20%, 50% and 90% calculated by default. Also switched from high density regions to quantiles. Custom credible intervals are now supported in all reporting and plotting functions.
  • Added mean and sd to all reporting summaries.
  • Added a summary of the growth rate and doubling time.
  • Added a new function regional_runtimes that summarises the run time across regions.
  • Updated the estimate_infections interface and expanded the range of options for the future_rt argument. Users can now choose to set Rt from any time point referenced to the forecast date.

Bug fixes

  • Fixed y axis max for plot_summary.
  • Fix to normalisation of delay and generation time distributions from @sbfnk. This will impact nowcast infections but not reproduction number estimate.
  • Updated discretised_gamma_pmf (discretised truncated Gamma PMF) to constrain gamma shape and (inverse) scale parameters to be positive and finite (alpha > 0 and beta > 0).
  • Fixed readLines incomplete final line warnings.
  • Fix from @medewitt from the internal fit_chain function where an interaction between rstan and timing out may have introduced an exception that caused whole regions to fail. This did not show on current unit tests or exploration using examples etc. indicating a gap in testing.

Other changes

  • Updates the interface for specifying how output is returned.
  • Moved all inherited from stan arguments into create_stan_args with the option to override using stan_args. This leads to breaking changes - see the examples for details of the new interface.
  • Updated all example and documentation to reflect the new interface.
  • Added a samples argument to get_regional_results to make loading in samples optional. This also allows samples to be dropped when using regional_epinow which reduces RAM usage.
  • Cleaned up wrapper functions to move individual jobs into functions.
  • Adds testing of high level functions and some low level unit testing.
  • Adds a csv download button the interactive table in the regional summary table.
  • Makevars updated to remove the dependency on GNU Make by @hsbadr
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