Changelog

Source: NEWS.md

epidemia 1.0.0

  • First version submitted to CRAN
  • Bug fixed for latent infections and first Rt with pop_adjust
  • reorganized files to correctly attribute copyright.
  • New model for adding vaccination adjustments
  • latent infections switched to normal, from log-normal
  • Additional vignettes and model description
  • Additional noise options for infection process
  • Significantly more flexible modeling of seeding process
  • Many small bug fixes

epidemia 0.7.0

  • Changes to general interface - new epiinf() function for representing infection model
  • Improved package website, with better description of the model and examples in the vignettes.
  • Ability to model latent infections explicitly - replacing renewal equation
  • Removed ‘pop’ and replaced with column of susceptibles in dataframe. This allows susceptible population to reduce over time due to vaccinations.
  • Improved error checking in epim(), with more informative messages
  • scaled_logit for epiobs
  • Full integration with Bayesplot package, and a plot.epimodel method which easily allows the user to choose different components of the model.
  • Fixed bug which meant “fullrank” was actually using “meanfield”
  • Ability to use random walks in the epiobs models
  • Choose between identity, scaled logit, and log link for epirt
  • Plot the (potentially transformed) linear predictors for both epiobs and epirt
  • Additional families for epiobs - normal and lognormal
  • Add summary method and printing for epimodel objects
  • Plots improved, allowing step for plot_rt, and improved formatting

epidemia 0.6.0

  • Substantial changes to interface: Added epirt and epiobs objects
  • Different and more flexible observation models
  • Improved structure to epimodel objects
  • Refactoring of main epim function
  • Improved plots, including interactive plots using plotly
  • Forecast evaluation using coverage and different metrics
  • Ability to do an initial run fit to cumulatives within epim
  • Updated tests, documentation and vignettes

epidemia 0.5.3

  • Improved model description in introduction vignette

epidemia 0.5.2

  • Passes R CMD Check with no warnings
  • Updated installation instructions

epidemia 0.5.1

  • Renamed stan files to avoid errors with Rstan 2.12.
  • Plotting vignette

epidemia 0.5.0

  • Random walk terms parsed separately as input to stan files. Variance parameter sampled in stan, and so can make predictions.
  • pseudo-log scales for plot_infections and plot_observations
  • control over date range for all plots
  • option to plot smoothed Rt in plot_rt

epidemia 0.4.0

  • Features for counterfactual analysis and predictions

epidemia 0.3.3

  • Added vignette describing priors
  • Description of collinearity issues in ‘resolving problems’ vignette
  • Form for potential beta testers

epidemia 0.3.2

  • Citation file
  • Fixes to documentation in website

epidemia 0.3.1

  • Website fixes
  • Separate index for website and github

epidemia 0.3.0

  • Website and more extensive vignettes

epidemia 0.2.0

  • Initial version.