NEWS.md

In ImperialCollegeLondon/epidemia: Modeling of Epidemics using Hierarchical Bayesian Models

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.

ImperialCollegeLondon/epidemia documentation built on June 26, 2021, 7:40 a.m.