NMB DASA Covid-19 User Guide
Overview
This WebApp contains a new extended SEIR model and simulation engine for tracking the progress of instances and mortality in the Covid-19 pandemic, based on a set of 20 model parameter inputs. The model and simulation are used to fit sample data and subsequently facilitate forecasting under various conditions.
The user creates a project by:
- Providing some initial settings for model inputs (default settings are available); and
- Uploading a CSV file containing sequences of incidence and mortality data over some span of days.
Model data are retained by the WebApp for use on all pages. Data will be retained even if the WebApp is reloaded. Model input settings are first tuned by fitting the simulation to the sample curves up to any point in their length. Forecasting with various scenarios can start at any point of fitting interval of the sample sequence. Forecasting begins with the model initialized to the state determined by the fit.
During forecasting two sets of data are used:
- Optimization Settings (shown in green) are the results of performing the data fit and are used until a selected Forecast Onset point, chosen in the range of the fit, to initialize the state of the model to the state obtained by the fit. Optimization settings also appear on the settings page.
- Forecast Settings (shown in red) kick in at the Forecast Onset and may include changes in slider values and switch positions. In particular, enabling the Det_Stoc switch introduces randomness into the simulation during the forecast.
An MCMC Metropolis-Hastings algorithm implementation page produces MCMC distributions for selected parameters. These can be used to select new parameter values for use from the point of Forecast Onset