What is the definition of the “priors” row?

These are the probabilities used in our simulations before we check their consistency with the observed data. They are reflected in the .pdf output of the “Prior” histograms. The “Posterior” histograms in the .pdf output show the distribution of each parameter that is compatible with the observed data.

Example:

Priors 5% 15% 60% 15% 5%
Basic reproductive number R0 before Intervention1 2.5 3 3.5 4 4.5
Number of Days from Infection to Becoming Infectious (Latent Period) 0 2 3 4 5

When we do our first simulation, we will draw an initial R0. Roughly speaking*, 60% of the time we will use R0 = 3.5, 15% of the time we use R0 = 4, etc. Then we draw the latent period; 60% of the time 3 days, 15% 4 days, etc. We do the same for each of the 19 parameters. Then use these 19 parameters to project hospitalization. If the projected hospitalization is compatabile** with the observed hospitalization, this set of parameters is accepted.

We repeat this process main.iterations times. We get our projected distributions by taking quantiles of the accepted projections.

*Actually we draw a normally distributed random variable with the same mean and standard deviation implied by this discrete distribution.

** Specifically, a scenario is accepted if required.in.bounds fraction of the projected hospitalization by day is within lower.bound.multiplier * LowerBound to upper.bound.multiplier * UpperBound. You can customize these in the Internals sheet and Hospitalization Data sheet.

How do the Re multipliers for interventions work?

The first Re multiplier is multiplied by the basic R0 to give the new Re after the first intervention. The second Re multiplier is multiplied by the basic R0 and the first Re multiplier to give the new Re after the second intervention.

Re after third intervention = R0 * intervention1.multiplier * intervention2.multiplier * intervention3.multiplier

What if I only have 2 interventions?

Set all values of intervention3.multiplier to 1. Or you can delete the rows with intervention3.date, intervention3.multiplier, intervention3.smooth.days.

What if I have 4 or more interventions?

You can have up to 9 interventions. To add more to the existing xlsx template:

  1. In Excel, unprotect the Parameters with Distributions sheet.
  2. Unhide Column A
  3. Add rows, e.g internal.name = intervention4.date, intervention4.multiplier, intervention4.smooth.days
  4. Make sure there is at least one blank line after the end of all the parameters