inst/hetTut/low.md

In ICI3D/ici3d-pkg: Materials for the International Clinics on Infectious Disease Dynamics and Data (ICI3D) Workshops

Part 1: Low Variance

First, let's run the model with very low variance so we can see what happens in a situation that is very similar to the homogenous population model. This is like the compartmental box models that we have been using in differential equation and discrete time versions of the SIR model.

This is the code running behind the scenes:

mxdst <- het.population(n = 100, beta.mean = 2, beta.var = 0.001)
het.hist(mxdst, beta.mean)
het.epidemic(mxdst, runs = 5, end.time = 10, gmma = 1)

To add another sample series, click the button above the graphs.

EXPLANATION OF VARIABLES

• beta.mean is the mean of your contact rate distribution
• beta.var is its variance
• end.time is how long to let the simulations go before cutting them off (if the outbreak hasn't already died)
• pop.size is the total population size
• gmma is the recovery rate (or 1/mean duration of infectiousness)
• rho is the waning rate (or 1/mean duration of immunity)

OUTPUT

The panel on the left is a histogram of the contact rate distribution. The middle shows the epidemic time series. The right panel shows the distribution of outbreak final size (i.e. total number of people infected before outbreak is over) from the runs.

ICI3D/ici3d-pkg documentation built on July 2, 2023, 1:59 p.m.