Interactive Documentation State 9.1

Serial Interval Data

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What you should see

Input Documentation

Choose your serial interval distribution

The parametric distribution to use when estimating the serial interval from data on dates of symptoms of pairs of infector/infected individuals.

Choose the posterior sample size (n1)

A positive integer giving the size of the sample of SI distributions to be drawn.

Choose the number of iterations used as MCMC burnin

A positive integer giving the burinin used in the MCMC when estimating the serial interval distribution.

Choose MCMC thin parameter

A positive integer corresponding to the thinning parameter. The MCMC Will be run for burnin+n1*thin iterations and then 1 in thin iterations will be recorded, after the burnin phase, leaving a sample size of n1.

Choose n2

The posterior sample size to be drawn for R for each SI distribution sampled

Set a seed (for MCMC)

An optional integer used as a seed for the random number generator inside MCMC. Useful to get reproducible results.

Choosing your own MCMC initial parameters

These are the initial values of the parameters to use for the MCMC. For every distribution except lognormal, param1 is the shape and param2 is the scale. For lognormal, param1 is the meanlog and param2 is the sdlog.

If these are not specified they are chosen automatically by the init_MCMC_params function of EpiEstim.

What Next?

Once you've filled in all your inputs as described above, click "Go" in the app.

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