gen_simobs_likelihood: Generate a likelihood function for single-county simulated...
In rplzzz/CovMitigation: COVID-19 infection model for Virginia

This likelihood function is greatly simplified from the one produced by gen_likelihood. It contains none of the adjustments for hospitalizaton fraction (since simulated data has no hospitalization to compare to), and it doesn't (yet) distinguish between symptomatic and asymptomatic cases.

1	gen_simobs_likelihood(simobs, timerange, verbose = FALSE)

`simobs`	Simulated observations, as returned by `simobs`.
`timerange`	Length-2 vector giving the earliest and latest dates to use in the calculation. If not specified, use all times in the dataset.
`verbose`	If `TRUE`, output additional diagnostic information to console.

The parameters to this model are beta, A0, D0, Ts, I0, b0, b1, mask_effect, and import_cases. Mask effect can be omitted; if so, it is fixed at zero.

The scenario runs are assumed to start at the earliest time in the observed dataset, even if the time range for comparing to data starts later. The population is initialized to I0 exposures at that time with the rest of the population initialized as susceptible.

Another change in this function is that we use the binomial distribution instead of the hypergeometric. This saves us some mucking about with ensuring that the susceptible population is greater than the number of positive observations.

rplzzz/CovMitigation documentation built on June 7, 2021, 8:48 a.m.