fit.epid {R0} | R Documentation |
Poisson log-likelihood for an observed epidemic
Description
Computes the Poisson log-likelihood of an observed epidemic, compared to the expected incidence values for a given R and generation time distirbution.
Usage
fit.epid(log.R, epid, GT, import, pred = FALSE, offset = 0)
Arguments
log.R |
The log-reproduction ratio. |
epid |
An epidemic curve, in the sense of passing |
GT |
Generation time distribution from |
import |
Vector of imported cases |
pred |
Boolean. By default ( |
offset |
Offset value for the log-likelihood (used to calculate confidence intervals). |
Details
For internal use. Called from est.R0.ML()
.
Computes and returns the Poisson log-likelihood of an observed epidemic, conditional on a given value of R and a generation time distribution.
Value
The Poisson log-likelihood of the observed epidemic passed as argument epid
,
or the Poisson-predicted incidence series given R and GT values.
Note
This function is also used in fit.epid.optim()
, which is a wrapper for the
joint optimization routine to determine the best-fitting R and GT values when
the est.R0.ML()
method is called and asked to jointly estimate reproduction
ratios and generation time distirbution.
Author(s)
Pierre-Yves Boelle, Thomas Obadia