fit.epid.optim

vector of parameters to be optimised. This should be provided as c(R0, GT.mean, GT.sd)

Compute the Poisson log - likelihood between epid and epidemic simulated with R and GT.

internal

Estimation of reproduction numbers for disease outbreak, based on
incidence data. The R0 package implements several documented methods. It is
therefore possible to compare estimations according to the methods used.
Depending on the methods requested by user, basic reproduction number
(commonly denoted as R0) or real-time reproduction number (referred to as
R(t)) is computed, along with a 95% Confidence Interval. Plotting outputs
will give different graphs depending on the methods requested : basic
reproductive number estimations will only show the epidemic curve
(collected data) and an adjusted model, whereas real-time methods will also
show the R(t) variations throughout the outbreak time period. Sensitivity
analysis tools are also provided, and allow for investigating effects of
varying Generation Time distribution or time window on estimates.

fit.epid.optim: Joint estimation of GT distribution and R

Description

Usage

Arguments

Details