sa.GT: Sensitivity analysis of reproduction ratio with varying GT distribution

Description

Sensitivity analysis of reproduction ratio with varying GT distribution.

Usage

sa.GT(incid, GT.type, 
    GT.mean.range, GT.sd.range, 
    begin = NULL, end = NULL, 
    est.method, t = NULL, 
    date.first.obs = NULL, 
    time.step = 1, ...)

Value

A data frame s.a with following components :

$GT.type: Distribution law for GT.
$GT.mean: Range of means used for tested GTs.
$GT.sd: Range of standard deviations used for tested GTs.
$R: Computed value for Reproduction Number given GT.type, GT.mean and GT.sd.
$conf.int[1]: The lower limit of 95% CI for R.
$conf.int[2]: The upper limit of 95% CI for R.

Arguments

incid: incident cases
GT.type: Type of distribution for GT (see generation.time for details)
GT.mean.range: mean used for all GT distributions throughout the simulation
GT.sd.range: Range of standard deviation used for GT distributions. Must be provided as a vector.
begin: begin date of the estimation of epidemic
end: end date of estimation of the epidemic
est.method: Estimation method used for sensitivity analysis. Requires a method computing a proper R0 value (and not an instantaneous R(t))
t: Dates vector to be passed to estimation function
date.first.obs: Optional date of first observation, if t not specified
time.step: Optional. If date of first observation is specified, number of day between each incidence observation
...: parameters passed to inner functions

Author

Pierre-Yves Boelle, Thomas Obadia

Details

By using different Generation Time (GT) distribution, different estimates of reproduction ratio can be analyzed.