sa.GT: Sensitivity of R0 to varying generation time distributions

Description

Sensitivity analysis to estimate the variation of reproduction numbers according to the disitrbution of generation time.

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: Type of distribution 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.
CI.lowe: The lower limit of 95% CI for R.
CI.upper: The upper limit of 95% CI for R.

Arguments

incid: A vector of incident cases.
GT.type: Type of distribution for GT (see GT.R for details).
GT.mean.range: Range of mean values used for all GT distributions throughout the simulation. Must be provided as a vector.
GT.sd.range: Range of standard deviation values used for GT distributions. Must be provided as a vector.
begin: Vector of begin dates for the estimation of epidemic.
end: Vector of end dates for estimation of the epidemic.
est.method: Estimation method used for sensitivity analysis.
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 the reproduction ratio can be analyzed.