sa.GT {R0}

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,
  ...
)

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

Details

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

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.

Author(s)

Pierre-Yves Boelle, Thomas Obadia