sa.time: Sensitivity analysis of basic reproduction ratio to begin/end dates

Description

Sensitivity analysis of reproduction ratio using supported estimation methods.

Usage

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

Value

A list with components as a data frame:

df: data.frame object with all results from sensitivity analysis.
df.clean: the same object, with NA rows removed. Used only for easy export of results.
mat.sen: Matrix with values of R0 given begin (rows) and end (columns) dates.
begin: A range of begin dates in epidemic.
end: A range of end dates in epidemic.

Arguments

incid: incident cases
GT: generation time distribution
begin: Vector of begins date of the estimation of epidemic
end: Vector of end dates of 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
res: If specified, will extract most of data from a R0.R-class result already generated by est.R0 and run sensitivity analysis on it.
...: parameters passed to inner functions

Author

Pierre-Yves Boelle, Thomas Obadia

Details

By varying different pairs of begin and end dates,different estimates of reproduction ratio can be analyzed.

'begin' and 'end' vector must have the same length for the sensitivity analysis to run. They can be provided either as "dates" or "numeric" values, depending on the other parameters (see check.incid). If some begin/end dates overlap, they are ignored, and corresponding uncomputed data are set to NA. Also, note that unreliable Rsquared values are achieved for very small time period (begin ~ end). These values are not representative of the epidemic outbreak behaviour.