sa.time: Sensitivity of R0 to time estimation windows

In tobadia/R0: Estimation of R0 and Real-Time Reproduction Number from Epidemics

Sensitivity of R0 to time estimation windows

Description

Sensitivity analysis to estimate the variation of reproduction numbers according to period over which the incidence is analyzed.

Usage

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

Arguments

incid	A vector of incident cases.
GT	Generation time distribution from generation.time().
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.
res	If specified, will extract most of data from a R0.R-class contained within the ⁠$estimate⁠ component of a result from estimate.R() and run sensitivity analysis with it.
...	Parameters passed to inner functions

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 periods (begin ~ end). These values are not representative of the epidemic outbreak behaviour.

Value

A list with components :

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.

Author(s)

Pierre-Yves Boelle, Thomas Obadia

tobadia/R0 documentation built on Sept. 24, 2023, 5:16 p.m.