est.R0.EG: Estimate R0 from exponential growth rate of an epidemic

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

Estimate R0 from exponential growth rate of an epidemic

Description

Estimate R0 from the initial phase of an epidemic when incident cases are presumed to follow an exponential distribution.

Usage

est.R0.EG(
  epid,
  GT,
  t = NULL,
  begin = NULL,
  end = NULL,
  date.first.obs = NULL,
  time.step = 1,
  reg.met = "poisson",
  checked = FALSE,
  ...
)

Arguments

epid	Object containing epidemic curve data.
GT	Generation time distribution from generation.time().
t	Vector of dates at which incidence was observed.
begin	At what time estimation begins.
end	Time at which to end computation.
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
reg.met	Regression method used. Default is "poisson" (for GLM), but can be forced to "linear".
checked	Internal flag used to check whether integrity checks were ran or not.
...	Parameters passed to inner functions.

Details

For internal use. Called by estimate.R().

Method "poisson" uses Poisson regression of incidence to estimate the exponential growth rate. Method "linear" uses linear regression of log(incidence) against time.

The 95% confidence interval is computed from the 1/M(-r) formula, using bounds on r from the Poisson or linear regression.

Value

A list with components:

R	The estimate of the reproduction ratio.
conf.int	The 95% confidence interval for the R estimate.
r	Exponential growth rate of the epidemic.
conf.int.r	Confidence interval of the exponential growth rate of the epidemic.
Rsquared	The deviance R-squared measure for the considered dates and model.
epid	Original epidemic data.
GT	Generation time distribution used in the computation.
data.name	Name of the data used in the fit.
begin	Starting date for the fit.
begin.nb	The number of the first day used in the fit.
end	The end date for the fit.
end.nb	The number of the las day used for the fit.
fit	Method used for fitting.
pred	Prediction on the period used for the fit.
method	Method for estimation.
method.code	Internal code used to designate method.

Note

This is the implementation of the method provided by Wallinga & Lipsitch (2007).

Author(s)

Pierre-Yves Boelle, Thomas Obadia

References

Wallinga, J., and M. Lipsitch. "How Generation Intervals Shape the Relationship Between Growth Rates and Reproductive Numbers." Proceedings of the Royal Society B: Biological Sciences 274, no. 1609 (2007): 599.

Examples

#Loading package
library(R0)

## Data is taken from the paper by Nishiura for key transmission parameters of an institutional
## outbreak during 1918 influenza pandemic in Germany)

data(Germany.1918)
mGT<-generation.time("gamma", c(3, 1.5))

est.R0.EG(Germany.1918, mGT, begin=1, end=27)
## Reproduction number estimate using  Exponential Growth 
## R :  1.525895[ 1.494984 , 1.557779 ]

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