R0 (version 1.2-10)

est.R0.EG: Estimate R from exponential growth rate

Description

Estimate R from exponential growth rate.

Usage

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

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.

Arguments

epid

object containing epidemic curve data. see Details.

GT

generation time distribution

t

Vector of dates at which incidence was calculated

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

Author

Pierre-Yves Boelle, Thomas Obadia

Details

For internal use. Called by est.R0.

method "poisson" uses Poisson regression of incidence. method "linear" uses linear regression of log(incidence)

CI is computed from the 1/M(-r) formula using bounds on r from the Poisson regression.

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 ]