est.R0.EG {R0} | R Documentation |
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 |
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 |
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 ]