est.R0.AR: Estimate R0 from attack rate of an epidemic

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

Estimate R0 from attack rate of an epidemic

Description

Estimate basic reproduction number R0 from Attack Rate (AR) of an epidemic.

Usage

est.R0.AR(
  AR = NULL,
  incid = NULL,
  pop.size = NULL,
  S0 = 1,
  checked = FALSE,
  ...
)

Arguments

AR	Attack rate as a percentage from total population.
incid	Sum of incident cases, possibly in the form of a vector of counts.
pop.size	Population size in which the incident cases were observed.
S0	Initial proportion of the population considered susceptible.
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().

In the simple SIR model, the relation between R0 and the Attack Rate is in the form R0 = -ln((1-AR)/S0) / (AR - (1-S0)). If the population size is provided, the variance of R0 is estimated using the delta method. The hypothesis are that of homogeneous mixing, no more transmission (epidemic ended), no change in transmission or interventions during the epidemic. This estimate may be correct in closed populations, and may be less valid in other cases.

The correction for incomplete susceptibility is based on the SIR model equations.

A 95% confidence interval is computed for the attack rate considering the total population size (CI(AR) = AR +/- 1.96*sqrt(AR*(1-AR)/n)), and so the confidence interval for the reproduction number is computed with these extreme values.

Value

A list with components:

epid	The vector of incidence, after being correctly formated by check.incid(). Used only by plotfit()
R	The estimate of the reproduction ratio.
conf.int	The 95% confidence interval for the R estimate.
AR	Original attack rate.
begin.nb	First date of incidence record. Used only by plotfit().
end.nb	Last date of incidence record. Used only by plotfit().
method	Method used for the estimation.
method.code	Internal code used to designate method.

Note

This is the implementation of the formula by Dietz (1993).

Author(s)

Pierre-Yves Boelle, Thomas Obadia

References

Dietz, K. "The Estimation of the Basic Reproduction Number for Infectious Diseases." Statistical Methods in Medical Research 2, no. 1 (March 1, 1993): 23-41.

Examples

#Loading package
library(R0)

## Woodall reported an attack rate of 0.31 in a population of 1732 during
## the 1957 H2N2 influenza pandemic ('Age and Asian Influenza, 1957', BMJ, 1958)

est.R0.AR(pop.size=1732, AR=0.31)
# Reproduction number estimate using Attack Rate method
# R :  1.19698[ 1.179606 , 1.215077 ]

est.R0.AR(AR=0.31)
# Reproduction number estimate using  Attack Rate  method.
# R :  1.19698

est.R0.AR(pop.size=1732, incid=31)
# Reproduction number estimate using Attack Rate method
# R :  1.009057[ 1.005873 , 1.012269 ]

est.R0.AR(pop.size=1732, incid=c(2,3,4,7,4,2,4,5))
# Reproduction number estimate using Attack Rate method
# R :  1.009057[ 1.005873 , 1.012269 ]

est.R0.AR(pop.size=1732, incid=c(2,3,0,7,4,2,0,5))
# Reproduction number estimate using Attack Rate method
# R :  1.006699[ 1.003965 , 1.009453 ]

R0 documentation built on Sept. 26, 2023, 5:10 p.m.