EpiEstim (version 1.1-2)

OverallInfectivity: Overall Infectivity Due To Previously Infected Individuals

Description

OverallInfectivity computes the overall infectivity due to previously infected individuals.

Usage

OverallInfectivity(I, SI.Distr)

Arguments

I

vector of non-negative integers containing an incidence time series.

SI.Distr

vector of probabilities giving the discrete distribution of the serial interval.

Value

OverallInfectivity(I, SI.Distr) returns a vector which contains the overall infectivity \(\lambda_t\) at each time step \(t\).

Details

The overall infectivity \(\lambda_t\) at time step \(t\) is equal to the sum of the previously infected individuals (given by the incidence vector \(I\)), weigthed by their infectivity at time \(t\) (given by the discrete serial interval distribution \(w_k\)).

In mathematical terms:

\(\lambda_t = \sum_{k=1}^{t-1}I_{t-k}w_k\)

References

Cori, A. et al. A new framework and software to estimate time-varying reproduction numbers during epidemics. (submitted)

See Also

DiscrSI, EstimateR

Examples

# NOT RUN {
## load data on pandemic flu in a school in 2009
data("Flu2009")

## compute overall infectivity
lambda <- OverallInfectivity(Flu2009$Incidence, Flu2009$SI.Distr)
par(mfrow=c(2,1))
plot(Flu2009$Incidence, type="s", xlab="time (days)", ylab="Incidence")
title(main="Epidemic curve")
plot(lambda, type="s", xlab="time (days)", ylab="Infectivity")
title(main="Overall infectivity")
# }