Overall Infectivity Due To Previously Infected Individuals
overall_infectivity computes the overall infectivity due to previously
infected individuals.
overall_infectivity(incid, si_distr)
incid |
One of the following
Note that the cases from the first time step are always all assumed to be imported cases. |
si_distr |
Vector of probabilities giving the discrete distribution of the serial interval. |
The overall infectivity λ_t at time step t is
equal to the sum of the previously infected individuals (given by the
incidence vector I, with I = incid$local + incid$imported if
I is a matrix), weigthed by their infectivity at time t (given by
the discrete serial interval distribution w_k). In mathematical terms:
λ_t = ∑_{k=1}^{t-1}I_{t-k}w_k
A vector which contains the overall infectivity λ_t at each time step
Anne Cori a.cori@imperial.ac.uk
Cori, A. et al. A new framework and software to estimate time-varying reproduction numbers during epidemics (AJE 2013).
## load data on pandemic flu in a school in 2009
data("Flu2009")
## compute overall infectivity
lambda <- overall_infectivity(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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.