Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/overall_infectivity.R

`overall_infectivity`

computes the overall infectivity due to previously
infected individuals.

1 | ```
overall_infectivity(incid, si_distr)
``` |

`incid` |
One of the following A vector (or a dataframe with a single column) of non-negative integers containing an incidence time series A dataframe of non-negative integers with two columns, so that `incid$local` contains the incidence of cases due to local transmission and`incid$imported` contains the incidence of imported cases (with`incid$local + incid$imported` the total incidence).
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).

1 2 3 4 5 6 7 8 9 10 | ```
## 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")
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.