sim.epid.indiv {R0}

Influenza-like illness simulation (individual-based model)

Description

Generates several epidemic curves with an individual-based model.

Usage

sim.epid.indiv(beta, Tmax, n = 1, family = "poisson", negbin.size = NULL)

Arguments

beta

Contact rate in the SEIR model.

Tmax

Maximum length of the epidemic (cases infected after this length will be truncated).

n

Number of epidemics to be simulated (defaults to 1)

family

Distribution of offspring. Can be either "poisson" (default) or "negbin".

negbin.size

If family is set to "negbin", sets the size parameter of the negative binomial distribution.

Details

The epidemic is simulated using a branching process, with infinite number of susceptibles to allow for exponential growth. The model used follows the Crump-Mode-Jagers description, with S/E/I/R description of the natural history.

Latent and infectious period follow parametrized Gamma distributions typical of influenza. An index case is first introduced, and offspring is sampled from a negative binomial distribution, with mean beta*I and variance negbin.size*beta*I, to allow for overdispersion.

Value

A matrix with epidemics stored as columns (incidence count).

Note

This is the exact function as used in the manuscript (Obadia et al., 2012).

Author(s)

Pierre-Yves Boelle, Thomas Obadia