Calculates the basic reproduction number for the specified SIR model and data set
epiBR0 (x = NULL, y = NULL, contact = NULL, alpha, beta, spark = NULL, infperiod, Sformula = NULL, tmax, niter, tempseed = NULL)
X coordinates of individuals
Y coordinates of individuals
Contact network(s)
Susceptibility parameter(>0)
Spatial parameter(s) (>0) or network parameter (s) (>0) if contact is used
Sparks parameter (>=0), representing infections unexplained by other parts of the model or infections coming in from outside the observed population, default value is zero
Length of infectious period for each individual
An object of class formula. See formula
Individual-level covariate information passable through this argument. An expression of the form ~ model is interpreted as a specification that the susceptibility function, \(\Omega_s(i) \) is modelled by a linear predictor specified symbolically by the model term. Such a model consists of a series of terms separated by + and - operators. If there is no covariate information, Sformula is null.
The last time point of simulation
Number of epidemic simulations to calculate basic reproduction number
Integer seed value to initialize the (Fortran) random number generator, default value is a random seed.
A list is returned with the following components:
The basic reproduction number value
Number of infections per simulation