epiBR0 {EpiILM} | R Documentation |
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 |
X coordinates of individuals |
y |
Y coordinates of individuals |
contact |
Contact network(s) |
alpha |
Susceptibility parameter(>0) |
beta |
Spatial parameter(s) (>0) or network parameter (s) (>0) if contact is used |
spark |
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 |
infperiod |
Length of infectious period for each individual |
Sformula |
An object of class formula. See formula Individual-level covariate information passable through this argument. An expression of the form |
tmax |
The last time point of simulation |
niter |
Number of epidemic simulations to calculate basic reproduction number |
tempseed |
Integer seed value to initialize the (Fortran) random number generator, default value is a random seed. |
A list is returned with the following components:
BasicR0 |
The basic reproduction number value |
simulated_BR0 |
Number of infections per simulation |