epiBR0: Basic reproduction number (R0)

Description Usage Arguments Value

Description

Calculates the basic reproduction number for the specified SIR model and data set

Usage

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epiBR0 (x = NULL, y = NULL, contact = NULL, alpha, beta, spark = NULL, infperiod, 

        Sformula = NULL, tmax, niter, tempseed = NULL)

Arguments

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 ~ model is interpreted as a specification that the susceptibility function, Ω_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.

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.

Value

A list is returned with the following components:

BasicR0

The basic reproduction number value

simulated_BR0

Number of infections per simulation


EpiILM documentation built on May 2, 2019, 12:20 p.m.