sirSpatmod {epimdr2}

Gradient function for a spatially-extended SIR model

Description

Gradient function for a spatially-extended SIR model given some spatial topology

Usage

sirSpatmod(t, y, parameters)

Arguments

t

Implicit argument for time

y

A vector of length L*3 with initial values for the states. The first 1:L represents initial S's, (L+1):2*L are initial I's and the last (2*L+1):3*L are initial R's

parameters

A vector with parameter values for the spatial SIR system

Value

A list of gradients

Examples

require(deSolve)
require(ncf)
data(usflu)
usdist = gcdist(usflu$Longitude, usflu$Latitude)
G = gravity(0.3, 0.6, 3, usflu$Pop, usdist)
gamma = 1/3.5
R0 = 1.8
beta = R0 * gamma/usflu$Pop
m = 1 / 1000 / sum(usflu$Pop)
parms = list(beta = beta, m = m, gamma  =  gamma, G = G) 
S = usflu$Pop
R = I = rep(0, length(usflu$Pop))
I[31] = 1 
inits = c(S = S, I = I, R = R)  
times = 0:200
out = ode(inits, times, sirSpatmod, parms)
L=length(usflu$Pop)
## Not run: matplot(out[, 50+(1:L)], type = "l", ylab = "Prevalence", xlab = "Day")