clear all;

% Supplement to Chapter 8 in book on Ranaviruses (Gray and Chinchar, eds.) 
% published in 2014 by Springer.

% This model is an SIR model in continuous time based on ordinary 
% differential equations with density dependent transmission to be run in matlab.

% Make sure the sir.m file is in the same folder as this file


% Parameters
t0 = 0; % initial time for the model- here is time zero
tf = 100; % final time evaluated for the model
N0 = [99 1 0]; % Number of idividuals in each population at t0. Refers to 
% population size of susceptibles, infected, and recovered.


% Integration
[t N] = ode45('sir',[t0 tf],N0); %  ode45 integrates the system of ordinary
% differential equations from time 0 (t0) to the final time (tf) for the
% function sir given the initial population distribution (N0). Outputs t
% (the time points evaluated) and the N for each population at each t.


% Plot the populations over time
plot(t,N(:,1),t,N(:,2),t,N(:,3)) 
title('SIR Model') 
xlabel('Time') 
ylabel('Population Size')
legend('Susceptible', 'Infected', 'Recovered')