%  abalone2
%
%   SI model of abalone with two populations each having recruits 
%    and supporting one way exchange
%
%    The model considers a number of benthic animals in a volume of water
%    Infectious particles can be released which spread the infection
%  
%    Units:
%      time is in days
%      populations are in number of animals/m^2
%      concentrations are in number/m^3
%
%        variables are 
%  y(1): S, susceptible, uninfected individuals [number/m^2]
%  y(2): I, infected individuals [number/m^2]
%  y(3): D, dead infected animals [number/m^2]
%  y(4): P, infectious particles close 
%            to the susceptible population [number/m^3]
%  y(5): S2, susceptible, uninfected individuals [number/m^2] 
%       in the second population
%   PAR is a structure containing the parameters for the model
%
%   PARabalone2.m sets the values of the various model parameters
%   RHSabalone2.m defines the equations and interaction
%
global PAR
%   array indexes of variables
nVar=5;  %  number of variables in the model
iS=1;iI=2;iD=3;iP=4;iS2=5;

PAR=PARabalone2;  %   define model parameters

y0=zeros(nVar,1);  %     initial conditions
y0(iS)=100;
y0(iI)=1;
y0(iP)=0;
y0(iS2)=100;

tspan=[0 100];  %   time span

[t,y]=ode45(@RHSabalone2,tspan,y0);
%   rename model results
S=y(:,1);I=y(:,2);D=y(:,3);P=y(:,4);S2=y(:,5);