%  SID marine model
%
%   SID model for  a single population
%
%    The model considers a number of individuals in a population
%    The model considers a number of individuals in a (surface) 

%  
%    Units:
%      time is in days
%      populations are in number of individuals (/m^2)

%
%     variables are 
%  y(1): S, susceptible, uninfected individuals [number/m^2]
%  y(2): I, infected individuals [number/m^2]
%  y(3): D, dead, individuals [number/m^2]

% Infection occurs by contact with dead infected animals

%   PAR is a structure containing the parameters for the model
%
%   PAR_SID.m sets the values of the various model parameters

%
global PAR

%   array indexes of variables

nVar=3;  %  number of variables in the model
iS=1;iI=2;iD=3;

PAR=PAR_SID;  %   define model parameters

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



tspan=[0 400];  %   time span,  simulation time
%tspan=[0 350];  %   time span sumulation time


% set up of the model

[t,y]=ode45(@RHS_SID,tspan,y0);

%   rename model results

S=y(:,1);I=y(:,2);D=y(:,3);