%  SEIR marine model
%
%   SEIR 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): E, EXPOSED, exposed individuals [number/m^2]
%  y(3): I, INFECTED, infected individuals [number/m^2]
%  y(4): R, RECOVERED, recovered for infection individuals [number/m^2]

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

%
global PAR

%   array indexes of variables
nVar=4;  %  number of variables in the model
iS=1;iE=2;iI=3;iR=4;

PAR=PAR_SEIR;  %   define model parameters

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


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

[t,y]=ode45(@RHS_SEIR,tspan,y0);
%   rename model results
S=y(:,1);E=y(:,2);I=y(:,3);R=y(:,4);