%  SIPF marine model (particle filtration model) 
%
%   SIPF 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): P, infectious particles (free-living pathogens, particles [number/m^3]
%  y(4): F, infectious particles inside susceptible population [number of
%  particles]

%  PAR is a structure containing the parameters for the model
%
%  PAR_SIP.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;iI=2;iP=3;iF=4; 

PAR=PAR_SIPF;  %   define model parameters

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

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


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

%   Rename model results. New names for the plots.

S=y(:,1);I=y(:,2);P=y(:,3);F=y(:,4);