function ydot=RHSinfct2(t,y)
%  RHSabalone2
%
%    define the RHS of the model equations. 
%        variables are 
%  y(1): S, susceptible, uninfected individuals [number]
%  y(2): I, infected individuals [number]
%  y(3): D, dead animals from the infected population [number]
%  y(4): P, infectious particles close 
%            to the susceptible population [number]
%  y(5): S2, susceptible, uninfected individuals [number/m^2] 
%       in the second population
%   array indexes of variables
nVar=5;
iS=1;iI=2;iD=3;iP=4;iS2=5;
global PAR 
%          most rates are 1/day
ydot=zeros(nVar,1);

D=y(iS2)-y(iS);if D < 0; D=0; end
K=(1 - (y(iS)+y(iI))/PAR.Carry);if K < 0; K=0;end
K2=(1 - y(iS2)/PAR.Carry2);if K2 < 0; K2=0;end

%   time changes of susceptable animals
ydot(iS)= - PAR.IPinfect * PAR.depth * y(iP) * y(iS)...
          - PAR.Iinfect * y(iI) * y(iS) ...
          - PAR.Dinfect * y(iD) * y(iS) ...
          - PAR.Bmort * y(iS) ...
          + PAR.ReproS * K * y(iS) ...
          + PAR.ReproI * K * y(iI) ...
          + PAR.Imm * y(iS2) + PAR.Diff * D;

%   time changes of susceptable animals in 2nd population
ydot(iS2)=  PAR.Repro2 *K2 * y(iS2) ...
          - PAR.Imm * y(iS2) - PAR.Diff * D;

%   time changes of infected animals
ydot(iI)= PAR.IPinfect * y(iP) * y(iS)... 
        + PAR.Iinfect * y(iI) * y(iS)... 
        + PAR.Dinfect * y(iD) * y(iS)... 
        - PAR.Imort * y(iI);

%   time changes of dead infected animals
ydot(iD)= PAR.Imort * y(iI) - PAR.DeadDecay * y(iD);

%   time changes of infectious particles
ydot(iP)= PAR.Irelease * y(iI) + PAR.Drelease * y(iD) ...
        - PAR.IPremove * y(iP);