%##################################################################################
%This is the Matlab code to set up and run model simulations for social-system %structured disease transmission in a basic 10 group metapopulation of primates.
%This code is not intended to be elegant and concise, rather, obvious and easy to 
%manipulate
%This code was written and annotated by Sadie J Ryan, commented on July 19th, 2013.
%#################################################################################

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%First, extract the following code to a separate function, and call it binan.m, so it can be %called inside the model simulations

%This file wants to be a function that makes sure that a binomial call which is passed 0,0 won't go crazy
function [a] = binan(n,p)
   n=floor(n);
if n==0
    a = 0;
else
     a = (binornd(n,p)/n);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%MAIN CODE STARTS HERE

%Setting up to run a ridiculous number of simulations to collect summaries at the %end

for q=1:20


nreps=100;
for j=1:nreps 

c=[q,j]

%If you want to know what iteration it's on, you can uncomment the next line
%c=j

%Setting up a 10 group SI model with between group movement

%DEMOGRAPHIC RATES - in this example code, we use the medium sized monkey

% Define the weaning age, ii, to obtain an infant transition category, i
    ii=3;
    irate=1/ii;
    i=irate;
    
%then the age of first reproduction for females, to derive the subadult female category, sf 
    mf = 5
    sfrate=1/mf;
    sf=sfrate;

%then the age of maturity for males, to derive subadult males, sm
    mm=6;
    smrate = 1/mm;
    sm=smrate;
    
% b, the birthrate
    %b=0.50
    b=brate;
 
    
%then longevity, to derive annual persistence, p
    le=15;
    p=1-(1/le);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Create the monkey metapopulation matrix, MM
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

MM=zeros(100,100);

%SET UP TOTAL POPULATION     
% Create overall NG population vector, X

AX=vertcat(5*ones(5,1),zeros(5,1));
BX=vertcat(5*ones(5,1),zeros(5,1));
CX=vertcat(5*ones(5,1),zeros(5,1));
DX=vertcat(5*ones(5,1),zeros(5,1));
EX=vertcat(5*ones(5,1),zeros(5,1));
FX=vertcat(5*ones(5,1),zeros(5,1));
GX=vertcat(5*ones(5,1),zeros(5,1));
HX=vertcat(5*ones(5,1),zeros(5,1));
IX=vertcat(5*ones(5,1),zeros(5,1));
JX=vertcat(5*ones(5,1),zeros(5,1));

X=vertcat(AX,BX,CX,DX,EX,FX,GX,HX,IX,JX);
%X=5*ones(100,1);
X(7)=1;

%We will want to run this one through some timesteps, tmax, and store NGs 
tmax=200;

%making a blank time series matrix, xx
xx=zeros(100,tmax);
xx(:,1)=X;

%The movement rate
m=q/20;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%        %DISEASE PARAMETERS AND TRANSMISSION STRUCTURES (Contact Vectors)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%    
    % define beta, B
    B=0.1;
    
    %Define alpha (death from disease), A
    A=0.05;
    
    %give a vertical transmission component, v
    v=0.0;
    
% We define a contact matrix, 5x5 binary, for the social system in question
% To run the model with a particular contact vector, uncomment it

%STD, Solitary
%C=[0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 0, 0, 0, 0, 1; 0, 0, 0,1, 0];
%STD, Monogamous
%C=[0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 0, 0, 0, 0, 1; 0, 0, 0,1, 0];
%STD, Unimale
%C=[0, 0, 0, 0, 0; 0, 0, 1, 0, 1; 0, 1, 0, 0, 0; 0, 0, 0, 0, 1; 0, 0, 0,1, 0];
%STD, Multimale
% C=[0, 0, 0, 0, 0; 0, 0, 1, 0, 1; 0, 1, 0, 0, 0; 0, 0, 0, 0, 1; 0, 0, 0,0, 0];
%STD, Fission-Fusion
%C=[0, 0, 0, 0, 0; 0, 1, 1, 1, 1; 0, 1, 1, 1, 1; 0, 1, 1, 1, 1; 0, 1, 1, 1, 1];

%FO, Solitary
% C=[1, 0, 0, 1, 1; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 1, 0, 0, 1, 1; 1, 0, 0, 1, 1];
%FO, Monogamous
% C=[1, 0, 0, 1, 1; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 1, 0, 0, 1, 1; 1, 0, 0,1, 1];
%FO, Unimale
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1];
%FO, Multimale
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1];
%FO, Fission-Fusion
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1,1, 1];

%Scratch, Solitary
% C=[0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 0, 0, 0, 1, 1; 0, 0, 0, 1, 1];
%Scratch, Monogamous
% C=[0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 0, 0, 0, 1, 1; 0, 0, 0, 1, 1];
%Scratch, Unimale
% C=[0, 0, 0, 0, 0; 0, 1, 1, 1, 1; 0, 0, 1, 0, 1; 1, 0, 0, 1, 0; 1, 0, 1, 0, 1];
%Scratch, Multimale
% C=[0, 0, 0, 0, 0; 0, 1, 1, 1, 1; 0, 0, 1, 1, 1; 1, 0, 1, 1, 1; 1, 0, 1, 1, 1];
%Scratch, Fission-Fusion
% C=[0, 0, 0, 0, 0; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1];

%Sneeze, Solitary
% C=[1, 0, 0, 1, 1; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 1, 0, 0, 1, 1; 1, 0, 0, 1, 1];
%Sneeze, Monogamous;
%Sneeze, Unimale
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1];
%Sneeze, Multimale
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1];
%Sneeze, Fission-Fusion
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1];

%Vector, Solitary
%C=[1, 0, 0, 1, 1; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 1, 0, 0, 1, 1; 1, 0, 0, 1, 1];
%Vector, Monogamous
% C=[1, 0, 0, 1, 1; 0, 0, 0, 0, 0; 0, 0, 0, 0, 0; 1, 0, 0, 1, 1; 1, 0, 0, 1, 1];
%Vector, Unimale
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1];
%Vector, Multimale
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1];
%Vector, Fission-Fusion
% C=[1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1, 1; 1, 1, 1, 1,1];


%start to run the model for a period of years

for t=2:tmax


%Within group persistence and infection
   %create an infection probability pinf, for each group AA to AJ
    %Define Infecteds   
	    AAI=xx(6:10, t-1);
        ABI=xx(16:20, t-1);
        ACI=xx(26:30, t-1);
        ADI=xx(36:40, t-1);
        AEI=xx(46:50, t-1);
        AFI=xx(56:60, t-1);
        AGI=xx(66:70, t-1);
        AHI=xx(76:80, t-1);
        AII=xx(86:90, t-1);
        AJI=xx(96:100, t-1);
    %Define within group population
        AAN = sum(xx(1:10, t-1));
        ABN = sum(xx(11:20, t-1));
        ACN = sum(xx(21:30, t-1));
        ADN = sum(xx(31:40, t-1));
        AEN = sum(xx(41:50, t-1));
        AFN = sum(xx(51:60, t-1));
        AGN = sum(xx(61:70, t-1));
        AHN = sum(xx(71:80, t-1));
        AIN = sum(xx(81:90, t-1));
        AJN = sum(xx(91:100, t-1));
        
   %Defining susceptibles for later use
        AAS=xx(1:5, t-1);
        ABS=xx(11:15, t-1);
        ACS=xx(21:25, t-1);
        ADS=xx(31:35, t-1);
        AES=xx(41:45, t-1);
        AFS=xx(51:55, t-1);
        AGS=xx(61:65, t-1);
        AHS=xx(71:75, t-1);
        AIS=xx(81:85, t-1);
        AJS=xx(91:95, t-1);
   
    %Set up the vector for freq-dep transmission within each group  
   
	if  AAN==0
        pinfAA=zeros(1,5)
    else
        pinfAA=1-exp(-B*C*AAI/AAN);
    end
    if  ABN==0
        pinfAB=zeros(1,5)
    else
        pinfAB=1-exp(-B*C*ABI/ABN);
    end
    if  ACN==0
        pinfAC=zeros(1,5)
    else
    pinfAC=1-exp(-B*C*ACI/ACN);
    end
    if  ADN==0
        pinfAD=zeros(1,5)
    else
    pinfAD=1-exp(-B*C*ADI/ADN);
    end
    if AEN==0
        pinfAE=zeros(1,5)
    else
    end
    pinfAE=1-exp(-B*C*AEI/AEN);
    if  AFN==0
        pinAF=zeros(1,5)
    else
    end
    pinfAF=1-exp(-B*C*AFI/AFN);
    if  AGN==0
        pinfAG=zeros(1,5)
    else
    end
    pinfAG=1-exp(-B*C*AGI/AGN);
    if  AHN==0
        pinfAH=zeros(1,5)
    else
    end
    pinfAH=1-exp(-B*C*AHI/AHN);
    if  AIN==0
        pinfAI=zeros(1,5)
    else
    end
    pinfAI=1-exp(-B*C*AII/AIN);
    if  AJN==0
        pinfAJ=zeros(1,5)
    else
    pinfAJ=1-exp(-B*C*AJI/AJN); 
    end   

  %Put the within-group demography and infection into the big matrix, MM
    
  %Susceptible births
  %Binomial flipped susceptible birthrates for susceptible mothers
  AAb = binan(xx(4,t-1)+xx(9,t-1), b);
  ABb = binan(xx(14,t-1)+xx(19,t-1), b);
  ACb = binan(xx(24,t-1)+xx(29,t-1), b);
  ADb = binan(xx(34,t-1)+xx(39,t-1), b);
  AEb = binan(xx(44,t-1)+xx(49,t-1), b);
  AFb = binan(xx(54,t-1)+xx(59,t-1), b);
  AGb = binan(xx(64,t-1)+xx(69,t-1), b);
  AHb = binan(xx(74,t-1)+xx(79,t-1), b);
  AIb = binan(xx(84,t-1)+xx(89,t-1), b);
  AJb = binan(xx(94,t-1)+xx(99,t-1), b);
    
  MM(1,4)   = AAb;
  MM(11,14) = ABb; 
  MM(21,24) = ACb; 
  MM(31,34) = ADb; 
  MM(41,44) = AEb; 
  MM(51,54) = AFb;
  MM(61,64) = AGb;
  MM(71,74) = AHb; 
  MM(81,84) = AIb; 
  MM(91,94) = AJb; 
  
  %from infected mothers
  %Binomial flipped birthrates for infected mothers
  MM(1,9)= AAb*(1-v);
  MM(11,19)= ABb*(1-v);
  MM(21,29)= ACb*(1-v);
  MM(31,39)= ADb*(1-v);
  MM(41,49)= AEb*(1-v);
  MM(51,59)= AFb*(1-v);
  MM(61,69)= AGb*(1-v);
  MM(71,79)= AHb*(1-v);
  MM(81,89)= AIb*(1-v);
  MM(91,99)= AJb*(1-v);
  
  %Infected births
  MM(6,9) = AAb*v;
  MM(16,19) = ABb*v;
  MM(26,29) = ACb*v;
  MM(36,39) = ADb*v;
  MM(46,49) = AEb*v;
  MM(56,59) = AFb*v;
  MM(66,69) = AGb*v;
  MM(76,79) = AHb*v;
  MM(86,89) = AIb*v;
  MM(96,99) = AJb*v;
  
  %Arrival of susceptible infants (those not infected and not transitioning)
  %Binomial flip on infant transition rate
  AAi = binan(xx(1, t-1)+xx(6,t-1),i);
  ABi = binan(xx(11, t-1)+xx(16,t-1),i);
  ACi = binan(xx(21, t-1)+xx(26,t-1),i);
  ADi = binan(xx(31, t-1)+xx(36,t-1),i);
  AEi = binan(xx(41, t-1)+xx(46,t-1),i);
  AFi = binan(xx(51, t-1)+xx(56,t-1),i);
  AGi = binan(xx(61, t-1)+xx(66,t-1),i);
  AHi = binan(xx(71, t-1)+xx(76,t-1),i);
  AIi = binan(xx(81, t-1)+xx(86,t-1),i);
  AJi = binan(xx(91, t-1)+xx(96,t-1),i);
    
  MM(1,1)= p*(1-pinfAA(1))*(1-AAi); 
  MM(11,11) = p*(1-pinfAB(1))*(1-ABi);
  MM(21,21) = p*(1-pinfAC(1))*(1-ACi);
  MM(31,31) = p*(1-pinfAD(1))*(1-ADi);
  MM(41,41) = p*(1-pinfAE(1))*(1-AEi);
  MM(51,51) = p*(1-pinfAF(1))*(1-AFi);
  MM(61,61) = p*(1-pinfAG(1))*(1-AGi);
  MM(71,71) = p*(1-pinfAH(1))*(1-AHi);
  MM(81,81) = p*(1-pinfAI(1))*(1-AIi);
  MM(91,91) = p*(1-pinfAJ(1))*(1-AJi);
  
  %Arrival of susceptible subadult females (sf)
  MM(2,1)=p*(1-pinfAA(1))*(AAi/2);
  MM(12,11)=p*(1-pinfAB(1))*(ABi/2);
  MM(22,21)=p*(1-pinfAC(1))*(ACi/2);
  MM(32,31)=p*(1-pinfAD(1))*(ADi/2);
  MM(42,41)=p*(1-pinfAE(1))*(AEi/2);
  MM(52,51)=p*(1-pinfAF(1))*(AFi/2);
  MM(62,61)=p*(1-pinfAG(1))*(AGi/2);
  MM(72,71)=p*(1-pinfAH(1))*(AHi/2);
  MM(82,81)=p*(1-pinfAI(1))*(AIi/2);
  MM(92,91)=p*(1-pinfAJ(1))*(AJi/2);
  
  %Arrival of susceptible subadult males (sm)
  MM(3,1)=p*(1-pinfAA(1))*(AAi/2);
  MM(13,11)=p*(1-pinfAB(1))*(ABi/2);
  MM(23,21)=p*(1-pinfAC(1))*(ACi/2);
  MM(33,31)=p*(1-pinfAD(1))*(ADi/2);
  MM(43,41)=p*(1-pinfAE(1))*(AEi/2);
  MM(53,51)=p*(1-pinfAF(1))*(AFi/2);
  MM(63,61)=p*(1-pinfAG(1))*(AGi/2);
  MM(73,71)=p*(1-pinfAH(1))*(AHi/2);
  MM(83,81)=p*(1-pinfAI(1))*(AIi/2);
  MM(93,91)=p*(1-pinfAJ(1))*(AJi/2);
  
  %Persistence of susceptible subadult females (sf)
 %Binomial flip on sf rates for susceptibles
  AAsf = binan(xx(2,t-1)+xx(7,t-1),sf);
  ABsf = binan(xx(12,t-1)+xx(17,t-1),sf);
  ACsf = binan(xx(22,t-1)+xx(27,t-1),sf);
  ADsf = binan(xx(32,t-1)+xx(37,t-1),sf);
  AEsf = binan(xx(42,t-1)+xx(47,t-1),sf);
  AFsf = binan(xx(52,t-1)+xx(57,t-1),sf);
  AGsf = binan(xx(62,t-1)+xx(67,t-1),sf);
  AHsf = binan(xx(72,t-1)+xx(77,t-1),sf);
  AIsf = binan(xx(82,t-1)+xx(87,t-1),sf);
  AJsf = binan(xx(92,t-1)+xx(97,t-1),sf);
  
  MM(2,2)= p*(1-pinfAA(2))*(1-AAsf);
  MM(12,12) = p*(1-pinfAB(2))*(1-ABsf);
  MM(22,22) = p*(1-pinfAC(2))*(1-ACsf);
  MM(32,32) = p*(1-pinfAD(2))*(1-ADsf);
  MM(42,42) = p*(1-pinfAE(2))*(1-AEsf);
  MM(52,52) = p*(1-pinfAF(2))*(1-AFsf);
  MM(62,62) = p*(1-pinfAG(2))*(1-AGsf);
  MM(72,72) = p*(1-pinfAH(2))*(1-AHsf);
  MM(82,82) = p*(1-pinfAI(2))*(1-AIsf);
  MM(92,92) = p*(1-pinfAJ(2))*(1-AJsf);
  
  %Persistence of susceptible subadult males (sm)
  %Binomial flips on susceptible sm
  AAsm = binan(xx(3,t-1)+xx(8,t-1),sm);
  ABsm = binan(xx(13,t-1)+xx(18,t-1),sm);
  ACsm = binan(xx(23,t-1)+xx(28,t-1),sm);
  ADsm = binan(xx(33,t-1)+xx(38,t-1),sm);
  AEsm = binan(xx(43,t-1)+xx(48,t-1),sm);
  AFsm = binan(xx(53,t-1)+xx(58,t-1),sm);
  AGsm = binan(xx(63,t-1)+xx(68,t-1),sm);
  AHsm = binan(xx(73,t-1)+xx(78,t-1),sm);
  AIsm = binan(xx(83,t-1)+xx(88,t-1),sm);
  AJsm = binan(xx(93,t-1)+xx(98,t-1),sm);
  
  MM(3,3) = p*(1-pinfAA(3))*(1-AAsm);
  MM(13,13)=p*(1-pinfAB(3))*(1-ABsm);
  MM(23,23)=p*(1-pinfAC(3))*(1-ACsm);
  MM(33,33)=p*(1-pinfAD(3))*(1-ADsm);
  MM(43,43)=p*(1-pinfAE(3))*(1-AEsm);  
  MM(53,53)=p*(1-pinfAF(3))*(1-AFsm);  
  MM(63,63)=p*(1-pinfAG(3))*(1-AGsm);
  MM(73,73)=p*(1-pinfAH(3))*(1-AHsm);
  MM(83,83)=p*(1-pinfAI(3))*(1-AIsm);
  MM(93,93)=p*(1-pinfAJ(3))*(1-AJsm);
  
  %Arrival of susceptible adult females (af)
  MM(4,2) = p*(1-pinfAA(2))*AAsf;
  MM(14,12) = p*(1-pinfAB(2))*ABsf;
  MM(24,22) = p*(1-pinfAC(2))*ACsf;
  MM(34,32) = p*(1-pinfAD(2))*ADsf;
  MM(44,42) = p*(1-pinfAE(2))*AEsf;
  MM(54,52) = p*(1-pinfAF(2))*AFsf;
  MM(64,62) = p*(1-pinfAG(2))*AGsf;
  MM(74,72) = p*(1-pinfAH(2))*AHsf;
  MM(84,82) = p*(1-pinfAI(2))*AIsf;
  MM(94,92) = p*(1-pinfAJ(2))*AJsf;
  
  %Arrival of susceptible adult males (am)
  MM(5,3) = p*(1-pinfAA(3))*AAsm;
  MM(15,13) = p*(1-pinfAB(3))*ABsm;
  MM(25,23) = p*(1-pinfAC(3))*ACsm;
  MM(35,33) = p*(1-pinfAD(3))*ADsm;
  MM(45,43) = p*(1-pinfAE(3))*AEsm;
  MM(55,53) = p*(1-pinfAF(3))*AFsm;
  MM(65,63) = p*(1-pinfAG(3))*AGsm;
  MM(75,73) = p*(1-pinfAH(3))*AHsm;
  MM(85,83) = p*(1-pinfAI(3))*AIsm;
  MM(95,93) = p*(1-pinfAJ(3))*AJsm;
  
  %Persistence of susceptible adult females (af)
  MM(4,4) = p*(1-pinfAA(4));
  MM(14,14) = p*(1-pinfAB(4));
  MM(24,24) = p*(1-pinfAC(4));
  MM(34,34) = p*(1-pinfAD(4));
  MM(44,44) = p*(1-pinfAE(4));
  MM(54,54) = p*(1-pinfAF(4));
  MM(64,64) = p*(1-pinfAG(4));
  MM(74,74) = p*(1-pinfAH(4));
  MM(84,84) = p*(1-pinfAI(4));
  MM(94,94) = p*(1-pinfAJ(4));
  
  %Persistence of susceptible adult males (am)
  MM(5,5) = p*(1-pinfAA(5));
  MM(15,15) = p*(1-pinfAB(5));
  MM(25,25) = p*(1-pinfAC(5));
  MM(35,35) = p*(1-pinfAD(5));
  MM(45,45) = p*(1-pinfAE(5));
  MM(55,55) = p*(1-pinfAF(5));
  MM(65,65) = p*(1-pinfAG(5));
  MM(75,75) = p*(1-pinfAH(5));
  MM(85,85) = p*(1-pinfAI(5));
  MM(95,95) = p*(1-pinfAJ(5));

  %Arrival of infected infants from susceptible
  MM(6,1) = p*pinfAA(1)*(1-AAi)*(1-A);
  MM(16,11) = p*pinfAB(1)*(1-ABi)*(1-A);
  MM(26,21) = p*pinfAC(1)*(1-ACi)*(1-A);
  MM(36,31) = p*pinfAD(1)*(1-ADi)*(1-A);
  MM(46,41) = p*pinfAE(1)*(1-AEi)*(1-A);
  MM(56,51) = p*pinfAF(1)*(1-AFi)*(1-A);
  MM(66,61) = p*pinfAG(1)*(1-AGi)*(1-A);
  MM(76,71) = p*pinfAH(1)*(1-AHi)*(1-A);
  MM(86,81) = p*pinfAI(1)*(1-AIi)*(1-A);
  MM(96,91) = p*pinfAJ(1)*(1-AJi)*(1-A);
  
  %Persistence of infected infants
  
  MM(6,6)= p*(1-AAi)*(1-A);
  MM(16,16)= p*(1-ABi)*(1-A);
  MM(26,26)= p*(1-ACi)*(1-A);
  MM(36,36)= p*(1-ADi)*(1-A);
  MM(46,46)= p*(1-AEi)*(1-A);
  MM(56,56)= p*(1-AFi)*(1-A);
  MM(66,66)= p*(1-AGi)*(1-A);
  MM(76,76)= p*(1-AHi)*(1-A);
  MM(86,86)= p*(1-AIi)*(1-A);
  MM(96,96)= p*(1-AJi)*(1-A);
    
  %Arrival of infected subadult females from susceptible infants (sf)
  MM(7,1) = p*pinfAA(1)*(AAi/2)*(1-A);
  MM(17,11) = p*pinfAB(1)*(ABi/2)*(1-A);
  MM(27,21) = p*pinfAC(1)*(ACi/2)*(1-A);
  MM(37,31) = p*pinfAD(1)*(ADi/2)*(1-A);
  MM(47,41) = p*pinfAE(1)*(AEi/2)*(1-A);
  MM(57,51) = p*pinfAF(1)*(AFi/2)*(1-A);
  MM(67,61) = p*pinfAG(1)*(AGi/2)*(1-A);
  MM(77,71) = p*pinfAH(1)*(AHi/2)*(1-A);
  MM(87,81) = p*pinfAI(1)*(AIi/2)*(1-A);
  MM(97,91) = p*pinfAJ(1)*(AJi/2)*(1-A);
  
  %Arrival of infected subadult males from susceptible infants (sm)
  MM(8,1) = p*pinfAA(1)*(AAi/2)*(1-A);
  MM(18,11) = p*pinfAB(1)*(ABi/2)*(1-A);
  MM(28,21) = p*pinfAC(1)*(ACi/2)*(1-A);
  MM(38,31) = p*pinfAD(1)*(ADi/2)*(1-A);
  MM(48,41) = p*pinfAE(1)*(AEi/2)*(1-A);
  MM(58,51) = p*pinfAF(1)*(AFi/2)*(1-A);
  MM(68,61) = p*pinfAG(1)*(AGi/2)*(1-A);
  MM(78,71) = p*pinfAH(1)*(AHi/2)*(1-A);
  MM(88,81) = p*pinfAI(1)*(AIi/2)*(1-A);
  MM(98,91) = p*pinfAJ(1)*(AJi/2)*(1-A);
  
  %Arrival of infected subadult females from susceptible subadult females (sf)
  MM(7,2) = p*pinfAA(2)*(1-AAsf)*(1-A);
  MM(17,12) = p*pinfAB(2)*(1-ABsf)*(1-A);
  MM(27,22) = p*pinfAC(2)*(1-ACsf)*(1-A);
  MM(37,32) = p*pinfAD(2)*(1-ADsf)*(1-A);
  MM(47,42) = p*pinfAE(2)*(1-AEsf)*(1-A);
  MM(57,52) = p*pinfAF(2)*(1-AFsf)*(1-A);
  MM(67,62) = p*pinfAG(2)*(1-AGsf)*(1-A);
  MM(77,72) = p*pinfAH(2)*(1-AHsf)*(1-A);
  MM(87,82) = p*pinfAI(2)*(1-AIsf)*(1-A);
  MM(97,92) = p*pinfAJ(2)*(1-AJsf)*(1-A);
  
  %Arrival of infected subadult males from susceptible subadult males (sm)
  MM(8,3) = p*pinfAA(3)*(1-AAsm)*(1-A);
  MM(18,13) = p*pinfAB(3)*(1-ABsm)*(1-A);
  MM(28,23) = p*pinfAC(3)*(1-ACsm)*(1-A);
  MM(38,33) = p*pinfAD(3)*(1-ADsm)*(1-A);
  MM(48,43) = p*pinfAE(3)*(1-AEsm)*(1-A);
  MM(58,53) = p*pinfAF(3)*(1-AFsm)*(1-A);
  MM(68,63) = p*pinfAG(3)*(1-AGsm)*(1-A);
  MM(78,73) = p*pinfAH(3)*(1-AHsm)*(1-A);
  MM(88,83) = p*pinfAI(3)*(1-AIsm)*(1-A);
  MM(98,93) = p*pinfAJ(3)*(1-AJsm)*(1-A);
  
  %Persistence of infected subadult females (sf)
 
  MM(7,6)= p*(AAi/2)*(1-A);
  MM(17,16)= p*(ABi/2)*(1-A);
  MM(27,26)= p*(ACi/2)*(1-A);
  MM(37,36)= p*(ADi/2)*(1-A);
  MM(47,46)= p*(AEi/2)*(1-A);
  MM(57,56)= p*(AFi/2)*(1-A);
  MM(67,66)= p*(AGi/2)*(1-A);
  MM(77,76)= p*(AHi/2)*(1-A);
  MM(87,86)= p*(AIi/2)*(1-A);
  MM(97,96)= p*(AJi/2)*(1-A);
  
  MM(7,7)= p*(1-AAsf)*(1-A);
  MM(17,17)= p*(1-ABsf)*(1-A);
  MM(27,27)= p*(1-ACsf)*(1-A);
  MM(37,37)= p*(1-ADsf)*(1-A);
  MM(47,47)= p*(1-AEsf)*(1-A);
  MM(57,57)= p*(1-AFsf)*(1-A);
  MM(67,67)= p*(1-AGsf)*(1-A);
  MM(77,77)= p*(1-AHsf)*(1-A);
  MM(87,87)= p*(1-AIsf)*(1-A);
  MM(97,97)= p*(1-AJsf)*(1-A);
  
  %Persistence of infected subadult males (sm)
  MM(8,6)= p*(AAi/2)*(1-A);
  MM(18,16)= p*(ABi/2)*(1-A);
  MM(28,26)= p*(ACi/2)*(1-A);
  MM(38,36)= p*(ADi/2)*(1-A);
  MM(48,46)= p*(AEi/2)*(1-A);
  MM(58,56)= p*(AFi/2)*(1-A);
  MM(68,66)= p*(AGi/2)*(1-A);
  MM(78,76)= p*(AHi/2)*(1-A);
  MM(88,86)= p*(AIi/2)*(1-A);
  MM(98,96)= p*(AJi/2)*(1-A);
   
  MM(8,8)= p*(1-AAsm)*(1-A);
  MM(18,18)= p*(1-ABsm)*(1-A);
  MM(28,28)= p*(1-ACsm)*(1-A);
  MM(38,38)= p*(1-ADsm)*(1-A);
  MM(48,48)= p*(1-AEsm)*(1-A);
  MM(58,58)= p*(1-AFsm)*(1-A);
  MM(68,68)= p*(1-AGsm)*(1-A);
  MM(78,78)= p*(1-AHsm)*(1-A);
  MM(88,88)= p*(1-AIsm)*(1-A);
  MM(98,98)= p*(1-AJsm)*(1-A);
  
  %Arrival of infected adult females from susceptible subadult females (af)
  MM(9,2) = p*pinfAA(2)*(AAsf)*(1-A);
  MM(19,12) = p*pinfAB(2)*(ABsf)*(1-A);
  MM(29,22) = p*pinfAC(2)*(ACsf)*(1-A);
  MM(39,32) = p*pinfAD(2)*(ADsf)*(1-A);
  MM(49,42) = p*pinfAE(2)*(AEsf)*(1-A);
  MM(59,52) = p*pinfAF(2)*(AFsf)*(1-A);
  MM(69,62) = p*pinfAG(2)*(AGsf)*(1-A);
  MM(79,72) = p*pinfAH(2)*(AHsf)*(1-A);
  MM(89,82) = p*pinfAI(2)*(AIsf)*(1-A);
  MM(99,92) = p*pinfAJ(2)*(AJsf)*(1-A);
  
  %Arrival of infected adult males from susceptible subadult males (sm)
  MM(10,3) = p*pinfAA(3)*(AAsm)*(1-A);
  MM(20,13) = p*pinfAB(3)*(ABsm)*(1-A);
  MM(30,23) = p*pinfAC(3)*(ACsm)*(1-A);
  MM(40,33) = p*pinfAD(3)*(ADsm)*(1-A);
  MM(50,43) = p*pinfAE(3)*(AEsm)*(1-A);
  MM(60,53) = p*pinfAF(3)*(AFsm)*(1-A);
  MM(70,63) = p*pinfAG(3)*(AGsm)*(1-A);
  MM(80,73) = p*pinfAH(3)*(AHsm)*(1-A);
  MM(90,83) = p*pinfAI(3)*(AIsm)*(1-A);
  MM(100,93) = p*pinfAJ(3)*(AJsm)*(1-A);
  
  %Arrival of infected adult females from susceptible adult females (af)
  MM(9,4) = p*pinfAA(4)*(1-A);
  MM(19,14) = p*pinfAB(4)*(1-A);
  MM(29,24) = p*pinfAC(4)*(1-A);
  MM(39,34) = p*pinfAD(4)*(1-A);
  MM(49,44) = p*pinfAE(4)*(1-A);
  MM(59,54) = p*pinfAF(4)*(1-A);
  MM(69,64) = p*pinfAG(4)*(1-A);
  MM(79,74) = p*pinfAH(4)*(1-A);
  MM(89,84) = p*pinfAI(4)*(1-A);
  MM(99,94) = p*pinfAJ(4)*(1-A);
  
  %Arrival of infected adult males from susceptible adults males (am)
  MM(10,5) = p*pinfAA(5)*(1-A);
  MM(20,15) = p*pinfAB(5)*(1-A);
  MM(30,25) = p*pinfAC(5)*(1-A);
  MM(40,35) = p*pinfAD(5)*(1-A);
  MM(50,45) = p*pinfAE(5)*(1-A);
  MM(60,55) = p*pinfAF(5)*(1-A);
  MM(70,65) = p*pinfAG(5)*(1-A);
  MM(80,75) = p*pinfAH(5)*(1-A);
  MM(90,85) = p*pinfAI(5)*(1-A);
  MM(100,95) = p*pinfAJ(5)*(1-A);
  
  %Persistence of infected adult females
  MM(9,7)= p*AAsf*(1-A);
  MM(19,17)= p*ABsf*(1-A);
  MM(29,27)= p*ACsf*(1-A);
  MM(39,37)= p*ADsf*(1-A);
  MM(49,47)= p*AEsf*(1-A);
  MM(59,57)= p*AFsf*(1-A);
  MM(69,67)= p*AGsf*(1-A);
  MM(79,77)= p*AHsf*(1-A);
  MM(89,87)= p*AIsf*(1-A);
  MM(99,97)= p*AJsf*(1-A);
  
  MM(9,9)= p*(1-A);
  MM(19,19)= p*(1-A);
  MM(29,29)= p*(1-A);
  MM(39,39)= p*(1-A);
  MM(49,49)= p*(1-A);
  MM(59,59)= p*(1-A);
  MM(69,69)= p*(1-A);
  MM(79,79)= p*(1-A);
  MM(89,89)= p*(1-A);
  MM(99,99)= p*(1-A);
  
  %Persistence of infected adult males
  MM(10,8)= p*AAsm*(1-A);
  MM(20,18)= p*ABsm*(1-A);
  MM(30,28)= p*ACsm*(1-A);
  MM(40,38)= p*ADsm*(1-A);
  MM(50,48)= p*AEsm*(1-A);
  MM(60,58)= p*AFsm*(1-A);
  MM(70,68)= p*AGsm*(1-A);
  MM(80,78)= p*AHsm*(1-A);
  MM(90,88)= p*AIsm*(1-A);
  MM(100,98)= p*AJsm*(1-A);
  
  MM(10,10)= p*(1-A);
  MM(20,20)= p*(1-A);
  MM(30,30)= p*(1-A);
  MM(40,40)= p*(1-A);
  MM(50,50)= p*(1-A);
  MM(60,60)= p*(1-A);
  MM(70,70)= p*(1-A);
  MM(80,80)= p*(1-A);
  MM(90,90)= p*(1-A);
  MM(100,100)= p*(1-A);
  

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
            %SUBADULT MALE MOVEMENT
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%AA is the NG vector after demography
AA = MM*xx(:,t-1);


%This script moves the monkeys around

%First, this chooses a group to move to using a uniform random variable to pick a group. 
%Second, if the group is the same as the one supplying the move, the vector TT gets a zero entry.
%Third, a binomial draw makes a stochastic rate based on the number of monkeys in that age category in the group.
%The vector TT gets a minus entry where the monkey leaves and a positive in the group in which it moves to.

%The vector TT, NG vector which holds the movers and moved
TT=zeros(100,1);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      %Loop thru groups
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    for z=0:9
    
    %Susceptible move
    %Make a random number representing the group where the monkey will go to
    GG=round(9*rand);

%If the group is the same as where it started, need to make sure it is sum zero
        if GG==z
            TT(10*z+3)=TT(10*z+3)+0;
        else

%Move gives the stochastic rate of monkey moving, based on the number of %monkeys in that category; if this number is zero, then zeros will be passed.   
            AAmove=binan(AA(10*z+3),m);

%Moved stores the actual quantity of monkey, which must then be removed %from the first group and put into the next one
            AAmoved=AAmove*AA(10*z+3);
            TT(10*z+3)= TT(10*z+3)-AAmoved;
            TT(10*GG+3)=TT(10*GG+3)+AAmoved;
        end

%Infective move
    GG=round(9*rand);
        if GG==z
            TT(10*z+8)=TT(10*z+8)+0;
        else
            AAmove=binan(AA(10*z+8),m);
            AAmoved=AAmove*AA(10*z+8);
            TT(10*z+8)= TT(10*z+8)-AAmoved;
            TT(10*GG+8)=TT(10*GG+8)+AAmoved;
        end

    end

xx(:,t) = AA+TT;
clear AA
end

NAA = sum(xx(1:10,tmax));
IAA = sum(xx(6:10,tmax));
NAB = sum(xx(11:20,tmax));
IAB = sum(xx(16:20,tmax));
NAC = sum(xx(21:30,tmax));
IAC = sum(xx(26:30,tmax));
NAD = sum(xx(31:40,tmax));
IAD = sum(xx(36:40,tmax));
NAE = sum(xx(41:50,tmax));
IAE = sum(xx(46:50,tmax));
NAF = sum(xx(51:60,tmax));
IAF = sum(xx(56:60,tmax));
NAG = sum(xx(61:70,tmax));
IAG = sum(xx(66:70,tmax));
NAH = sum(xx(71:80,tmax));
IAH = sum(xx(76:80,tmax));
NAI = sum(xx(81:90,tmax));
IAI = sum(xx(86:90,tmax));
NAJ = sum(xx(91:100,tmax));
IAJ = sum(xx(96:100,tmax));

Ntmax=sum(xx(:,tmax));

Prevtmax=(IAA+IAB+IAC+IAD+IAE+IAF+IAG+IAH+IAI+IAJ)/Ntmax;
NN(j)=Ntmax;
PP(j)=Prevtmax;
GROUPS(j,:)=[NAA,NAB,NAC,NAD,NAE,NAF,NAG,NAH,NAI,NAJ];

end

Nmean=mean(NN);
Nste=std(NN)/sqrt(j);
Prevmean=mean(PP);
Prevste=std(PP)/sqrt(j);
GROUPSmean=mean(GROUPS);
GROUPSste=std(GROUPS)/sqrt(j);

QQ(q,1)=Nmean;
QQ(q,2)=Nste;
RR(q,1)=Prevmean;
RR(q,2)=Prevste;
end

QQ
RR