function [M_PARAM_SPACE,PARAM_SPACE] = PAPER1_PAREMETER_SPACE_CONECSTREGTHvsDATASIZE(ADJ0)
%23-09-2014 esta funcion es creada para formar el parameter space para el
%paper para analizar connection stregth vs data size

rr=0;
rrr=0;
for i=0.01:0.0007:0.15
    i
    r=0;
    [CLM]=ANY_TOPOLOGY_LOGISTIC_MAPS_CREATION_2(100001,i*ADJ0);
    rr=rr+1;
    for j=1000:250:50000
        rrr=rrr+1;
        inp=sprintf('Strength %s, Size %s',num2str(i),int2str(j));
        disp(inp);
        r=r+1;
        data=CLM(end-j:end,:);
        [a,b]=PAPER1_Loop_Comparison_reconstruction_DIFF_LENGTH(data,ADJ0);
        if a==1
            PARAM_SPACE(rrr,:)=[rrr i j 1];
            M_PARAM_SPACE(rr,r)=1;
        else
            PARAM_SPACE(rrr,:)=[rrr i j b];
            M_PARAM_SPACE(rr,r)=b;
        end
    end
end
imagesc(PARAM_SPACE)
end
function [signo,cero_C]=PAPER1_Loop_Comparison_reconstruction_DIFF_LENGTH(DATA0,ADJ)
%23-09-2014 codigo para el primer Paper
%15-07-2013 version 4 not calculates DMIR because is very time demanding
%15-07-2013 code running for partial reconstructions.
%la funcion reconstruye la network para los 5 metodos siguientes
%{
1_ MI
2_ MIR_cumulative
3_ MIR_Good partition
4_ MCIR_cumulative
5_ MCIR_Good partition
%}
%% PATHS
%path_code ='/home/s11ca2/Dropbox/Chris-Ezequiel/22-10-2013_codes';
%path_results ='/home/s11ca2/Dropbox/Chris-Ezequiel/22-10-2013_codes/RESULTS/MIR_PLATO/';

%% PATH EZE

path_code ='/home/eze/Dropbox/Chris-Ezequiel/22-10-2013_codes';
path_results ='/home/eze/Dropbox/Chris-Ezequiel/22-10-2013_codes/RESULTS/PAPER1/';

%% 

GRAPHIC = 0;

data_length=length(DATA0);

clear data
DATA=DATA0;
    
    
M = size(DATA,1);
N = size(DATA,2);
loop_cero=zeros(5,1);


metodos =1% how many method we have

signo=zeros(metodos,1);
metodo{4}='MIR AVERAGE ER';
metodo{5}='MIR ER-PLAT';
metodo{1}='MIR LYAP-PLATO';
metodo{2}='MIR CUMULATIVE LYAP';
metodo{3}='MI';
% metodo{6}='TOP_ENT AVERAGE';
% metodo{7}='TOP_ENT N-Markov';
for i=1:metodos
        if i==1
            
%             str = sprintf('Method %s Running.', metodo{i});
%             disp(str);
            %[ADJ_IP,PLOT_INFO_C]=PAPER1_DeMATRIX_QINF_MIR_Average(DATA0,4,20);
            %[PLOT_INFO_C,ADJ_IP]=PAER1_De_MATRIX_MIR_COMPUTATION_SHORT_PATH(DATA0,4,20);
            %% --------------NEW 15/10/2015
            rr=0;
            for I=1:size(DATA0,2)-1
                I
                for J=I+1:size(DATA0,2)
                    rr=rr+1;
                int=[2 4 8 16 32];
                r=0;
                    for i=int
                        r=r+1;
                    %[PLOT_INFO_C,ADJ_IP]=PAPER1_De_MATRIX_MIR_COMPUTATION_SHORT_PATH(DATA0,4,20);
                    [Is,CORD] = MI_from_DIFF_PARATITIONS([DATA0(:,I) DATA0(:,J)],i,i);
                    [~,T3]=Transitive_matrix_row_SPACE_FROM_COORDS(CORD(:,4));
                    TT(r,:)=[i r Is T3]; 
                    end
                    ADJ_IP(I,J)=sum(abs(diff(TT(:,3))))/TT(end,4); 
                    PLOT_INFO_C(rr,:)=[I J sum(abs(diff(TT(:,3))))/TT(end,4)];
                end
            end
                    PLOT_INFO_C(:,3)=(PLOT_INFO_C(:,3)-min(PLOT_INFO_C(:,3)))/(max(PLOT_INFO_C(:,3))-min(PLOT_INFO_C(:,3)));
                    l=ADJ_IP>0.1e-100;
                    ADJ_IP=(ADJ_IP-min(ADJ_IP(l)))/(max(ADJ_IP(:))-min(ADJ_IP(l)));
                    l=ADJ_IP<0;
                    ADJ_IP(l)=0;
                  i=1
            %% --------------FIN NEW 15/10/2015
            
            %{
            cd(path_results)
            dlmwrite('adj_IP_PLATAU.txt',ADJ_IP);
            dlmwrite('PLOT_INFO_PLATAU.txt',PLOT_INFO_C);
            cd(path_code)
            %}
            [cero_C,V_Cero_C,signo1] = PAPER1_Comparison_reconstruction(ADJ_IP,ADJ);
            signo(i)=signo1;
            loop_cero(i)=cero_C;
            T_PLOT{i}=PLOT_INFO_C;
            T_cero(i)=cero_C;
            T_V_Cero{i}=V_Cero_C;
            if signo(i)>0
                txt=sprintf('Method %s -- Recons Length %s \n',metodo{i},num2str(cero_C));
            else
                txt=sprintf('Method %s -- Recons Porcentage %s \n',metodo{i},num2str(-1*cero_C));
                loop_cero(i)=-1*loop_cero(i);
            end
            disp(txt);
        end 
end
    
C_text_metodos=metodo;
if GRAPHIC==1
    figure
for J=1:metodos
   a=T_PLOT;
   b=T_cero;
   c=T_V_Cero;
    d=signo;
    bar(a{J},'g');
    hold on
    %------------Shadow
    x = linspace(0, 1+N*(N-1)/2); % 100 points between intersections
    yy1 =c{J}(1)*ones(1,100);   %lower function
    yy2 =c{J}(end)*ones(1,100); % upper function
    x = [x,x(end:-1:1)];        % repeat x values
    yy = [yy1,yy2];   % vector of upper & lower boundaries
    if d(J)>0
        f=fill(x,yy,'r');    % fill area defined by x & yy in blue
        txt={C_text_metodos{J},'Recons Length=',num2str(b(J))};
    else
        f=fill(x,yy,'y');    % fill area defined by x & yy in blue
        txt={C_text_metodos{J},'Recons Porcentage',num2str(-1*b(J))};
    end
    alpha(f,b(J));
    %____________End Shadow
    set(gca,'XLim',[0 1+N*(N-1)/2])
    hold off
    
end
end
end

function [ceroF,V_Cero,signo] = PAPER1_Comparison_reconstruction(adj_IP,adj,int )
%15-07-2013 porcentage added to analize the non-total reconstruction

M=length(adj);
adj=triu(adj);
if size(adj_IP,1)==M-1
    adj(end,:)=[];
end
l0=adj_IP==0;
if nargin<3
    int=0.01;
end
r=0;
rr=0;

for tr=int:int:max(adj_IP(~l0))
    l_adj_IP=adj_IP>=tr;
    diff=abs(sum(sum(abs(adj-l_adj_IP))));
    if diff==0
        r=r+1;
        cero{1}(r)=tr;
    else
        rr=rr+1;
        diff_negative=(adj-l_adj_IP);
        lpos1=diff_negative>0;
        lneg1=diff_negative<0;
        lneg{rr}=sum(lneg1(:));
        lpos{rr}=sum(lpos1(:));
        cero{2}(rr,:)=[tr 1-diff/sum(sum(adj)) rr];
        if r~=0
        end
    end
end

if isempty(cero{1})
    max_cero2=max(cero{2}(:,2));
    lmax=cero{2}(:,2)==max_cero2;
    V_Cero=cero{2}(lmax,1);
    if max_cero2<0.00001
        max_cero2=0;
        ceroF=max_cero2;
    else
        ceroF=max_cero2;
    end
    signo=-1;
else
    V_Cero=cero{1};
    ceroF=cero{1}(end)-cero{1}(1);
    signo=1;
end
end