% Figure making loop for Rostock workshop
%   for output from Nstochseq_rostock07_workshop
%   October 2007
%this will work for up to 12 environmental states
% 
%
%  the limiting factor is the no. of rows of the plotsyms matrix
%  another limiting factor is the no. of columns of the stuff matrix...this
%   program will work in that sense up to and including 99 environmental states

close all
clear all

load AE_base
load AE_Markov
load AE_survmarkov

plotsyms=['b ';'g ';'r ';'c ';'m ';'y ';'b:';'g:';'r:';'c:';'m:';'y:'];     

for i=1:nstates
    if i<10
stuff1(i,:)=['initial state  ' num2str(i)]; %pads the spaces so we can then have two digits
stuff2(i,:)=['constant state  ' num2str(i)];
stuff3(i,:)=['state  ' num2str(i)];
xvalues2(i,:)=[' ' num2str(i)]; %string labels
xtick2(i)=i; %numeric values
    else 
stuff1(i,:)=['initial state ' num2str(i)];
stuff2(i,:)=['constant state ' num2str(i)];
stuff3(i,:)=['state ' num2str(i)];
xvalues2(i,:)=[num2str(i)]; %string labels
xtick2(i)=i; %numeric values
    end
    end;

stuff1=[stuff1
        'plateau         '];
stuff2=[stuff2
       'constant mean    '];

for i=1:nstages
       if i<10
stagelegend(i,:)=['stage  ' num2str(i)]; %pads the spaces so we can then have two digits
 xvalues1(i,:)=[' ' num2str(i)]; %string labels
 xtick1(i)=i; %numeric values
   
       else 
stagelegend(i,:)=['stage ' num2str(i)];
xvalues1(i,:)=[num2str(i)]; %string labels
xtick1(i)=i; %numeric values

       end ;
end;

figure(1)
subplot(2,1,1)
for i=1:nstates
plot(mu_markov(i,:),plotsyms(i,:),'linewidth',2);
hold on;
end;
plot(repmat(plateau_markov,1,maxage),'k','linewidth',2);
legend(stuff1);
%text(maxage/10,1.2*slope_markov,['-log(\lambda)']) 
title(['Markov environment, ' name(1,:), '\it{-log \lambda_{m}} = ' num2str(plateau_markov) ]);
ylabel('Mortality rate, \it{\mu_{a}(x)}','FontName','Helvetica','FontSize',16);
%xlabel('Age{\it x}, yrs','FontName','Helvetica','FontSize',16);
axis( [0 maxage min(min(mu_markov)) max(max(mu_markov))] );
hold off;

subplot(2,1,2)
for i=1:nstates
plot(qcon_mu(i,:),plotsyms(i,:),'linewidth',2);
hold on;
end;
plot(qbar_mu,'k','linewidth', 2)
legend(stuff2);
title(['Deterministic environment, \it{-log \lambda_{qbar}}= ' num2str(qbar_plateau)])
ylabel('Mortality rate, \it{\mu_x}','FontName','Helvetica','FontSize',16);
xlabel('Age{\it x}, yrs','FontName','Helvetica','FontSize',16);
axis( [0 maxage min(min(mu_markov)) max(max(mu_markov))] );
hold off;

figure(2)
bar(qbar_deaths(1,:))
title(['Deterministic environment: ' stuff2(end,:)])
ylabel('Proportion of Deaths','FontName','Helvetica','FontSize',16);
xlabel('Age{\it x}, yrs','FontName','Helvetica','FontSize',16);
axis( [0 maxage/3 0 max(max(deaths_markov))]);

for i=1:nstates
    figure(2+i)
    bar(deaths_markov(i,:))
    title(['Markov environment: ' stuff1(i,:)])
    ylabel('Proportion of Deaths','FontName','Helvetica','FontSize',16);
    xlabel('Age{\it x}, yrs','FontName','Helvetica','FontSize',16);
    axis( [0 maxage/3 0 max(max(deaths_markov))]);
end

figure
bar(lifeexp_markov');
ylabel('Remaining life expectancy, yrs')
title(['Markov environment'])
legend(stuff1(1:nstates,:))
xlabel('stage')

figure;
subplot(2,1,1)
barh(us_markov','stacked');
legend(stagelegend);
ylabel('State')
xlabel('Proportion in dominant eigenvector')
subplot(2,1,2)
barh(u_markov)
ylabel('Stage')
xlabel('Proportion in dominant eigenvector')

figure
%xtick=[1 2 3 4 5 6 7 8];
%xvalues=['seed     ';'sdling   ';'juvenile ';'pre-rep  ';'smallrep ';'medrep   ';'largerep ';'xlargerep']; % ares only
bar(qcon_oneperiodsurvival');
ylabel('One period survival')
legend(stuff3(1:nstates,:))
%set(gca,'XTick',xtick); %ares only
%set(gca,'XTickLabel',{xvalues},'FontName','Helvetica','FontSize',14)
xlabel('Stage')




figure
subplot(1,2,2)
bar(pis)
ylabel('Frequency','FontName','Helvetica','FontSize',16);
xlabel('Habitat state','FontName','Helvetica','FontSize',16);
subplot(1,2,1)
compass(hab_eigs);
title([name(1,:)])


%dot patterns for demography in each environmental state
for kk=1:nstates;% starts the loop over states
mat= qs(:,:,kk); % the first q matrix is in when kk=1 

dotsize=[100 85 70 55 40 25 10 5 1]; %defines dot sizes 
dotsize=dotsize/2; %rescale for multiple subplots

% get the structure of the matrix by transition magnitude 
mats=zeros(nstages,nstages,length(dotsize));

mats(:,:,1) =  mat>=1;
mats(:,:,2) = (mat>=.75 & mat<1);
mats(:,:,3) = (mat>=.50 & mat<.75);
mats(:,:,4) = (mat>=.25 & mat<.5);
mats(:,:,5) = (mat>=.1 & mat<.25);
mats(:,:,6) = (mat>=0.01 & mat<.1);
mats(:,:,7) = (mat>=0.001 & mat<.01);
mats(:,:,8) = (mat>=0.0001 & mat<.001);
mats(:,:,9) = (mat<0.0001 & mat>0);

matdiag = eye(nstages);

figure %since the brujo plot matrices in positions 5-8, 
%subplot(2,2,b-4)
for i=1:length(dotsize)
%spy(mats(:,:,i),dotsize(i),'k'); %makes the dots black, does not work in
%MATLAB 7
spy(mats(:,:,i),dotsize(i));
hold on;
end;
%spy(matdiag,10,'w+'); %mark the diagonal with white plus
text(5,1,[stuff3(kk,:)]); 
%xvalues=['1';'2';'3';'4';'5';'6';'7';'8']; now defined at outset
set(gca,'XTick',xtick1);
set(gca,'XTickLabel',{xvalues1},'FontName','Helvetica','FontSize',10)
set(gca,'YTick',xtick1);
set(gca,'YTickLabel',{xvalues1},'FontName','Helvetica','FontSize',10)
xlabel('Stage at time {\it t}','FontName','Helvetica','FontSize',12)
ylabel('Stage at time {\it t+1}','FontName','Helvetica','FontSize',12)
hold off;
end; %ends the loop over states

%dot patterns for habitat transitions
mat= cmat; % the habitat transition matrix 

dotsize=[100 85 70 55 40 25 10 5 1]; %defines dot sizes 
dotsize=dotsize/2; %rescale for multiple subplots

% get the structure of the matrix  
mats=zeros(nstates,nstates,length(dotsize));

mats(:,:,1) =  mat>=1;
mats(:,:,2) = (mat>=.75 & mat<1);
mats(:,:,3) = (mat>=.50 & mat<.75);
mats(:,:,4) = (mat>=.25 & mat<.5);
mats(:,:,5) = (mat>=.1 & mat<.25);
mats(:,:,6) = (mat>=0.01 & mat<.1);
mats(:,:,7) = (mat>=0.001 & mat<.01);
mats(:,:,8) = (mat>=0.0001 & mat<.001);
mats(:,:,9) = (mat<0.0001 & mat>0);

matdiag = eye(nstages);

figure  
for i=1:length(dotsize)
%spy(mats(:,:,i),dotsize(i),'k'); %makes the dots black, does not work in
%MATLAB 7
spy(mats(:,:,i),dotsize(i));
hold on;
end;
%spy(matdiag,10,'w+'); %mark the diagonal with white plus
text(5,1,['Habitat transitions']); 
%xvalues=['1';'2';'3';'4';'5';'6';'7';'8']; now defined at outset
set(gca,'XTick',xtick2);
set(gca,'XTickLabel',{xvalues2},'FontName','Helvetica','FontSize',10)
set(gca,'YTick',xtick2);
set(gca,'YTickLabel',{xvalues2},'FontName','Helvetica','FontSize',10)
xlabel('State at time {\it t}','FontName','Helvetica','FontSize',12)
ylabel('State at time {\it t+1}','FontName','Helvetica','FontSize',12)
hold off;

%dot patterns megamatrix
mat= m; % the megamatrix 

dotsize=[100 85 70 55 40 25 10 5 1]; %defines dot sizes 
dotsize=dotsize/2; %rescale for multiple subplots

% get the structure of the matrix  
mats=zeros(nstates*nstages,nstates*nstages,length(dotsize));

mats(:,:,1) =  mat>=1;
mats(:,:,2) = (mat>=.75 & mat<1);
mats(:,:,3) = (mat>=.50 & mat<.75);
mats(:,:,4) = (mat>=.25 & mat<.5);
mats(:,:,5) = (mat>=.1 & mat<.25);
mats(:,:,6) = (mat>=0.01 & mat<.1);
mats(:,:,7) = (mat>=0.001 & mat<.01);
mats(:,:,8) = (mat>=0.0001 & mat<.001);
mats(:,:,9) = (mat<0.0001 & mat>0);

matdiag = eye(nstages);

figure  
for i=1:length(dotsize);
%spy(mats(:,:,i),dotsize(i),'k'); %makes the dots black, does not work in
%MATLAB 7
spy(mats(:,:,i),dotsize(i));
hold on;
end;
%spy(matdiag,10,'w+'); %mark the diagonal with white plus
text(5,1,['State-stage transitions']); 
%xvalues=['1';'2';'3';'4';'5';'6';'7';'8']; now defined at outset
%set(gca,'XTick',xtick2);
%set(gca,'XTickLabel',{xvalues2},'FontName','Helvetica','FontSize',10)
%set(gca,'YTick',xtick2);
%set(gca,'YTickLabel',{xvalues2},'FontName','Helvetica','FontSize',10)
xlabel('State-stage at time {\it t}','FontName','Helvetica','FontSize',12)
ylabel('State-stage at time {\it t+1}','FontName','Helvetica','FontSize',12)
hold off;