function N = old_generate_data(N0,q,s,M, filename, cohorts, years, surveys, observations,year_offset);
% filegenerator(N0,q,s,M, filename, cohorts, years, surveys, observations, year_offset)
%
% Generates text file for herring problem. Left out parameters are
% randomly generated.
%
% VERSION WITH SIMPLE MODEL - no random effects, and just one M!
%
% Written by Lennart Frimannslund

fprintf(2,'Hey there!\n\nThis is the OLD version. A problem with this version is that\n');
fprintf(2,'it produces survey indices for age 0, which apparently won%st happen in reality \n',char(39));
fprintf(2,'and that the constant cfactor = 1 is too large, which causes the catch to be too\n');
fprintf(2,'large.\n');



if (exist('year_offset','var')==0 | length(year_offset) == 0),
  year_offset = 1980;
end;

% Generate filename if not specified
if (exist('filename','var') == 0 | length(filename) == 0),
  c = clock;
  filename = sprintf('herring-%s-%02d.%02d.%02d',date,c(4),c(5), ...
                     floor(c(6)));
  clear c;
end;


% Get number of surveys
if (exist('q','var') ~= 0 & length(q) ~= 0),
  surveys = length(q);
end;

% s - Generate random number between 0 and 1
if (exist('s','var') == 0 | length(s) == 0),
  s = rand;
end;

% M - Generate random number between 0 and 0.2
if (exist('M','var') == 0 | length(M) == 0),
  M = rand(1,1) * 0.2;
end;


% If no of cohorts not specified - generate random number between 1 and 6
if (exist('cohorts','var') == 0 | length(cohorts) == 0),
  cohorts = ceil((rand*5)) + 1;
end;

% years - if not specified, generate random number between 5 and 25
if (exist('years','var') == 0 | length(years) == 0),
  years = ceil((rand*20)) + 5;
end;

% surveys - if not specified, generate random number between 1 and 6
if (exist('surveys','var') == 0 | length(surveys) == 0),
  surveys = ceil((rand*5)) + 1;
end;

% if not specified - generate which fraction of maximum possible
% observations available
if (exist('observations','var') == 0 | length(observations) == 0),
  observations = ceil(rand * surveys * years * cohorts);
end;


% Define N0 if not supplied 
% exp(N0) between 0 and 3
%if (exist('N0','var') == 0 | length(N0) == 0),
%  N0 = 3 * rand(1,1);
%end;

% Generate q - between 0.1 and 0.8 
if (exist('q','var') == 0 | length(q) == 0),
  q = 0.7 * rand(1,surveys) + 0.1;
end;



% Input variables now in place - generate data set itself
%
% For the most part translated line-by-line from r/s-code.
  
n = years;
m = cohorts;
%sM = t;

logs = log(s);

cfactor = 1;
alpha = 0;
%Z = (rand(1,cohorts)) - 0.5;

% TRANSPOSE OF ITS USUAL FORM!
N = zeros(n,m);

%N(1,:) = N0;
% Added "* 100" 01032010
N(1,:) = N0(:)'; 

% SAME HERE, TRANSPOSE!
CC = zeros(size(N));

%u = randn(n+m-1,1) * sM;

%for (i=2:n),
%  
%  if (i>10),
%    CC(i-1,:) = rand(1,m) * cfactor/n  .* N(i-1,:);
%  end;
%  
%  N(i,:)  = (N(i-1,:) - CC(i-1,:)) * exp(-(M+u(i)));
%  
%end;

% NEW loop, replaces the one above
for (j=1:m),
  for (i=2:n),

    if (i>2),
      CC(i-1,j) = rand(1,1) * cfactor/n * N(i-1,j);
    end;

    N(i,j) = (N(i-1,j) - CC(i-1,j)) * exp(-M);
  end;
end;

%fprintf(1,'Population trajectory:\n');
%N'

II = cell(surveys,1);
for (i=1:surveys),
 
  II{i} = q(i) * N .* exp(randn(n,m) * exp(logs));
end;

surveyraw = [];
% now create surveyraw matrix, to be put in file
for (l=1:surveys),
  surveyraw_l = zeros(years*cohorts,4);
  III = II{l};
  
  for (i = 1:cohorts),
    for (j=1:years),
      
      surveyraw_l((i-1)*years+j,:) = [i j-1 l III(j,i)];

      
    end;
  end;
  
  surveyraw = [surveyraw; surveyraw_l];
end;

% Surveyraw matrix now in place, extract #observations number of rows from
% it randomly
permutation = randperm(years*cohorts*surveys);

      
% Write to file
fid = fopen([filename '.dat'],'w');
% disp(fopen('all'));
fprintf(fid,'# Randomly generated herring file\n');
fprintf(fid,'# True values:\n');
fprintf(fid,'#\tN0: ');
fprintf(fid,'%s ',num2str(N0));
fprintf(fid,'\n');
fprintf(fid,'#\tq: ');
fprintf(fid,'%s ',num2str(q));
fprintf(fid,'\n');
fprintf(fid,'#\ts: %8.5f \n#\tM: %8.5f\n#\n',s,M);
fprintf(fid,'# True population trajectory, transpose(N):\n#\n');
for (i=1:size(N,1)),
  fprintf(fid,'# ');
  for (j=1:size(N,2)),
   fprintf(fid,'%s ',num2str(N(i,j)));
  end;
  fprintf(fid,'\n');
end;
fprintf(fid,'#\n');
fprintf(fid,'\n# m (Antall kohorter)\n %3d \n\n',cohorts);

% Endret 01032010 -- gammel kode hadde et sluttår for mye
fprintf(fid,'# Startaar for kohorter\n');
fprintf(fid,'%i ',[0:cohorts-1]+year_offset);
fprintf(fid,'\n# Sluttaar for kohorter\n');
fprintf(fid,'%i ',[years-1:years-1+cohorts-1]+year_offset);
fprintf(fid,'\n# Catches (one cohort per line)\n');

for (j=1:cohorts),
  fprintf(fid,'%5.3f ',CC(:,j)');
  fprintf(fid,'\n');
end;

fprintf(fid,'\n#Number of surveys\n %3d \n',surveys);
fprintf(fid,'#Number of survey indices\n %4d \n',observations);
fprintf(fid,'# Survey table\n');


for (i=1:observations),
  fprintf(fid,'%3d %3d %3d %6.3f\n',surveyraw(permutation(i),:));
end;

%
%for (i=1:n),
%  for (j=1:m),
%    fprintf(fid,'%3d %3d %3d %6.3f\n',j,i,1,II(i,j)); 
%
%  end;
%end;

fclose(fid);


%
%  Now generate start values for optimisation, namely
%  true values as above

% ADMB format
fid = fopen([filename '.pin'],'w');

%Changed 01032010
%fprintf(fid,'%8.3f',(N0 / 100));
fprintf(fid,'# N0\n %s \n# q',num2str(N0));

fprintf(fid,'\n');
fprintf(fid,'%8.5f',q);
fprintf(fid,'\n#logs\n');
fprintf(fid,'%8.5f',log(s));
%fprintf(fid,'\n#log(tau)\n');
%fprintf(fid,'%8.5f',log(t));
fprintf(fid,'\n#M\n');
fprintf(fid,'%8.5f\n',M);
%fprintf(fid,'\n#Z\n');
%fprintf(fid,'%d ',zeros(1,cohorts));
%fprintf(fid,'\n#epsilon\n');
%fprintf(fid,'%d ',zeros(1,years+cohorts-1));
fclose(fid);

% Added 25032010 -- input file with N0, not Z, as the variable
%fid = fopen([filename '-noZ.pin'],'w');
%
%fprintf(fid,'# N0\n');
%fprintf(fid,' %8.3f ',N(1,:)/100);
%
%fprintf(fid,'\n#q\n');
%fprintf(fid,'%8.5f',q);
%fprintf(fid,'\n#logs\n');
%fprintf(fid,'%8.5f',log(s));
%fprintf(fid,'\n#log(tau)\n');
%fprintf(fid,'%8.5f',log(t));
%fprintf(fid,'\n#M\n');
%fprintf(fid,'%8.5f',M);
%fprintf(fid,'\n#Z\n');
%fprintf(fid,'%d ',zeros(1,cohorts));
%fprintf(fid,'\n#epsilon\n');
%fprintf(fid,'%d ',zeros(1,years+cohorts-1));
%fclose(fid);

return;