% EXAMPLE script which runs the simple model on synthetic data,
% and then plots the results.

% If on Octave, turn off the pausing of text output
try,
  more off;
end;

% Enter the proper directory
% cd ~lennartfr/common_files/mfiles

% Define parameters for data generation
N0 = [200 400 600];
q = [0.4 0.6];
s = 0.1;
M = 0.15;
startyear = 1980;
num_survey_indices = inf;
num_years = 15;
catch_factor = 2;

% Define directories and file names
cod_dir = '../cod_admb';
base_dir = pwd;
filename = [cod_dir '/cod'];

% Generate data This will create (or overwrite)
% the files cod.dat and cod.pin in the directory defined by cod_dir.
% The return variable Nt is the true trajectory (transposed)
Nt = generate_data(N0,q,s,M,filename,length(N0),num_years, ...
     length(q),num_survey_indices,startyear,catch_factor);

% Enter directory where admb program is found
cd(cod_dir);

% Run ADMB
unix('unset LD_LIBRARY_PATH; ./cod');

% Return to mfile directory and plot
cd(base_dir);
datpar2plot(filename);
% Add true trajectory to plot 
add_N_to_plot(Nt,startyear,gcf)