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mfiles:mfiles [2010/12/13 15:19] – lennartfrmfiles:mfiles [2010/12/13 15:34] (current) – lennartfr
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 ====== Matlab / Octave Utilities ====== ====== Matlab / Octave Utilities ======
 +
 +This page list the various Matlab and octave utilities which interact with ADMB, typically generating input for and interpreting output from ADMB. It is meant to be as complete as possible. This means that it is likely to contain many non-essential files as well as the essential files, for defining and running data sets.
  
 ====== Files written spring 2010 ====== ====== Files written spring 2010 ======
Line 1111: Line 1113:
  
 ====== Files written autumn 2010 ====== ====== Files written autumn 2010 ======
 +
 +==== table2allCohortsModel.m ====
 +
 +<file txt table2allCohortsModel.m>
 +function table2allCohortsModel(startyear, endyear, minage, maxage, catchfile, ...
 +     surveyfile, datfile, include_weight_maturity);
 +% table2allCohortsModel(startyear, endyear, minage, maxage, catchfile, surveyfile, datfile, include_weight_and_maturity);
 +
 +
 +fid = fopen(datfile,'w');
 +
 +try,
 +  fprintf(fid,'# Auto-generated datfile\n\n');
 +
 +  fprintf(fid,'# Startyear\n%i\n\n# Endyear\n%i\n\n',startyear,endyear);
 +
 +  fprintf(fid,'# Min age\n%i\n\n# Max age\n%i\n\n',minage,maxage);
 +
 +  fprintf(fid,'# Catch\n');
 +
 +  C = load(catchfile);
 +
 +  startyear_row = find(C(:,1) == startyear);
 +  endyear_row = find(C(:,1) == endyear);
 +  
 +  minage_col = find(C(1,:) == minage);
 +  maxage_col = find(C(1,:) == maxage);
 +  
 +  for (i=startyear_row:endyear_row),
 +    for (j=minage_col:maxage_col),
 +      fprintf(fid,'%10.6f ',C(i,j));
 +    end;
 +    fprintf(fid,'\n');
 +  end;
 +  
 +  
 +  fprintf(fid,'# Survey data\n');
 +  S = load(surveyfile);
 +  
 +  startyear_row = find(S(:,1) == startyear);
 +  endyear_row = find(S(:,1) == endyear);
 +  
 +  minage_col = find(S(1,:) == minage);
 +  maxage_col = find(S(1,:) == maxage);
 +  
 +  for (i=startyear_row:endyear_row),
 +    for (j=minage_col:maxage_col),
 +      fprintf(fid,'%10.6f ',S(i,j));
 +    end;
 +    fprintf(fid,'\n');
 +  end;
 +  
 +  if (exist('include_weight_maturity','var') && include_weight_maturity == 1),
 +    
 +    mature_3_12_2009;
 +    weight_3_11_2009;
 +    mature = mature';
 +    weight = weight';
 +    
 +    fprintf(fid,'# Proportion mature at age\n');
 +    startyear_row = find(mature(:,1) == startyear);
 +    endyear_row = find(mature(:,1) == endyear);
 +    
 +    minage_col = find(mature(1,:) == minage);
 +    maxage_col = find(mature(1,:) == maxage);
 +    
 +    for (i=startyear_row:endyear_row),
 +      for (j=minage_col:maxage_col),
 + fprintf(fid,'%10.6f ',mature(i,j));
 +      end;
 +      fprintf(fid,'\n');
 +    end;
 +    
 +    
 +    
 +    fprintf(fid,'# Weight at age\n');
 +    startyear_row = find(weight(:,1) == startyear);
 +    endyear_row = find(weight(:,1) == endyear);
 +    
 +    minage_col = find(weight(1,:) == minage);
 +    maxage_col = find(weight(1,:) == maxage);
 +    
 +    for (i=startyear_row:endyear_row),
 +      for (j=minage_col:maxage_col),
 + fprintf(fid,'%10.6f ',weight(i,j));
 +      end;
 +      fprintf(fid,'\n');
 +    end;
 +    
 +    get_sondre_data;
 +    csd = [nan sondre_ages; sondre_years' sondre_sigma];
 +    
 +    fprintf(fid,'# Catch standard deviations\n');
 +    startyear_row = find(csd(:,1) == startyear);
 +    endyear_row = find(csd(:,1) == endyear);
 +    
 +    minage_col = find(csd(1,:) == minage);
 +    maxage_col = find(csd(1,:) == maxage);
 +    
 +    for (i=startyear_row:endyear_row),
 +      for (j=minage_col:maxage_col),
 + fprintf(fid,'%10.6f ',csd(i,j));
 +      end;
 +      fprintf(fid,'\n');
 +    end;
 +    
 +    
 +  end;
 +  
 +  
 +  fclose(fid);
 +
 +catch,
 +  fprintf(2,'%s\n',lasterr);
 +  fclose(fid);
 +end;
 +
 +
 +</file>
mfiles/mfiles.1292253561.txt.gz · Last modified: 2010/12/13 15:19 by lennartfr