Differences

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--- mfiles:mfiles [2010/05/05 13:23] – lennartfr
+++ mfiles:mfiles [2010/12/13 15:34] (current) – lennartfr
@@ Line 1: / Line 1: @@
 ====== 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 ======
 Here various .m-files which interact with ADMB will be listed.
@@ Line 18: / Line 22: @@
 % Enter the proper directory
-cd ~lennartfr/common_files/mfiles
+%cd ~lennartfr/common_files/mfiles
 % Define data files
@@ Line 41: / Line 45: @@
 % Run ADMB
-unix('./cod');
+unix('unset LD_LIBRARY_PATH; ./cod');
 % Return to mfile directory and plot
@@ Line 1106: / Line 1110: @@
   fclose(fid);
 end;
+</file>
+====== 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>