[avida-cvs] avida CVS commits: /current/doc analyze_mode.html

[mercere99]

mercere99		Fri Dec  5 13:40:39 2003 EDT

  Modified files:              
    /avida/current/doc	analyze_mode.html 
  Log:
  Modified documentation to include new analyze commands.
  Also: last commit should have also included a new '-i' command line
  option to start analyze mode interactively.
  
  
Index: avida/current/doc/analyze_mode.html
diff -u avida/current/doc/analyze_mode.html:1.4 avida/current/doc/analyze_mode.html:1.5
--- avida/current/doc/analyze_mode.html:1.4	Sat Oct 11 09:34:30 2003
+++ avida/current/doc/analyze_mode.html	Fri Dec  5 13:40:39 2003
@@ -53,6 +53,19 @@
         symbol associated with each instruction; this command is simply
         followed by a sequence of such symbols that is than translated back
         into a proper genotype.
+<tr><td><b>LOAD_MULTI_DETAIL [<font color="#0000AA">start-UD</font>] [<font color="#0000AA">step-UD</font>] [<font color="#0000AA">stop-UD</font>] [<font color="#008800">dir='./'</font>] [<font color="#008800">start batch=0</font>]</b><br>
+   Allows the user to load in multiple detail files at once, one per
+   batch.  This is helpful when you're trying to do parallel analysis
+   on many detail files, or else to create a phylogenetic depth map.<br>
+
+   Example: <tt>LOAD_MULTI_DETAIL 100 100 100000 ../my_run/run100/</tt><br>
+
+   This would load in the files detail_pop.100 through detail_pop.100000 
+   in steps of 100, from the directory of my choosing.  Since 1000 files will
+   be loaded and we didn't specify starting batch, they will be put in
+   batches 0 through 999.
+
+
 </table>
 
 <p>
@@ -234,6 +247,13 @@
         The cells in the chart indicate the fitness were a mutation to
         occur at the position in the matrix, to the listed instruction.
         If the "html" flag is used, the charts will be output in HTML format.
+<tr><td><b>MAP_DEPTH [<font color="#008800">filename='depth_map.dat'</font>] [<font color="#008800">min_batch=0</font>] [<font color="#008800">max_batch=cur_batch-1</font>]</b><br>
+       This will create a depth map (like those we use for phylogeny
+       visualization) in the filename specified.  You can direct which
+       batches to take this from, but by default it will work perfectly after
+       a LOAD_MULTI_DETAIL.
+
+    
 <tr><td><b>AVERAGE_MODULATITY [<font color="#008800">file="modularity.dat"</font>]
 	[<font color="#008800">task.0 task.1 task.2 task.3 task.4 task.5      
 	task.6 task.7 task.8</font>] </b><br>