[Avida-SVN] r2943 - development/documentation
blwalker at myxo.css.msu.edu
blwalker at myxo.css.msu.edu
Fri Nov 14 14:26:03 PST 2008
Author: blwalker
Date: 2008-11-14 17:26:03 -0500 (Fri, 14 Nov 2008)
New Revision: 2943
Modified:
development/documentation/analyze.html
development/documentation/inst_set.html
Log:
Fixing some documentation files that ended up with obsolete versions after the collect-branch merge. Sorry about that, guys.
Thanks to Ben for bringing this to my attention.
Modified: development/documentation/analyze.html
===================================================================
--- development/documentation/analyze.html 2008-11-14 19:15:49 UTC (rev 2942)
+++ development/documentation/analyze.html 2008-11-14 22:26:03 UTC (rev 2943)
@@ -6,7 +6,7 @@
<body>
<div class="revision">
-Revised 2006-09-03 DMB
+Revised 2007-07-01 CAO
</div>
<p><a href="index.html">Return to the Index</a></p>
@@ -370,7 +370,7 @@
format indicates the layout of columns in the file. If the filename
specified ends in <kbd>.html</kbd>, html formatting will be used instead of
plain text. For the format, see the section on
- <a href="#OUTPUT_FORMATS">Output Formats</a> below.
+ <a href="#GENOTYPE_STATS">Genotype Statistics</a> below.
</dd>
<dt><strong>
DETAIL_TIMELINE [<span class="cmdargopt">file='detail_timeline.dat'</span>]
@@ -573,13 +573,14 @@
<p> </p>
-<h2><a name="OUTPUT_FORMATS">Output Formats</a></h2>
+<h2><a name="GENOTYPE_STATS">Genotype Statistics</a></h2>
<p>
-Several commands (such as DETAIL and MAP) require format parameters
-to specify what genotypic features should be output. Before the
-such commands are used, other collection functions may need to be
-run.
+ Avida analyze mode recognizes several keywords that correspond to information about genotypes.
+ Several commands (such as DETAIL and MAP) require the use of these as format parameters
+ to specify what genotypic features should be output. Others (such as FILTER) use them to identify
+ specific genotypes that possess certain qualities. Before these commands are used, other
+ processing functions may need to be run.
</p>
<p>
Allowable formats after a normal load (assuming these values were available
@@ -590,17 +591,21 @@
<tr>
<td width="33%"><strong>id</strong> (Genome ID)</td>
<td width="33%"><strong>parent_id</strong> (Parent ID)</td>
- <td width="33%"><strong>num_cpus</strong> (Number of CPUs)</td>
+ <td width="33%"><strong>parent2_id</strong> (Second Parent ID in sexual genotypes)</td>
</tr>
<tr>
+ <td width="33%"><strong>num_cpus</strong> (Number of CPUs)</td>
<td><strong>total_cpus</strong> (Total CPUs Ever)</td>
<td><strong>length</strong> (Genome Length)</td>
- <td><strong>update_born</strong> (Update Born)</td>
</tr>
<tr>
+ <td><strong>update_born</strong> (Update Born)</td>
<td><strong>update_dead</strong> (Update Dead)</td>
<td><strong>depth</strong> (Tree Depth)</td>
+</tr>
+<tr>
<td><strong>sequence</strong> (Genome Sequence)</td>
+ <td><strong>task_list</strong> (List of all tasks performed)</td>
</tr>
</table>
</div>
@@ -627,6 +632,12 @@
<td><strong>div_type</strong> (Divide type used; 1 is default)</td>
</tr>
<tr>
+ <td><strong>mate_id</strong> (Mate Selection ID Number
+ (sexual genotypes))</td>
+ <td><strong>executed_flags</strong> (Executed Flags)</td>
+ <td><strong>task_order</strong> (Task Performance Order)</td>
+</tr>
+<tr>
<td><strong>task.n</strong> (# of times task number n is done)</td>
<td><strong>task.n:binary</strong> (is task n done, 0/1)</td>
<td><strong>total_task_count</strong> (# of different tasks done)</td>
@@ -652,14 +663,17 @@
<table width="95%">
<tr>
<td width="50%"><strong>parent_dist</strong> (Parent Distance)</td>
+ <td width="50%"><strong>ancestor_dist</strong> (Ancestor Distance)</td>
+</tr>
+<tr>
<td width="50%"><strong>comp_merit_ratio</strong>, (Computational Merit Ratio with parent)</td>
+ <td><strong>efficiency_ratio</strong> (Replication Efficiency Ratio with parent)</td>
</tr>
<tr>
- <td><strong>efficiency_ratio</strong> (Replication Efficiency Ratio with parent)</td>
<td><strong>fitness_ratio</strong> (Fitness Ratio with parent)</td>
+ <td><strong>parent_muts</strong> (Mutations from Parent)</td>
</tr>
<tr>
- <td><strong>parent_muts</strong> (Mutations from Parent)</td>
<td><strong>html.sequence</strong> (Genome Sequence in Color; html format)</td>
</tr>
</table>
Modified: development/documentation/inst_set.html
===================================================================
--- development/documentation/inst_set.html 2008-11-14 19:15:49 UTC (rev 2942)
+++ development/documentation/inst_set.html 2008-11-14 22:26:03 UTC (rev 2943)
@@ -5,9 +5,7 @@
</head>
<body>
-<div class="revision">
-Revised 2006-09-05 DMB
-</div>
+<div class="revision">Revised 2007-03-20 BEB</div>
<p><a href="index.html">Return to the Index</a></p>
<hr />
@@ -22,7 +20,7 @@
define how that instruction should be used. The exact format is as follows:
</p>
<p>
-<code>inst-name redundancy cost ft_cost prob_fail</code>
+<code>inst-name redundancy cost ft_cost energy_cost prob_fail</code>
</p>
@@ -50,13 +48,17 @@
executed. This is used to lower the diversity of instructions
inside an organism. The default value here is 0.
</dd>
-<dt><strong>prob_fail</strong></dt>
+<dt><strong>energy_cost</strong></dt>
<dd>
+ The number of Energy units required to execute this instruction. Zero is the default if this value is not specified.
+</dd>
+<dt><strong>prob_fail</strong>
+<dd>
The probability of this instruction not working properly. If an
instruction fails it will simply do nothing, but still cost the
CPU cycles to execute. The defailt probability of failure is zero.
</dd>
-</dl>
+ </dl>
<p>
Normally only the first column of numbers is used in the file.
@@ -301,6 +303,10 @@
it has made a full 360 degree turn, or else it finds an organism that
possesses the complement label.
+<h3><code>rotate-label</code></h3>
+
+Rotates the calling organism to the direction specified by the label that follows. If no label is present the organisms rotates to face south.
+
<h3><code>div-asex</code></h3>
Same as h-divide (added for symetry with the divide-sex).
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