[Avida-cvs] [avida-svn] r907 - development/documentation
brysonda at myxo.css.msu.edu
brysonda at myxo.css.msu.edu
Tue Aug 29 18:31:05 PDT 2006
Author: brysonda
Date: 2006-08-29 21:31:04 -0400 (Tue, 29 Aug 2006)
New Revision: 907
Modified:
development/documentation/actions.html
development/documentation/analyze.html
development/documentation/analyze_samples.html
development/documentation/config.html
development/documentation/inst_set.html
development/documentation/print_data.html
development/documentation/structure.html
development/documentation/svn.html
Log:
Update Analyze Samples and PrintData Options documentation.
Modified: development/documentation/actions.html
===================================================================
--- development/documentation/actions.html 2006-08-29 18:36:08 UTC (rev 906)
+++ development/documentation/actions.html 2006-08-30 01:31:04 UTC (rev 907)
@@ -160,7 +160,7 @@
<h2><a name="PrintActions">Print Actions</a></h2>
<p>
-Output events are the primary way of saving data from an avida experiments.
+Output events are the primary way of saving data from an Avida experiments.
The main two types are <em>continuous output</em>, which append to a single file
every time the event is trigged, and <em>singular output</em>, which produce
a single, complete file for each trigger.
@@ -924,7 +924,7 @@
Save a clone of this organism to the file specified; if no filename is
given, use the name clone.<em>update</em>. The update number allows regular
clones with distinct filenames to be saved with the same periodic event.
- Running <kbd>avida -l filename</kbd> will start an avida population with the
+ Running <kbd>avida -l filename</kbd> will start an Avida population with the
saved clone. Note that a clone only consists of the genomes in
the population, and their current state is lost, so the run may not
proceed identically as to if it had continued as it was going.
Modified: development/documentation/analyze.html
===================================================================
--- development/documentation/analyze.html 2006-08-29 18:36:08 UTC (rev 906)
+++ development/documentation/analyze.html 2006-08-30 01:31:04 UTC (rev 907)
@@ -57,7 +57,7 @@
<dt><strong>LOAD_ORGANISM [<font color="#0000AA">filename</font>]</strong></dt>
<dd>
Load in a normal single-organism file of the type that is output
- from avida. These consist of lots of organismal information inside
+ from Avida. These consist of lots of organismal information inside
of comments, and then the full genome of the organism with one
instruction per line.
</dd>
Modified: development/documentation/analyze_samples.html
===================================================================
--- development/documentation/analyze_samples.html 2006-08-29 18:36:08 UTC (rev 906)
+++ development/documentation/analyze_samples.html 2006-08-30 01:31:04 UTC (rev 907)
@@ -1,24 +1,32 @@
<html>
-<title>Sample Programs from Analyze Mode</title>
-<body
- bgcolor="#FFFFFF"
- text="#000000"
- link="#0000AA"
- alink="#0000FF"
- vlink="#000044">
+<head>
+ <title>Avida : Sample Programs from Analyze Mode</title>
+</head>
+<body>
-<h2 align=center>Sample Programs from Analyze Mode</h2>
+<div style="float: right">
+Revised 2006-08-29 DMB
+</div>
+<p><a href="index.html">Return to the Index</a></p>
+<hr />
+
+<div align="center">
+<h1>Sample Programs from Analyze Mode</h1>
+</div>
+
<p>
This document gives some example analyze programs and explains how they
function.
+</p>
-<h3>Testing a genome sequence</h3>
+<p> </p>
+<h2>Testing a genome sequence</h2>
<p>
The following program will load in a genome sequence, run it through a test
CPU, and output the information about it in a couple of formats.
-
+</p>
<pre>
VERBOSE
LOAD_SEQUENCE rmzavcgmciqqptqpqcpctletncogcbeamqdtqcptipqfpgqxutycuastttva
@@ -29,7 +37,7 @@
</pre>
<p>
-This program starts off with the "VERBOSE" command so that avida will print
+This program starts off with the VERBOSE command so that Avida will print
to the screen all of the details about what is going on as it runs the
analyze script; I recommend you begin all of your programs this way for
debugging purposes. The program then uses the LOAD_SEQUENCE command to allow
@@ -37,7 +45,7 @@
will translate the genome into the proper genotype as long as you are using
the correct instruction set file, since that file determines the mappings of
letters to instructions).
-
+</p>
<p>
The RECALCULATE command places the genome sequence into a test CPU, and
determines its fitness, merit, gestation time, etc. so that the DETAIL
@@ -46,46 +54,48 @@
and PRINT commands will then print individual files about this genome, the
first tracing its execution line-by-line, and the second summarizing all
sorts of statistics about it and displaying the genome.
-Since no directory was specified for these commands, "<tt>genebank/</tt>" is
-assumed, and the filenames are "<tt>org-S1.trace</tt>" and
-"<tt>org-S1.gen</tt>". If a genotype has a name when it is loaded, that
+Since no directory was specified for these commands, <kbd>archive/</kbd> is
+assumed, and the filenames are <kbd>org-S1.trace</kbd> and
+<kbd>org-S1.gen</kbd>. If a genotype has a name when it is loaded, that
name will be kept, but if it doesn't, it will be assigned a name starting at
org-S1, then org-S2, and so on counting higher. The TRACE and PRINT commands
add their own suffixes to the genome's name to determine the filename they
will be printed as.
-<h3>Using Variables</h3>
+<p> </p>
+<h2>Using Variables</h2>
+
<p>
Often, you will want to run the same section of analyze code with multiple
-different "inputs" each time through, or else you might simply want a single
+different inputs each time through, or else you might simply want a single
value to be easy to change throughout the code. To facilitate such
programming practices, variables are available in analyze mode that can be
altered for each repitition through the code.
-
+</p>
<p>
There are actually several types of variables, all of which are a single
letter of number. For a command that requires a variable name as an input,
you simply put that variable where it is requested. For example, if you
were going to set the variable i to be equal to the number 12, you would
type:
-
+</p>
<pre>
SET i 12
</pre>
<p>
-But later on in the code, how does avida know when you type an i if you
+But later on in the code, how does Avida know when you type an i if you
really want the letter 'i' there, or if you prefer the number 12 to be there?
-To distinguish these cases, you must put a dollar sign ("$") before a variable
+To distinguish these cases, you must put a dollar sign '$' before a variable
wherever you want it to be translated to its value instead of just using
the variable name itself.
-
+</p>
<p>
There are a few different commands that allow you to manipulate a variable's
value, and sometimes execute a section of code multiple times based off of
each of the possible values. Here is one example:
-
+</p>
<pre>
FORRANGE i 100 199
SET d /home/charles/dev/avida/runs/evo-neut/evo_neut_$i
@@ -102,7 +112,7 @@
Thus the first time through the loop, 'i' will be equal to the value '100',
then '101', '102', all the way up to '199'. In this particular case, we have
100 runs (numbered 100 through 199) that we want to work with.
-
+</p>
<p>
The first thing we do once we're inside the loop is set the value of the
variable 'd' to be the name of the directory we're going to be working
@@ -110,31 +120,34 @@
it over every time we need it. If we set it to the variable d, then all we
need to do is type '$d' in the future, and it will be translated to the
full name. Note that in this case we are setting a variable to a string
-instead of a number; that's just fine and avida will figure out how to
+instead of a number; that's just fine and Avida will figure out how to
handle it properly. This directory we are working with will change each
time through the loop, and that it is no problem to use one variable as part
of setting another.
-
+</p>
<p>
After we know what directory we are using, we run a PURGE_BATCH to get rid of
all of the genotypes from the last time through
the loop (lest we just keep building up more and more genotypes in the
current batch)
and then we refill the batch by using LOAD_DETAIL_DUMP to load in all of the
-genotypes saved in the file "<tt>detail_pop.100000</tt>" within our chosen
+genotypes saved in the file <kbd>detail-100000.pop</kbd> within our chosen
directory. The RECALCULATE command runs all of the genotypes through a
test CPU so we have all the statistics we need, and finally DETAIL will print
-out the stats we want to the file "<tt>detail.dat</tt>", again
+out the stats we want to the file <kbd>detail.dat</kbd>, again
placing it in the proper directory. The END command signifies the end of the
FORRANGE loop.
+</p>
-<h3>Finding Lineages</h3>
+<p> </p>
+<h2>Finding Lineages</h2>
+
<p>
-Quite often, the portion of an avida run that we will be most interested
+Quite often, the portion of an Avida run that we will be most interested
in is the lineage from the final dominant genotype back to the original
-ancestor. As such, there are tools in avida to get at this information.
-
+ancestor. As such, there are tools in Avida to get at this information.
+</p>
<pre>
FORRANGE i 100 199
SET d /home/charles/dev/avida/runs/evo-neut/evo_neut_$i
@@ -160,12 +173,12 @@
pick out a single genotype, and discard everything else except for its
lineage. In this case, we pick the genotype with the highest abundance
(the most virtual CPUs associated with it) at the time of printing.
-
+</p>
<p>
As before, the RECALCULATE command gets us any additional information we
may need about the genotypes, and then we print that information to a file
using the DETAIL command. The filenames that we are using this time
-have the format "<tt>lineage.$i.html</tt>", so they are all being written
+have the format <kbd>lineage.$i.html</kbd>, so they are all being written
to the current directory with filenames that incorporate the run number
right in them. Also, because the filename ends in the suffix '.html', Avida
knows to print the file in a proper html format. Note that the specific
@@ -173,16 +186,19 @@
lineage (and hence measured things like the genetic distance to the parent)
and are in html mode (and thus can print the sequence using colors to specify
where exactly mutations occurred).
+</p>
-<h3>Working with Batches</h3>
+<p> </p>
+<h2>Working with Batches</h2>
+
<p>
In analyze mode, we can load genotypes into multiple batches and we then
operate on a single batch at a time. So, for example, if we wanted
to only consider the dominant genotypes at time points 100 updates apart, but
-all we had to work with were the detail files (containing <i>all</i>
+all we had to work with were the detail files (containing <em>all</em>
genotypes at each time point) we might write a program like:
-
+</p>
<pre>
SET d /home/charles/avida/runs/mydir/here-it-is
SET_BATCH 0
@@ -205,17 +221,20 @@
over into batch one. By the time we're done, we have all of the dominant
genotypes inside of batch one, so we can print anything we need right from
there.
+</p>
-<h3>Building your own Commands</h3>
+<p> </p>
+<h2>Building your own Commands</h2>
+
<p>
One really useful feature that I have added to the analyze mode is the
ability for the user to construct a variety of their own commands without
modifying the source code. This is done with the FUNCTION command.
For example, if you know you will always need a file called
-"<tt>lineage.html</tt>" with very specific information in it, you might write
+<kbd>lineage.html</kbd> with very specific information in it, you might write
a helper command for yourself as follows:
-
+</p>
<pre>
FUNCTION MY_HTML_LINEAGE # arg1=run_directory
PURGE_BATCH
@@ -230,13 +249,13 @@
<p>
This works identically to how we found lineages and printed their data in
the section above. Only this time, it has created the new command called
-"MY_HTML_LINEAGE" that you can use anytime thereafter. Arguments to functions
+MY_HTML_LINEAGE that you can use anytime thereafter. Arguments to functions
work similar to variables, but they are numbers instead of letters. Thus
$1 translates to the first arguments, $2 becomes the second, and so on. You
are limited to 9 arguments at this point, but that should be enough for
most tasks. $0 is the name of the function you are running, in case you
ever need to use that.
-
+</p>
<p>
You may be interested in also using functions in conjunction with the
SYSTEM command. Anything you type as arguments to this command gets run on
@@ -244,7 +263,7 @@
otherwise be done were you at the shell prompt. For example, imagine that
you were going to use a lot of compressed files in your analysis that you
would first need to uncompress. You might right a function like:
-
+</p>
<pre>
FUNCTION UNZIP # Arg1=filename
SYSTEM gunzip $1
@@ -254,14 +273,14 @@
<p>
This is a shorter example than you might typically want to write a function
for, but it does get the point across. This would allow you to just type
-"UNZIP <filename>" whenever you needed to uncompress something.
-
+<code>UNZIP <filename></code> whenever you needed to uncompress something.
+</p>
<p>
Functions are particularly useful in conjunction with the INCLUDE command.
-You can create a file called something like "<tt>my_functions.cfg</tt>" in
-your avida work directory, define a bunch of functions there, and then start
-all of your <tt>analyze.cfg</tt> files with the line:
-
+You can create a file called something like <kbd>my_functions.cfg</kbd> in
+your Avida work directory, define a bunch of functions there, and then start
+all of your <kbd>analyze.cfg</kbd> files with the line:
+</p>
<pre>
INCLUDE my_functions.cfg
</pre>
@@ -271,54 +290,60 @@
this language becomes more flexible, so will your ability to
create functions within the language, so you will be able to develop
flexible and useful libraries for yourself.
+</p>
-<h3>Try it Out...</h3>
+<p> </p>
+<h2>Try it Out...</h2>
+
<p>
Here are a couple of example problems you can try to see how well you can
use analyze mode. These should get you used to working with it for future
projects.
-
+</p>
<p>
-<b>Problem 1</b>. A detail file in avida contains one line associated with
- each genotype, in order from the most abundant to the least. Currently,
- the LOAD_DETAIL_DUMP command will load the entire file's worth of
- genotypes into the current batch, but what if you only wanted the top
- few? You should write a function called "LOAD_DETAIL_TOP" that takes
- two arguments. The first ($1) is the name file that needs to be loaded
- in (just as in the original command), and the second is the number of
- lines you want to load.
-
+<strong>Problem 1</strong>. A detail file in Avida contains one line associated with
+each genotype, in order from the most abundant to the least. Currently,
+the LOAD_DETAIL_DUMP command will load the entire file's worth of
+genotypes into the current batch, but what if you only wanted the top
+few? You should write a function called LOAD_DETAIL_TOP that takes
+two arguments. The first ($1) is the name file that needs to be loaded
+in (just as in the original command), and the second is the number of
+lines you want to load.
+</p>
<p>
- The easiest way to go about doing this is by using the SYSTEM command
- along with the Unix command "<tt>head</tt>" which will output the very
- top of a file. If you typed the line:
-
+The easiest way to go about doing this is by using the SYSTEM command
+along with the Unix command <kbd>head</kbd> which will output the very
+top of a file. If you typed the line:
+</p>
<pre>
- head -42 detail_pop.1000 > my_temp_file
+ head -42 detail_pop.1000 > my_temp_file
</pre>
<p>
- The file "<tt>my_temp_file</tt>" would be created, and its contents would
- be the first 42 lines of <tt>detail_pop.1000</tt>. So, what you need this
- function to do is create a temporary file with proper number of lines from
- the detail file in it, load that temp file into the current batch, and
- then delete the file (using the <tt>rm</tt> command).
- <i>Warning</i>: be very careful with the automated deletions -- you don't
- want to accidentally remove something that you really need! I recommend
- that you use the command "rm -i" until you finish debugging. This
- problem may end up being a little tricky for you, but you should be able to
- work your way through it.
-
+The file <kbd>my_temp_file</kbd> would be created, and its contents would
+be the first 42 lines of <kbd>detail-1000.pop</kbd>. So, what you need this
+function to do is create a temporary file with proper number of lines from
+the detail file in it, load that temp file into the current batch, and
+then delete the file (using the <kbd>rm</kbd> command).
+<em>Warning</em>: be very careful with the automated deletions -- you don't
+want to accidentally remove something that you really need! I recommend
+that you use the command <kbd>rm -i</kbd> until you finish debugging. This
+problem may end up being a little tricky for you, but you should be able to
+work your way through it.
+</p>
<p>
-<b>Problem 2</b>. Now that you have a working LOAD_DETAIL_TOP command, you
- can run "LOAD_DETAIL_TOP <filename> 1" in order to only load the most
- dominant genotype from the detail file. Rewrite the example program from
- the section "Working with Batches" above such that you now only need to
- work within a single batch.
+<strong>Problem 2</strong>. Now that you have a working LOAD_DETAIL_TOP command, you
+can run <code>LOAD_DETAIL_TOP <filename> 1</code> in order to only load the most
+dominant genotype from the detail file. Rewrite the example program from
+the section "Working with Batches" above such that you now only need to
+work within a single batch.
+</p>
-<br><hr>
-Project hosted by:<br>
-<a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=46761&type=2" width="125" height="37" border="0" alt="SourceForge.net"/></a>
+<hr />
+<p><a href="index.html">Return to the Index</a></p>
+
+</body>
+</html>
\ No newline at end of file
Modified: development/documentation/config.html
===================================================================
--- development/documentation/config.html 2006-08-29 18:36:08 UTC (rev 906)
+++ development/documentation/config.html 2006-08-30 01:31:04 UTC (rev 907)
@@ -274,7 +274,7 @@
that it will be mutated each update. In other words, this should
be a very low value if it is turned on at all. If a mutation occurs,
that site is replaced with a random instruction. In practice this
- also slows avida down if it is non-zero because it requires so many
+ also slows Avida down if it is non-zero because it requires so many
random numbers to be tested every update.
</td>
</tr>
@@ -448,7 +448,7 @@
<h2>Geneology Info</h2>
<p>
-These settings control how avida monitors and deals with genotypes,
+These settings control how Avida monitors and deals with genotypes,
species, and lineages.
</p>
<table border="1">
@@ -498,7 +498,7 @@
<tr>
<td valign="top"><strong><code>SPECIES_RECORDING</code></strong></td>
<td>
- This entry sets if and how species should be recorded in avida. A
+ This entry sets if and how species should be recorded in Avida. A
setting of 0 turns all species tests off. A setting of 1 means that
every time a genotype reaches threshold, it is tested against all
currently existing species to determine if it is part of any of them.
@@ -536,7 +536,7 @@
<tr style="background-color: #AAFFAA">
<td valign="top"><strong><code>TRACK_MAIN_LINEAGE</code></strong></td>
<td>
- In a normal avida run, the genebank keeps track of all existing
+ In a normal Avida run, the genebank keeps track of all existing
genotypes, and deletes them when the last organism of that genotype
dies out. With this flag set, a genotype will not be deleted unless
both it and <em>all of its descendents</em> have died off. This allows
Modified: development/documentation/inst_set.html
===================================================================
--- development/documentation/inst_set.html 2006-08-29 18:36:08 UTC (rev 906)
+++ development/documentation/inst_set.html 2006-08-30 01:31:04 UTC (rev 907)
@@ -181,7 +181,7 @@
operation on them. The result of this operation is placed in the
<a href="glossary/help.Nop-Register-Notation.html">?BX?</a> register. Note that
this is the only <a href="glossary/help.Logic.html">logic</a> operation provided in
-the basic avida instruction set.
+the basic Avida instruction set.
<h3>(q) <code>IO</code></h3>
Modified: development/documentation/print_data.html
===================================================================
--- development/documentation/print_data.html 2006-08-29 18:36:08 UTC (rev 906)
+++ development/documentation/print_data.html 2006-08-30 01:31:04 UTC (rev 907)
@@ -1,65 +1,89 @@
-<h3>Event: <tt>print_data</tt> options</h3>
+<html>
+<head>
+ <title>Avida : PrintData Options</title>
+</head>
+<body>
-<table cellpadding=5 border=2>
-<tr><th>Keyword <th>Description
-<tr><td><tt>update</tt> <td>Current Update
-<tr><td><tt>sub_update</tt> <td>Instructions executed within update
-<tr><td><tt>generation</tt> <td>Average Generation in Population
-<tr><td><tt>entropy</tt> <td>Genotype Entropy (Diversity)
-<tr><td><tt>species_entropy</tt> <td>Species Entropy (Diversity)
-<tr><td><tt>energy</tt> <td>Average Inferiority (Energy)
-<tr><td><tt>dom_merit</tt> <td>Ave Merit of Dominant Genotype
-<tr><td><tt>dom_gest</tt> <td>Ave Gestation Time of Dominant Genotype
-<tr><td><tt>dom_fitness</tt> <td>Ave Fitness of Dominant Genotype
-<tr><td><tt>dom_repro</tt> <td>Ave Repro-Rate of Dominant Genotype
-<tr><td><tt>dom_length</tt> <td>Genome Length of Dominant Genotype
-<tr><td><tt>dom_copy_length</tt> <td>Copied Length of Dominant Genotype
-<tr><td><tt>dom_exe_length</tt> <td>Executed Length of Dominant Genotype
-<tr><td><tt>dom_id</tt> <td>ID of Dominant Genotype
-<tr><td><tt>dom_name</tt> <td>Name of Dominant Genotype
-<tr><td><tt>dom_births</tt> <td>Birth Count of Dominant Genotype
-<tr><td><tt>dom_breed_true</tt> <td>Breed-True Count of Dominant Genotype
-<tr><td><tt>dom_breed_in</tt> <td>Breed-In Count of Dominant Genotype
-<tr><td><tt>dom_breed_out</tt> <td>Breed-Out Count of Dominant Genotype
-<tr><td><tt>dom_num_cpus</tt> <td>Abundance of Dominant Genotype
-<tr><td><tt>dom_depth</tt> <td>Tree Depth of Dominant Genotype
-<tr><td><tt>dom_sequence</tt> <td>Sequence of Dominant Genotype
-<tr><td><tt>num_births</tt> <td>Count of Births in Population
-<tr><td><tt>num_deaths</tt> <td>Count of Deaths in Population
-<tr><td><tt>breed_in</tt> <td>Count of Non-Breed-True Births
-<tr><td><tt>breed_true</tt> <td>Count of Breed-True Births
-<tr><td><tt>bred_true</tt> <td>Count of Organisms that have Bred True
-<tr><td><tt>num_cpus</tt> <td>Count of Organisms in Population
-<tr><td><tt>num_genotypes</tt> <td>Count of Genotypes in Population
-<tr><td><tt>num_threshold</tt> <td>Count of Threshold Genotypes
-<tr><td><tt>num_species</tt> <td>Count of Species in Population
-<tr><td><tt>thresh_species</tt> <td>Count of Threshold Species
-<tr><td><tt>num_lineages</tt> <td>Count of Lineages in Population
-<tr><td><tt>num_parasites</tt> <td>Count of Parasites in Population
-<tr><td><tt>num_no_birth</tt> <td>Count of Childless Organisms
-<tr><td><tt>tot_cpus</tt> <td>Total Organisms ever in Population
-<tr><td><tt>tot_genotypes</tt> <td>Total Genotypes ever in Population
-<tr><td><tt>tot_threshold</tt> <td>Total Threshold Genotypes Ever
-<tr><td><tt>tot_species</tt> <td>Total Species ever in Population
-<tr><td><tt>tot_lineages</tt> <td>Total Lineages ever in Population
-<tr><td><tt>ave_repro_rate</tt> <td>Average Repro-Rate (1/Gestation)
-<tr><td><tt>ave_merit</tt> <td>Average Merit
-<tr><td><tt>ave_age</tt> <td>Average Age
-<tr><td><tt>ave_memory</tt> <td>Average Memory Used
-<tr><td><tt>ave_neutral</tt> <td>Average Neutral Metric
-<tr><td><tt>ave_lineage</tt> <td>Average Lineage Label
-<tr><td><tt>ave_gest</tt> <td>Average Gestation Time
-<tr><td><tt>ave_fitness</tt> <td>Average Fitness
-<tr><td><tt>ave_gen_age</tt> <td>Average Genotype Age
-<tr><td><tt>ave_length</tt> <td>Average Genome Length
-<tr><td><tt>ave_copy_length</tt> <td>Average Copied Length
-<tr><td><tt>ave_exe_length</tt> <td>Average Executed Length
-<tr><td><tt>ave_thresh_age</tt> <td>Average Threshold Genotype Age
-<tr><td><tt>ave_species_age</tt> <td>Average Species Age
-<tr><td><tt>max_fitness</tt> <td>Maximum Fitness in Population
-<tr><td><tt>max_merit</tt> <td>Maximum Merit in Population
+<div style="float: right">
+Revised 2006-08-29 DMB
+</div>
+
+<p>
+<a href="index.html">Return to the Index</a> |
+<a href="actions.html#PrintData">List of Actions (PrintData)</a>
+</p>
+<hr />
+
+<div align="center">
+<h1>PrintData Options</h1>
+</div>
+
+<table border="1" cellpadding="2">
+<tr><th>Keyword</th><th>Description</th></tr>
+<tr><td><code>update</code</td><td>Current Update</td></tr>
+<tr><td><code>sub_update</code</td><td>Instructions executed within update</td></tr>
+<tr><td><code>generation</code</td><td>Average Generation in Population</td></tr>
+<tr><td><code>entropy</code</td><td>Genotype Entropy (Diversity)</td></tr>
+<tr><td><code>species_entropy</code</td><td>Species Entropy (Diversity)</td></tr>
+<tr><td><code>energy</code</td><td>Average Inferiority (Energy)</td></tr>
+<tr><td><code>dom_merit</code</td><td>Ave Merit of Dominant Genotype</td></tr>
+<tr><td><code>dom_gest</code</td><td>Ave Gestation Time of Dominant Genotype</td></tr>
+<tr><td><code>dom_fitness</code</td><td>Ave Fitness of Dominant Genotype</td></tr>
+<tr><td><code>dom_repro</code</td><td>Ave Repro-Rate of Dominant Genotype</td></tr>
+<tr><td><code>dom_length</code</td><td>Genome Length of Dominant Genotype</td></tr>
+<tr><td><code>dom_copy_length</code</td><td>Copied Length of Dominant Genotype</td></tr>
+<tr><td><code>dom_exe_length</code</td><td>Executed Length of Dominant Genotype</td></tr>
+<tr><td><code>dom_id</code</td><td>ID of Dominant Genotype</td></tr>
+<tr><td><code>dom_name</code</td><td>Name of Dominant Genotype</td></tr>
+<tr><td><code>dom_births</code</td><td>Birth Count of Dominant Genotype</td></tr>
+<tr><td><code>dom_breed_true</code</td><td>Breed-True Count of Dominant Genotype</td></tr>
+<tr><td><code>dom_breed_in</code</td><td>Breed-In Count of Dominant Genotype</td></tr>
+<tr><td><code>dom_breed_out</code</td><td>Breed-Out Count of Dominant Genotype</td></tr>
+<tr><td><code>dom_num_cpus</code</td><td>Abundance of Dominant Genotype</td></tr>
+<tr><td><code>dom_depth</code</td><td>Tree Depth of Dominant Genotype</td></tr>
+<tr><td><code>dom_sequence</code</td><td>Sequence of Dominant Genotype</td></tr>
+<tr><td><code>num_births</code</td><td>Count of Births in Population</td></tr>
+<tr><td><code>num_deaths</code</td><td>Count of Deaths in Population</td></tr>
+<tr><td><code>breed_in</code</td><td>Count of Non-Breed-True Births</td></tr>
+<tr><td><code>breed_true</code</td><td>Count of Breed-True Births</td></tr>
+<tr><td><code>bred_true</code</td><td>Count of Organisms that have Bred True</td></tr>
+<tr><td><code>num_cpus</code</td><td>Count of Organisms in Population</td></tr>
+<tr><td><code>num_genotypes</code</td><td>Count of Genotypes in Population</td></tr>
+<tr><td><code>num_threshold</code</td><td>Count of Threshold Genotypes</td></tr>
+<tr><td><code>num_species</code</td><td>Count of Species in Population</td></tr>
+<tr><td><code>thresh_species</code</td><td>Count of Threshold Species</td></tr>
+<tr><td><code>num_lineages</code</td><td>Count of Lineages in Population</td></tr>
+<tr><td><code>num_parasites</code</td><td>Count of Parasites in Population</td></tr>
+<tr><td><code>num_no_birth</code</td><td>Count of Childless Organisms</td></tr>
+<tr><td><code>tot_cpus</code</td><td>Total Organisms ever in Population</td></tr>
+<tr><td><code>tot_genotypes</code</td><td>Total Genotypes ever in Population</td></tr>
+<tr><td><code>tot_threshold</code</td><td>Total Threshold Genotypes Ever</td></tr>
+<tr><td><code>tot_species</code</td><td>Total Species ever in Population</td></tr>
+<tr><td><code>tot_lineages</code</td><td>Total Lineages ever in Population</td></tr>
+<tr><td><code>ave_repro_rate</code</td><td>Average Repro-Rate (1 / Gestation)</td></tr>
+<tr><td><code>ave_merit</code</td><td>Average Merit</td></tr>
+<tr><td><code>ave_age</code</td><td>Average Age</td></tr>
+<tr><td><code>ave_memory</code</td><td>Average Memory Used</td></tr>
+<tr><td><code>ave_neutral</code</td><td>Average Neutral Metric</td></tr>
+<tr><td><code>ave_lineage</code</td><td>Average Lineage Label</td></tr>
+<tr><td><code>ave_gest</code</td><td>Average Gestation Time</td></tr>
+<tr><td><code>ave_fitness</code</td><td>Average Fitness</td></tr>
+<tr><td><code>ave_gen_age</code</td><td>Average Genotype Age</td></tr>
+<tr><td><code>ave_length</code</td><td>Average Genome Length</td></tr>
+<tr><td><code>ave_copy_length</code</td><td>Average Copied Length</td></tr>
+<tr><td><code>ave_exe_length</code</td><td>Average Executed Length</td></tr>
+<tr><td><code>ave_thresh_age</code</td><td>Average Threshold Genotype Age</td></tr>
+<tr><td><code>ave_species_age</code</td><td>Average Species Age</td></tr>
+<tr><td><code>max_fitness</code</td><td>Maximum Fitness in Population</td></tr>
+<tr><td><code>max_merit</code</td><td>Maximum Merit in Population</td></tr>
</table>
-<br><hr>
-Project hosted by:<br>
-<a href="http://sourceforge.net"><img src="http://sourceforge.net/sflogo.php?group_id=46761&type=2" width="125" height="37" border="0" alt="SourceForge.net"/></a>
-
\ No newline at end of file
+
+
+<hr />
+<p>
+<a href="index.html">Return to the Index</a> |
+<a href="actions.html#PrintData">List of Actions (PrintData)</a>
+</p>
+
+</body>
+</html>
Modified: development/documentation/structure.html
===================================================================
--- development/documentation/structure.html 2006-08-29 18:36:08 UTC (rev 906)
+++ development/documentation/structure.html 2006-08-30 01:31:04 UTC (rev 907)
@@ -84,7 +84,7 @@
<h3>Top Level Directory</h3>
-All of the files for the current version of avida reside in the directory
+All of the files for the current version of Avida reside in the directory
labeled <kbd style="color: #008844">trunk/</kbd> by default when checked
out of Subversion. In addition to the subdirectories
<kbd style="color: #008844">documentation/</kbd>,
@@ -96,7 +96,7 @@
<dl>
<dt><kbd style="color: #000088">AUTHORS</kbd></dt>
<dd>
-This file contains information about the authorship of avida.
+This file contains information about the authorship of Avida.
</dd>
<dt><kbd style="color: #000088">Avida.xcodeproj</kbd></dt>
<dd>
@@ -265,7 +265,7 @@
<dt><kbd style="color: #000088">cAvidaConfig.??</kbd></dt>
<dd>
These files define the cAvidaConfig object that maintains the
-current configuration state of avida. This class is initialized
+current configuration state of Avida. This class is initialized
by the avida.cfg file and processed command line arguments and can be modified
via various events during the run.
</dd>
@@ -281,7 +281,7 @@
</dd>
<dt><kbd style="color: #000088">cInstruction.??</kbd></dt>
<dd>
-The cInstruction class is very simple, maintaining a single instruction in avida.
+The cInstruction class is very simple, maintaining a single instruction in Avida.
</dd>
<dt><kbd style="color: #000088">cInstLibBase.h</kbd></dt>
<dd>
Modified: development/documentation/svn.html
===================================================================
--- development/documentation/svn.html 2006-08-29 18:36:08 UTC (rev 906)
+++ development/documentation/svn.html 2006-08-30 01:31:04 UTC (rev 907)
@@ -83,7 +83,7 @@
<p>
If you are just using the SVN in order to have the most up-to-date version
-of avida, than you should never have any problems with it. An occasional
+of Avida, than you should never have any problems with it. An occasional
"<tt>svn update</tt>" when you need a newly implemented feature should do
the trick. However, if you are going to edit the code (even if you never
plan to commit your changes) there are some other things you need to worry
More information about the Avida-cvs
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