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8
eo/tutorial/html/eoLesson1.html
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@ -86,13 +86,13 @@ below, or go directly to the <a href="#exercise1">exercises</a>.
<b><font color="#993300">General includes:</font></b><font color="#000000">Like
all C-like code, the file starts with include directives (<a href="FirstBitGA.html#start">Bit</a>
- <a href="FirstRealGA.html#start">Real</a>). Apart from standard includes,
the spedific file to include is </font><b><font color="#FF6600">eo</font></b><font color="#000000">:
the specific file to include is </font><b><font color="#FF6600">eo</font></b><font color="#000000">:
this is a file that contains the list of the most important EO files.</font></li>
<br>&nbsp;
<li>
<b><font color="#999900">Representation</font></b><font color="#000000">:
you then have to delclare the type of individuals you will be handling.
you then have to declare the type of individuals you will be handling.
All evolution-related objects you will need are templatized w.r.t. the
type of individuals.</font></li>
@ -147,7 +147,7 @@ Random Number Generator</font><font color="#000000"> is called </font><b><tt><fo
and should be used everywhere you need a realization of a random variable
of known law. Moreover, this RNG requires a </font><b><tt><font color="#660000"><font size=+1>seed</font></font></tt></b><font color="#000000">,
which is set here (<a href="FirstBitGA.html#random">Bit</a> - <a href="FirstRealGA.html#random">Real</a>):
everytime you run the algorithm with the </font><font color="#FF6600">same
every time you run the algorithm with the </font><font color="#FF6600">same
seed</font><font color="#000000">, you will get the </font><font color="#FF6600">same
result</font><font color="#000000">. Hence, to test the robustness of your
algorithm, you should run it with different seeds. This is rather time
@ -245,7 +245,7 @@ is the standard <font color="#CC33CC">arithmetic crossover</font> for real-value
vectors, that chooses a point randomly on the segment between both parents
(also termed <font color="#CC33CC">BLX-0</font>). <b><font face="Arial,Helvetica"><font size=+1><a href="doc/html/class_eouniformmutation.html">eoUniformMutation</a></font></font></b>
is the <font color="#CC33CC">uniform mutation</font> for real-valued vectors
that choses a new value for each variable uniformly on an interval centered
that chooses a new value for each variable uniformly on an interval centered
on the parent value. The width of the interval is an <font color="#FF6600">internal
parameter</font> of the object, here called <b><tt>EPSILON</tt></b>.</li>

14
eo/tutorial/html/eoLesson2.html
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@ -70,7 +70,7 @@ object that is a sub-class of the corresponding STL vector class.</font></li>
<p><b><font color="#FF0000">Note:</font></b> <font color="#000000">Also,
a non-templatized fitness can be </font><b><font color="#FF6600">compiled
separately</font></b><font color="#000000"> (not done here) into an object
file once and forall (<a href="eoProgramming.html#templates">remember</a>
file once and for all (<a href="eoProgramming.html#templates">remember</a>
that templates forbid that).</font>
<br>&nbsp;
<li>
@ -134,12 +134,12 @@ sum up to 1, all rates are scaled anyway.
<p><b><font color="#FF0000">Note:</font></b> The operators have to be encapsulated
into an <b><tt><font color="#CC33CC">eoTransform</font></tt></b> object
(<a href="FirstBitEA.html#transform">Bit</a> - <a href="FirstRealEA.html#transform">Real</a>)
to be passed to the <b><tt><font color="#FF6666">eoEasyEA </font></tt></b>algorihtm.
to be passed to the <b><tt><font color="#FF6666">eoEasyEA </font></tt></b>algorithm.
The <b><tt><font color="#CC33CC">eoSGATransform</font></tt></b> is a simple
<b><tt><font color="#CC33CC">eoTransform</font></tt></b>
that does exactly the same thing than <b><tt><font color="#FF6666">eoSGA</font></tt></b>:
each pair from the selected parents undergoes the <font color="#CC33CC">crossover
operator with given probablity</font>, and all individuals (after crossover
operator with given probability</font>, and all individuals (after crossover
eventually) undergo <font color="#CC33CC">mutation with given probability</font>.
The arguments to the <b><tt><font color="#CC33CC">eoSGATransform</font></tt></b>
are an <b><tt><font color="#CC33CC">eoQuadOp</font></tt></b> with its probability
@ -182,7 +182,7 @@ a population (his <b><tt><font color="#660000">operator()</font></tt></b>&nbsp;
returns a population). This was done internally in the&nbsp; <a href="doc/html/class_eosga.html#a0">constructor
of eoSGA</a>&nbsp; - see lesson1.</ul>
<hr WIDTH="100%"><a NAME="Exercise1"></a><b><font size=+2><font color="#000099">Exercice
<hr WIDTH="100%"><a NAME="Exercise1"></a><b><font size=+2><font color="#000099">Exercise
1: </font><font color="#FF0000">minimizing</font></font></b>
<br><font color="#000000">Modify the algorithm so that it minimizes the
fitness.</font>
@ -201,16 +201,16 @@ the file <b><tt><a href="real_value.html">real_value.h</a></tt></b> so
that it returns the sum of squares instead of its inverse. And again there
is something else to modify...</font></li>
</ul>
<a NAME="exercise2"></a><b><font size=+2><font color="#000099">Exercice
<a NAME="exercise2"></a><b><font size=+2><font color="#000099">Exercise
2: </font><font color="#FF0000">initialization</font></font></b>
<br><font color="#000000">Use different initializers: for instance, on
the real-valued sphere function minimization, try to initialize half of
the population in [-2,-1] and the other half in [1,2], with and without
the segment and arithmetic crossovers (and for large values of VEC_SIZE,
the size of the vectors). Amazing, isn't it! Explain that result.</font>
<p><a NAME="Exercise3"></a><b><font size=+2><font color="#000099">Exercice
<p><a NAME="Exercise3"></a><b><font size=+2><font color="#000099">Exercise
3:&nbsp; </font><font color="#FF0000">replacement</font></font></b>
<br><font color="#000000">You can now twidle the number of offspring that
<br><font color="#000000">You can now twiddle the number of offspring that
will be generated from the parents. But of course you need to adjust the
replacement to keep a constant population size.</font>
<ul>

40
eo/tutorial/html/eoLesson3.html
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@ -28,7 +28,7 @@ file</li>
<li>
<a href="#state">save</a> the population to disk, together with every part
of the algrithm you could think of - so you can decide to <font color="#FF6600">reload</font>
of the algorithm you could think of - so you can decide to <font color="#FF6600">reload</font>
everything later to continue the same run, eventually with different parameters.</li>
<li>
@ -79,7 +79,7 @@ after the encapsulation of our </font><font color="#CC0000">binary_function</fon
into an </font><b><tt><font color="#CC0000"><font size=+1>eoEvalFunc</font></font></tt></b><font color="#000000">
object, which again encapsulate the </font><b><tt><font color="#CC0000"><font size=+1>eoEvalFunc</font></font></tt></b><font color="#000000">
into an </font><b><tt><font color="#CC0000"><font size=+1>eoEvalFuncCounter</font></font></tt></b><font color="#000000">.
As its name says, thisobject will, in addition to computing the fitness,
As its name says, this object will, in addition to computing the fitness,
count the </font><b><font color="#FF6600">actual</font></b><font color="#000000">
number of evaluations: the fitness of non-modified individuals is of course
not recomputed - and this is taken care of by this object. Moreover, it
@ -129,11 +129,11 @@ for volunteers to create a Graphical User Interface :-)</font>
<li>
<font color="#000000">The </font><b><tt><font color="#3366FF">eoValueParam</font></tt></b><font color="#000000">
class, </font><font color="#FF6600">templatized by the type of the variable</font><font color="#000000">
you want to handle (i.e. i</font><b><tt><font color="#660000">nteger, double,
you want to handle (i.e. i</font><b><tt><font color="#660000">integer, double,
yourPrivateClass</font></tt></b><font color="#000000">, ...). In this lesson,
we will not go into details: e.g. we will not tell you that the
<b><font face="Arial,Helvetica"><font size=+1><a href="doc/html/class_eovalueparam.html">eoValueParam</a></font></font></b>
is actually a templatized sub-class of abstract class eoParam (oups, I
is actually a templatized sub-class of abstract class eoParam (oops, I
said it!), nor will we deal with parameters outside their use from an eoParser.
See the parameter section of the Bottom-up tutorial, or wait until <a href="eoLesson4.html">lesson
4</a>).</font></li>
@ -153,7 +153,7 @@ are read, by order of priority</font>
<font color="#000000">from a text file</font></li>
<li>
<font color="#000000">from the environement</font></li>
<font color="#000000">from the environment</font></li>
<li>
<font color="#000000">from default values</font></li>
@ -186,7 +186,7 @@ in</li>
But you can now type in
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
<b><tt><font color="#FF6666">SecondBitEA --vecSize=100</font></tt></b>
<br>and see the output of the optimization of OneMax on 100-bit bitstings.
<br>and see the output of the optimization of OneMax on 100-bit bitstrings.
<br>&nbsp;
<li>
Take a look at all available parameters by typing in</li>
@ -271,7 +271,7 @@ mechanism offers you better ways to do that - and it's so easy ....</font>
<p>
<hr WIDTH="100%"><a NAME="checkpoint"></a><b><font color="#000099"><font size=+2>eoCheckpoint:
every generation I'd like to ...</font></font></b>
<br><font color="#000000">The checkpointing mechanism is a very powerfull
<br><font color="#000000">The checkpointing mechanism is a very powerful
construct to perform some </font><b><font color="#FF6600">systematic actions</font></b><font color="#000000">
every generation - like </font><font color="#FF6600">saving things</font><font color="#000000">
(using eoState objects described above), computing </font><font color="#FF6600">statistics</font><font color="#000000">
@ -330,14 +330,14 @@ whatever this is).</li>
<li>
<b><tt><font color="#3366FF">eoAverageStat</font></tt></b> and <b><tt><font color="#3366FF">eoSecondMomentStat</font></tt></b>
respectiveley return the average (type double, assumes that <b><tt><font color="#660000">FitnessType</font></tt></b>
respectively return the average (type double, assumes that <b><tt><font color="#660000">FitnessType</font></tt></b>
is castable to a double) and a pair made of the average and the standard
deviation (type <b><tt><font color="#660000">pair&lt;double></font></tt></b>)
of the fitnesses in the populations.</li>
<li>
<b><tt><font color="#3366FF">eoDiversityStat</font></tt></b> returns the
diversity in the population: asssuming that there is a distance function
diversity in the population: assuming that there is a distance function
defined among individuals, it returns the average inter-individuals distance.
See also Exercise 2.</li>
</ul>
@ -346,8 +346,8 @@ within your algorithm, simply <a href="SecondBitEA.html#stat_declare">declare</a
the corresponding eoStat objects, and <a href="SecondBitEA.html#stat_pass">add</a>
them to the <b><tt><font color="#3366FF">eoCheckpoint</font></tt></b> you
use in the algorithm.
<p><b><font color="#FF0000">Note</font></b>: actually, there are 2 disctinct
classes that compute and gove access to statistics: <b><tt><font color="#3366FF">eoStat</font></tt></b>
<p><b><font color="#FF0000">Note</font></b>: actually, there are 2 distinct
classes that compute and give access to statistics: <b><tt><font color="#3366FF">eoStat</font></tt></b>
and <b><tt><font color="#3366FF">eoSortedStat</font></tt></b>. As its name
indicate, the latter is used whenever computing the statistics require
a sorted population: not only this avoids to sort the population many times,
@ -368,8 +368,8 @@ are available in th eEO distribution:
<b><tt><font color="#3366FF">eoStdoutMonitor</font></tt></b> displays its
parameters in <font color="#FF6600">text format on the screen</font>. The
(optional) boolean value in the constructor modifies the output: when true
(the default), vebose output is used, with one line per parameter. When
false, parcimonious output displays one line for all parameters.</li>
(the default), verbose output is used, with one line per parameter. When
false, parsimonious output displays one line for all parameters.</li>
<li>
<b><tt><font color="#3366FF">eoStdoutMonitor</font></tt></b> writes its
@ -414,7 +414,7 @@ are available in the EO distribution:
<b><tt><font color="#3366FF">eoIncrementor</font></tt></b> A simple updater
which maintains a <font color="#FF6600">counter</font> (an <b><tt><font color="#3366FF">eoValueParam</font></tt></b>
that needs to be created beforehand, and passed in the constructor). It
is incremented everytime the <b><tt><font color="#660000">operator()</font></tt></b>
is incremented every time the <b><tt><font color="#660000">operator()</font></tt></b>
method is called (every generation at the moment). You can of course also
give an increment in the constructor (1 by default).</li>
@ -442,7 +442,7 @@ the state to some state-saver - and don't forget to <a href="SecondBitEA.html#st
the statesavers to the current <b><tt><font color="#3366FF">eoCheckpoint</font></tt></b>.
<br>
<hr WIDTH="100%">
<br><b><font color="#000099"><font size=+2>Exercice 1:</font></font></b>
<br><b><font color="#000099"><font size=+2>Exercise 1:</font></font></b>
<ul>
<li>
<font color="#000000">The code of </font><b><tt><font color="#660000"><font size=+1>SecondBitEA</font></font></tt></b><font color="#000000">
@ -459,25 +459,25 @@ otherwise the standard deviations won't make any sense here.</font></li>
<li>
<font color="#000000">Please try to understand why the average is always
0 before taking alook at the solution (file <a href="NoWay.html">exercise1.cpp</a>).</font></li>
0 before taking a look at the solution (file <a href="NoWay.html">exercise1.cpp</a>).</font></li>
<li>
<font color="#000000">Then run</font></li>
<br><b><tt><font color="#660000"><font size=+1>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
exercise1 --vecSize=1000 --maxGen=1000</font></font></tt></b>
<br><font color="#000000">to get a chance to see something hapenning before
<br><font color="#000000">to get a chance to see something happening before
the program ends!</font></ul>
<hr WIDTH="100%"><b><font color="#000099"><font size=+2>Exercice 2:</font></font></b>
<hr WIDTH="100%"><b><font color="#000099"><font size=+2>Exercise 2:</font></font></b>
<br><font color="#000000">Write the </font><b><tt><font color="#3366FF">eoDiversityStat</font></tt></b><font color="#000000">
stat computation and test it. Thanks to send us the code!</font>
<br>
<hr WIDTH="100%">
<br><b><font color="#000099"><font size=+2>Exercice 3:</font></font></b>
<br><b><font color="#000099"><font size=+2>Exercise 3:</font></font></b>
<br><font color="#000000">Write the code for an </font><b><tt><font color="#3366FF"><font size=+1>eoGnuplot1DwithErrorbarsMonitor</font></font></tt></b><font color="#000000">
that would take into account the standard deviations and display them as
errorbars.</font>
error-bars.</font>
<br><font color="#000000">Again, send us the code afterwards, thanks :-)</font>
<br>
<hr WIDTH="100%">

22
eo/tutorial/html/eoProgramming.html
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@ -57,7 +57,7 @@ are that
functors are functions with private data</li>
<li>
you can have different funtors objects of the same class, i.e. you can
you can have different functors objects of the same class, i.e. you can
use the same functionality with different parameters</li>
<li>
@ -165,15 +165,15 @@ function.
<p><b><font color="#000099">Drawbacks</font></b>
<br>The main drawback I see in using STL is that it makes it almost
<b><font color="#FF6600">impossible
to use a debugger </font></b>normally: whereas acess to data is made simple
to the progammer, data structures are actually so complex, and debuggers
so willing to display everything that you get lines of template instanciation
to use a debugger </font></b>normally: whereas access to data is made simple
to the programmer, data structures are actually so complex, and debuggers
so willing to display everything that you get lines of template instantiation
when asking your debugger what is inside some container! For instance I
could never visualize some
<tt><font color="#FF6600"><font size=+1>v[i]</font></font></tt>
with <tt><font color="#FF6600"><font size=+1>gbd</font></font></tt>, v
being an STL vector!
<br>But there nonehteless are so many advantages !!!
<br>But there nonetheless are so many advantages !!!
<p>
<hr WIDTH="100%">
<br><a NAME="random"></a><b><font color="#000099"><font size=+1>Random
@ -183,7 +183,7 @@ numbers are simulated in computers by using <font color="#FF6600">pseudo-random<
number generators (RNGs for short), i.e. functions that return series of
numbers who look random (w.r.t. some statistical criteria).
<p>To make sure the random number generator is as good as possible, and
to ensure reproducibility of the results across diffrerent platforms, EO
to ensure reproducibility of the results across different platforms, EO
has its own RNG, the ``<font color="#FF6600">Mersenne Twister</font>''
random number generator MT19937 (thanks to <font color="#FF0000">Takuji
Nishimura</font>, see <font face="Arial,Helvetica"><font size=+1><a href="../../doc/html/class_eorng.html">eoRNG.h</a></font></font>
@ -205,12 +205,12 @@ use the RNG seeding procedure, see e.g. in <a href="FirstBitGA.html#random">Less
<li>
to simulate "true" random runs, you can just seed the RNG with a machine-clock
realted number, e.g. calling time(0), as done for isntance in <a href="SecondBitEA.html#random">Lesson3</a>
related number, e.g. calling time(0), as done for instance in <a href="SecondBitEA.html#random">Lesson3</a>
(and after).</li>
</ul>
As RNGs only produce (by definition) numbers that are uniformly distributed
integers between 0 and some maximal number, EO provides you with random
numbers follwing <b><font color="#FF6600">different probability distribution</font></b>
numbers following <b><font color="#FF6600">different probability distribution</font></b>
(e.g. floating point following <font face="Arial,Helvetica"><font size=+1><a href="../../doc/html/class_eorng.html#a8">normal
distribution</a></font></font>).
<p>EO also provides <a href="../../doc/html/rnd_generators.h-source.html">random_generators</a>
@ -225,14 +225,14 @@ and naming style</font></font></b>
EO:
<ul>
<li>
The name of local varoiables shoudl start with a lower case letter</li>
The name of local variables should start with a lower case letter</li>
<li>
The name of the parameters to a function shoudl start with an underscore
The name of the parameters to a function should start with an underscore
(_)</li>
<br>The initialization parameters of constructors, for instance,&nbsp;
shoudl be named from the names of the variables they are used to initialize.
should be named from the names of the variables they are used to initialize.
<li>
The names of classes should start with eo + an Uppercase letter</li>

4
eo/tutorial/html/eoTopDown.html
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@ -48,7 +48,7 @@ populations,
...).</li>
<p><br>Current version (Nov. 29, 2000) stops here, but here are the plans
(sujected to many changes, of course!)
(subjected to many changes, of course!)
<br>&nbsp;
<li>
Lesson 4 - More about checkpointing: write your first <font color="#FF6600">adaptive
@ -69,7 +69,7 @@ Lesson 7 - ...</li>
</ul>
Of course, in each lesson, you have links to the Bottom-Up page of the
corresponding component of an EA you are modifying.
<br>( ... Well, to tell you the truth, as of today, november 28, this is
<br>( ... Well, to tell you the truth, as of today, November 28, this is
not true :-)
<br>
<hr WIDTH="100%">

12
eo/tutorial/html/eoTutorial.html
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@ -25,7 +25,7 @@ EAs :-)
This tutorial can be used in 2 different ways: top-down and bottom-up.
<ul>
<li>
<a href="eoTopdown.html">Top-down</a> means you start from a <font color="#FF6600">very
<a href="eoTopDown.html">Top-down</a> means you start from a <font color="#FF6600">very
simple, ready-to-run algorithm,</font> and gradually modify it, making
it both more powerful and more complex.</li>
@ -63,7 +63,7 @@ brief introduction</a>).</li>
<p><br><b><font color="#000099"><font size=+2>Colors and navigation:</font></font></b>
<p>You will see this diagram in quite many places, as for instance at the
top of all examples - usually it will be clicable and will help you navigate
top of all examples - usually it will be clickable and will help you navigate
among the different parts of an EO program. See the <a href="eoIntroEA.html">brief
introduction to Evolutionary Computation</a> for a detailed explanation.
<center>
@ -108,8 +108,8 @@ any of the above, i.e. random number generator, or basic C++/STL syntax
.</li>
<li>
Note that <font color="#FF6666">pink</font> will be used to desctibe the
syntax of compile orders (i.e. at the oepratoring system level, see e.g.
Note that <font color="#FF6666">pink</font> will be used to describe the
syntax of compile orders (i.e. at the operating system level, see e.g.
<a href="#install">below</a>).</li>
<li>
@ -120,10 +120,10 @@ will use the Helvetica typeface, like this line you are now reading.</font></li>
<ul>
<li>
an interface that would allow you to build your Evolutionary Programs by
a few clics; such a thing does exist, is called <a href="http://www-rocq.inria.fr/EASEA/">EASEA</a>,
a few clicks; such a thing does exist, is called <a href="http://www-rocq.inria.fr/EASEA/">EASEA</a>,
and is complementary to this tutorial as it helps the user to build some
simple EO programs from simple description. But there are things that EASEA
cannot do, and you will have to do it yourself and will need to imcrease
cannot do, and you will have to do it yourself and will need to increase
your knowledge about EO for that.</li>
</ul>
<a NAME="install"></a>