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tutorial part2: minor language fixes
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fmder committed Nov 1, 2014
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Operators and Algorithms
========================

Before starting with complex algorithms, we will see some basis of DEAP.
Before starting with complex algorithms, we will see some basics of DEAP.
First, we will start by creating simple individuals (as seen in the
:ref:`creating-types` tutorial) and make them interact with each other using
different operators. Afterwards, we will learn how to use the algorithms and
Expand All @@ -12,7 +12,7 @@ other tools.
A First Individual
------------------

First import the required modules and register the different functions required to create individuals that are a list of floats with a minimizing two objectives fitness.
First import the required modules and register the different functions required to create individuals that are lists of floats with a minimizing two objectives fitness.

.. literalinclude:: /code/tutorials/part_3/3_next_step.py
:lines: 2-16
Expand All @@ -34,11 +34,11 @@ Evaluation

The evaluation is the most personal part of an evolutionary algorithm, it is
the only part of the library that you must write yourself. A typical
evaluation function takes one individual as argument and return its fitness as
evaluation function takes one individual as argument and returns its fitness as
a :class:`tuple`. As shown in the in the :ref:`core` section, a fitness is a list of floating point values and has a
property :attr:`~deap.base.Fitness.valid` to know if this individual shall be re-evaluated. The
fitness is set by setting the :attr:`~deap.base.Fitness.values` to the
associated :class:`tuple`. For example, the following evaluates the previously created individual ``ind1`` and assign its fitness to the corresponding values.
associated :class:`tuple`. For example, the following evaluates the previously created individual ``ind1`` and assigns its fitness to the corresponding values.

.. literalinclude:: /code/tutorials/part_3/3_next_step.py
:lines: 24-32
Expand All @@ -49,21 +49,21 @@ Mutation
--------
The next kind of operator that we will present is the mutation operator.
There is a variety of mutation operators in the :mod:`deap.tools` module.
Each mutation has its own characteristics and may be applied to different type
of individual. Be careful to read the documentation of the selected operator
Each mutation has its own characteristics and may be applied to different types
of individuals. Be careful to read the documentation of the selected operator
in order to avoid undesirable behaviour.

The general rule for mutation operators is that they **only** mutate, this
means that an independent copy must be made prior to mutating the individual
if the original individual has to be kept or is a *reference* to an other individual (see the selection operator).
if the original individual has to be kept or is a *reference* to another individual (see the selection operator).

In order to apply a mutation (here a gaussian mutation) on the individual ``ind1``,
simply apply the desired function.

.. literalinclude:: /code/tutorials/part_3/3_next_step.py
:lines: 35-37

The fitness' values are deleted because they not related to the individual anymore. As stated above, the mutation does mutate and only mutate an individual it is not responsible of invalidating the fitness nor anything else. The following shows that ``ind2`` and ``mutant`` are in fact the same individual.
The fitness' values are deleted because they're not related to the individual anymore. As stated above, the mutation does mutate and only mutate an individual it is neither responsible of invalidating the fitness nor anything else. The following shows that ``ind2`` and ``mutant`` are in fact the same individual.

.. literalinclude:: /code/tutorials/part_3/3_next_step.py
:lines: 39-40
Expand All @@ -73,13 +73,13 @@ Crossover

The second kind of operator that we will present is the crossover operator.
There is a variety of crossover operators in the :mod:`deap.tools` module.
Each crossover has its own characteristics and may be applied to different type
Each crossover has its own characteristics and may be applied to different types
of individuals. Be careful to read the documentation of the selected operator
in order to avoid undesirable behaviour.

The general rule for crossover operators is that they **only** mate individuals, this
means that an independent copies must be made prior to mating the individuals
if the original individuals have to be kept or is are *references* to other
if the original individuals have to be kept or are *references* to other
individuals (see the selection operator).

Lets apply a crossover operation to produce the two children that are cloned beforehand.
Expand All @@ -104,7 +104,7 @@ Selection
---------

Selection is made among a population by the selection operators that are
available in the :mod:`deap.operators` module. The selection operator usually
available in the :mod:`deap.tools` module. The selection operator usually
takes as first argument an iterable container of individuals and the number of
individuals to select. It returns a list containing the references to the
selected individuals. The selection is made as follow.
Expand All @@ -130,7 +130,7 @@ Using the Toolbox

The toolbox is intended to contain all the evolutionary tools, from the object
initializers to the evaluation operator. It allows easy configuration of each
algorithms. The toolbox has basically two methods,
algorithm. The toolbox has basically two methods,
:meth:`~deap.toolbox.Toolbox.register` and
:meth:`~deap.toolbox.Toolbox.unregister`, that are used to add or remove tools
from the toolbox.
Expand Down Expand Up @@ -163,22 +163,22 @@ very simple generational evolutionary algorithm.
This is a complete algorithm. It is generic enough to accept any kind of
individual and any operator, as long as the operators are suitable for the
chosen individual type. As shown in the last example, the usage of the toolbox
allows to write algorithms that are as close as possible to the pseudo code.
Now it is up to you to write and experiment your own.
allows to write algorithms that are as close as possible to pseudo code.
Now it is up to you to write and experiment on your own.

Tool Decoration
+++++++++++++++
Tool decoration is a very powerful feature that helps to control very precise
thing during an evolution without changing anything in the algorithm or
things during an evolution without changing anything in the algorithm or
operators. A decorator is a wrapper that is called instead of a function. It
is asked to make some initialization and termination work before and after the
actual function is called. For example, in the case of a constrained domain,
one can apply a decorator to the mutation and crossover in order to keep any
individual from being out-of-bound. The following defines a decorator that
checks if any attribute in the list is out-of-bound and clips it if it is the
checks if any attribute in the list is out-of-bound and clips it if this is the
case. The decorator is defined using three functions in order to receive the
*min* and *max* arguments. Whenever the mutation or crossover is called,
bounds will be check on the resulting individuals.
bounds will be checked on the resulting individuals.

.. literalinclude:: /code/tutorials/part_3/3_6_2_tool_decoration.py
:lines: 8-
Expand All @@ -194,28 +194,28 @@ and `Python Decorator Libary <http://wiki.python.org/moin/PythonDecoratorLibrary

Variations
----------
Variations allows to build simple algorithms using predefined small building blocks. In
Variations allow to build simple algorithms using predefined small building blocks. In
order to use a variation, the toolbox must be set to contain the required
operators. For example in the lastly presented complete algorithm, the
crossover and mutation are regrouped in the :func:`~deap.algorithms.varAnd`
function, this function requires the toolbox to contain the :func:`~deap.mate`
and :func:`~deap.mutate` functions. The variations can be used to simplify
the writing of an algorithm as follow.
and :func:`~deap.mutate` functions. This variation can be used to simplify
the writing of an algorithm as follows.

.. literalinclude:: /code/tutorials/part_3/3_7_variations.py
:lines: 33-

This last example shows that using the variations makes it straight forward to
build algorithms that are very close to the pseudo-code.
build algorithms that are very close to pseudo code.

Algorithms
----------
There is several algorithms implemented in the :mod:`~deap.algorithms` module.
There are several algorithms implemented in the :mod:`~deap.algorithms` module.
They are very simple and
reflect the basic types of evolutionary algorithms present in the literature.
The algorithms use a :class:`~deap.base.Toolbox` as defined in the last
sections. In order to setup a toolbox for an algorithm, you must register the
desired operators under a specified names, refer to the documentation of the
desired operators under the specified names, refer to the documentation of the
selected algorithm for more details. Once the toolbox is ready, it is time to
launch the algorithm. The simple evolutionary algorithm takes 5 arguments, a
*population*, a *toolbox*, a probability of mating each individual at each
Expand All @@ -225,8 +225,8 @@ generation (*mutpb*) and a number of generations to accomplish (*ngen*).
.. literalinclude:: /code/tutorials/part_3/3_8_algorithms.py
:lines: 33-

The best way to understand what the simple evolutionary algorithm does, it to
take a look at the documentation or the source code
The best way to understand what the simple evolutionary algorithm does, is to
take a look at the documentation or the source code.

Now that you built your own evolutionary algorithm in python, you are welcome
to gives us feedback and appreciation. We would also really like to hear about
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