The geco Reference Manual

This is the geco Reference Manual, version 2.1, generated automatically by Declt version 4.0 beta 2 "William Riker" on Sun Sep 15 05:14:21 2024 GMT+0.

Table of Contents


1 Introduction


2 Systems

The main system appears first, followed by any subsystem dependency.


2.1 geco

GECO: Genetic Evolution through Combination of Objects A CLOS-based Framework for Prototyping Genetic Algorithms

Author

George P. W. Williams, Jr

Contact

License

GPL 2.0

Version

2.1

Source

geco.asd.

Child Components

3 Modules

Modules are listed depth-first from the system components tree.


3.1 geco/definitions

Dependency

packages.lisp (file).

Source

geco.asd.

Parent Component

geco (system).

Child Components

3.2 geco/utilities

Dependency

packages.lisp (file).

Source

geco.asd.

Parent Component

geco (system).

Child Components

3.3 geco/methods

Dependencies
Source

geco.asd.

Parent Component

geco (system).

Child Components

4 Files

Files are sorted by type and then listed depth-first from the systems components trees.


4.1 Lisp


4.1.1 geco/geco.asd

Source

geco.asd.

Parent Component

geco (system).

ASDF Systems

geco.


4.1.2 geco/packages.lisp

Source

geco.asd.

Parent Component

geco (system).

Packages

4.1.3 geco/definitions/generics.lisp

Source

geco.asd.

Parent Component

definitions (module).

Public Interface

4.1.4 geco/definitions/classes.lisp

Source

geco.asd.

Parent Component

definitions (module).

Public Interface

4.1.5 geco/utilities/dbg.lisp

Source

geco.asd.

Parent Component

utilities (module).

Public Interface
Internals

*dbg-flags* (special variable).


4.1.6 geco/utilities/random.lisp

Source

geco.asd.

Parent Component

utilities (module).

Public Interface
Internals

4.1.7 geco/methods/chromosome-methods.lisp

Source

geco.asd.

Parent Component

methods (module).

Public Interface

4.1.8 geco/methods/organism-methods.lisp

Source

geco.asd.

Parent Component

methods (module).

Public Interface

4.1.10 geco/methods/pop-stats-methods.lisp

Source

geco.asd.

Parent Component

methods (module).

Public Interface

4.1.11 geco/methods/population-methods.lisp

Source

geco.asd.

Parent Component

methods (module).

Public Interface

4.1.12 geco/methods/genetic-plan-methods.lisp

Source

geco.asd.

Parent Component

methods (module).

Public Interface

4.1.13 geco/methods/ecosystem-methods.lisp

Source

geco.asd.

Parent Component

methods (module).

Public Interface

5 Packages

Packages are listed by definition order.


5.1 geco

Source

packages.lisp.

Nickname

ga

Use List

common-lisp.

Used By List

geco-user.

Public Interface
Internals

5.2 geco-user

Source

packages.lisp.

Nickname

gu

Use List
  • common-lisp.
  • geco.

6 Definitions

Definitions are sorted by export status, category, package, and then by lexicographic order.


6.1 Public Interface


6.1.1 Ordinary functions

Function: dbg (&rest flags)

If there are no FLAGS, then turn on all debug code, else add each FLAG to the *DBG-FLAGS* list.

Package

geco.

Source

dbg.lisp.

Function: dbg-p (&rest flags)

If *DBG-FLAGS* is not a list, return its value, else test for presence of any of FLAGS on the *DBG-FLAGS* list.

Package

geco.

Source

dbg.lisp.

Function: dbg? ()

Tell me what debugging flags are active.

Package

geco.

Source

dbg.lisp.

Function: dbgo (fmt-string &rest fmt-args)
Package

geco.

Source

dbg.lisp.

Function: geco-random-float (number)

Accept a positive floating-point number and returns a number of the same kind between zero (inclusive) and the number (exclusive).

Package

geco.

Source

random.lisp.

Function: geco-random-integer (number)

Accept a positive integer and returns a number of the same kind between zero (inclusive) and the number (exclusive).

Package

geco.

Source

random.lisp.

Function: roulette-pick-random-weight-index (weights-table &key invert-p)

Select a random index into a table of weights, using the roulette wheel approach. Assumes that the weights-table has been normalized to sum to 1.0

Package

geco.

Source

selection-methods.lisp.

Function: undbg (&rest flags)

If there are no FLAGS, then turn off all debug code, else remove each FLAG from the *DBG-FLAGS* list.

Package

geco.

Source

dbg.lisp.


6.1.2 Generic functions

Generic Function: 2x-cross-chromosomes (parent1 parent2 child1 child2 locus-index1 locus-index2)
Package

geco.

Methods
Method: 2x-cross-chromosomes ((parent1 chromosome) (parent2 chromosome) (child1 chromosome) (child2 chromosome) locus-index1 locus-index2)

[Two-point crossover] Cross a chromosome segment between two parents two specified locations in the children. Both chromosomes must be the same size. When locus-index1 > locus-index2, the copied segment wraps
around the end of the chromosomes; When the designated segment indicates the entire chromosome, nothing is copied.

Source

chromosome-methods.lisp.

Generic Function: 2x-cross-organisms (parent1 parent2 child1 child2 &key chromosome-index parent1-chromosome locus-index1 locus-index2)
Package

geco.

Methods
Method: 2x-cross-organisms ((parent1 organism) (parent2 organism) (child1 organism) (child2 organism) &key chromosome-index parent1-chromosome locus-index1 locus-index2)

Two-point crossover of random chromosomes between two organisms.

Source

organism-methods.lisp.

Generic Function: allele-code-to-value (chromosome locus-index allele-code)

Returns the allele which would be represented by allele-code for the given locus-index on chromosome.

Package

geco.

Source

generics.lisp.

Methods
Method: allele-code-to-value ((self binary-chromosome) locus-index allele-code)

A much more efficient implementation than the general case of indexing into the vector returned by allele-values.

Source

chromosome-methods.lisp.

Method: allele-code-to-value ((self chromosome) locus-index allele-code)
Source

chromosome-methods.lisp.

Generic Function: allele-values (chromosome locus-index)

Returns a vector of allele values which represents the possible values of the allele at the indicated locus of the chromosome.

Package

geco.

Source

generics.lisp.

Methods
Method: allele-values ((self binary-chromosome) locus-index)
Source

chromosome-methods.lisp.

Generic Function: as-good-as-test (pop)
Package

geco.

Methods
Method: as-good-as-test ((pop minimizing-score-mixin))
Source

population-methods.lisp.

Method: as-good-as-test ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Reader: avg-normalized-score (object)
Package

geco.

Methods
Reader Method: avg-normalized-score ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

avg-normalized-score.

Generic Writer: (setf avg-normalized-score) (object)
Package

geco.

Methods
Writer Method: (setf avg-normalized-score) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

avg-normalized-score.

Generic Reader: avg-score (object)
Package

geco.

Methods
Reader Method: avg-score ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

avg-score.

Generic Writer: (setf avg-score) (object)
Package

geco.

Methods
Writer Method: (setf avg-score) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

avg-score.

Generic Reader: b2g-map (object)
Package

geco.

Methods
Reader Method: b2g-map ((gray-code-translation gray-code-translation))

automatically generated reader method

Source

classes.lisp.

Target Slot

b2g-map.

Generic Writer: (setf b2g-map) (object)
Package

geco.

Methods
Writer Method: (setf b2g-map) ((gray-code-translation gray-code-translation))

automatically generated writer method

Source

classes.lisp.

Target Slot

b2g-map.

Generic Function: best-organism (pop)
Package

geco.

Methods
Method: best-organism ((pop minimizing-score-mixin))
Source

population-methods.lisp.

Method: best-organism ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Function: best-organism-accessor (pop)
Package

geco.

Methods
Method: best-organism-accessor ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Function: better-than-test (pop)
Package

geco.

Methods
Method: better-than-test ((pop minimizing-score-mixin))
Source

population-methods.lisp.

Method: better-than-test ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Function: bin2gray (self bin)
Package

geco.

Methods
Method: bin2gray ((self gray-code-translation) bin)
Source

chromosome-methods.lisp.

Generic Function: chromosome-classes (organism)

Returns a list of classes of chromosomes for the organism. The size of this list determines the number of chromosomes. Typically this is a class allocated slot on the instantiated class.

Package

geco.

Source

generics.lisp.

Generic Function: compute-binary-allele-statistics (population)
Package

geco.

Methods
Method: compute-binary-allele-statistics ((population population))

Returns a list of vectors (one per binary chromosome in the organisms of the population) of counts by locus of non-zero alleles.

Source

population-methods.lisp.

Generic Function: compute-normalized-statistics (self)
Package

geco.

Methods
Method: compute-normalized-statistics ((self population-statistics))
Source

pop-stats-methods.lisp.

Generic Function: compute-statistics (thing)

Compute the statistics for the relevent thing.

Package

geco.

Source

generics.lisp.

Methods
Method: compute-statistics ((pop population))

This method should only be used if the statistics need to be recomputed.
They are initially computed when the population-statistics instance is first created for the population.

Source

population-methods.lisp.

Method: compute-statistics ((self population-statistics))
Source

pop-stats-methods.lisp.

Generic Function: converged-p (population)

A predicate which returns true (non-NIL) when the population is converged.

Package

geco.

Source

generics.lisp.

Methods
Method: converged-p ((pop population))

A predicate which returns true (non-NIL) when the population has converged.
This method defines convergence as either of the following:
1. The entire population is converged to a single score value; or
2. At least convergence-fraction of the current population has a normalized score value which is as good as convergence-threshold-margin of the population.
Here, as good as is determined using the function returned by the as-good-as-test generic function of the population.

Source

population-methods.lisp.

Generic Function: convergence-fraction (population)

Returns a number in the range (0,1] which indicates the portion of the population which has converged to the current best score in the population.

Package

geco.

Source

generics.lisp.

Methods
Method: convergence-fraction ((pop minimizing-score-mixin))
Source

population-methods.lisp.

Method: convergence-fraction ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Function: convergence-threshold-margin (population)

Returns a number in the range (0,1] which indicates the fraction of the current population’s best score which the convergence-fraction of the population must be as good as to be converged.

Package

geco.

Source

generics.lisp.

Methods
Method: convergence-threshold-margin ((pop minimizing-score-mixin))
Source

population-methods.lisp.

Method: convergence-threshold-margin ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Function: copy-chromosome (chromosome owner-organism)

Creates a copy of chromosome, which will belong to owner-organism. The score is not copied, forcing the organism to be EVALUATEd.

Package

geco.

Source

generics.lisp.

Methods
Method: copy-chromosome ((self chromosome) owner-organism)
Source

chromosome-methods.lisp.

Generic Function: copy-chromosome-with-score (chromosome owner-organism)

Creates a copy of chromosome, including its score, which will belong to owner-organism.

Package

geco.

Source

generics.lisp.

Generic Function: copy-organism (organism &key new-population)

Creates a copy of organism, which will optionally belong to new-population.

Package

geco.

Source

generics.lisp.

Methods
Method: copy-organism ((self organism) &key new-population)
Source

organism-methods.lisp.

Generic Function: copy-organism-with-score (self &key new-population)
Package

geco.

Methods
Method: copy-organism-with-score ((self organism) &key new-population)
Source

organism-methods.lisp.

Generic Function: count-allele-codes (chromosome from-index loci-to-count allele-code)
Package

geco.

Methods
Method: count-allele-codes ((chromosome chromosome) from-index loci-to-count allele-code)

Returns the number of loci in the loci-to-count loci of chromosome, starting at from-index, wich have allele-code

Source

chromosome-methods.lisp.

Generic Function: cross-chromosomes (parent1 parent2 child1 child2 locus-index)
Package

geco.

Methods
Method: cross-chromosomes ((parent1 chromosome) (parent2 chromosome) (child1 chromosome) (child2 chromosome) locus-index)

[One-point crossover] Cross a chromosome segment between two parents at a specified location in the children. Both chromosomes must be the same size.

Source

chromosome-methods.lisp.

Generic Function: cross-organisms (parent1 parent2 child1 child2 &key chromosome-index parent1-chromosome locus-index)
Package

geco.

Methods
Method: cross-organisms ((parent1 organism) (parent2 organism) (child1 organism) (child2 organism) &key chromosome-index parent1-chromosome locus-index)

Crossover random chromosomes between two organisms.

Source

organism-methods.lisp.

Generic Function: decode (organism)

Convert an organism’s chromosomal representation (it’s genotype) into it’s phenotype,
i.e., what the genotype is intended to represent, and save it in the phenotype slot of the organism.
This may or may not be of practical value to a particular implementation. The function is invoked immediately before the organism is evaluated.

Package

geco.

Source

generics.lisp.

Generic Function: decode-binary-loci-value (chromosome from-index loci-to-decode)
Package

geco.

Methods
Method: decode-binary-loci-value ((chromosome binary-chromosome) from-index loci-to-decode)

Returns the binary value represented by the loci-to-decode loci of chromosome, starting at from-index. chromosome is assumed to be an array of bit.

Source

chromosome-methods.lisp.

Generic Reader: ecosystem (object)
Package

geco.

Methods
Reader Method: ecosystem ((population population))

automatically generated reader method

Source

classes.lisp.

Target Slot

ecosystem.

Reader Method: ecosystem ((genetic-plan genetic-plan))

automatically generated reader method

Source

classes.lisp.

Target Slot

ecosystem.

Generic Writer: (setf ecosystem) (object)
Package

geco.

Methods
Writer Method: (setf ecosystem) ((population population))

automatically generated writer method

Source

classes.lisp.

Target Slot

ecosystem.

Writer Method: (setf ecosystem) ((genetic-plan genetic-plan))

automatically generated writer method

Source

classes.lisp.

Target Slot

ecosystem.

Generic Function: eidetic (thing1 thing2)

Predicate, true if both things are the same class and have the same genetic makeup.

Package

geco.

Source

generics.lisp.

Methods
Method: eidetic ((org1 organism) (org2 organism))

Predicate, true if the organisms are of the same class and have the same chromosomes.

Source

organism-methods.lisp.

Method: eidetic ((chr1 chromosome) (chr2 chromosome))

Predicate, true if the chromosomes are of the same class and have the same alleles.

Source

chromosome-methods.lisp.

Generic Function: evaluate (thing plan)

Determine the score of the thing, be it ecosystem, population, or organism, with respect to plan.

Package

geco.

Source

generics.lisp.

Methods
Method: evaluate ((self ecosystem) (plan genetic-plan))
Source

ecosystem-methods.lisp.

Method: evaluate ((pop population) (plan genetic-plan))
Source

population-methods.lisp.

Method: evaluate :after ((self organism) (plan genetic-plan))
Source

organism-methods.lisp.

Method: evaluate :before ((self organism-phenotype-mixin) (plan genetic-plan))
Source

organism-methods.lisp.

Generic Reader: evaluation-limit (object)
Generic Writer: (setf evaluation-limit) (object)
Package

geco.

Methods
Reader Method: evaluation-limit ((genetic-plan genetic-plan))
Writer Method: (setf evaluation-limit) ((genetic-plan genetic-plan))

If non-nil, it should be an integer, the final generation number.

Source

classes.lisp.

Target Slot

evaluation-limit.

Generic Reader: evaluation-number (object)
Package

geco.

Methods
Reader Method: evaluation-number ((ecosystem ecosystem))

automatically generated reader method

Source

classes.lisp.

Target Slot

evaluation-number.

Generic Writer: (setf evaluation-number) (object)
Package

geco.

Methods
Writer Method: (setf evaluation-number) ((ecosystem ecosystem))

automatically generated writer method

Source

classes.lisp.

Target Slot

evaluation-number.

Generic Function: evolution-termination-p (plan)

A predicate which returns true (non-NIL) when evolution should terminate.
A default method is provided on the class genetic-plan which returns T when the generation-number of the ecosystem reaches the generation-limit of the plan,
or when the evaluation-number of the ecosystem reaches the evaluation-limit of the plan, or when the population has converged, based on the converged-p predicate.

Package

geco.

Source

generics.lisp.

Methods
Method: evolution-termination-p ((self genetic-plan))
Source

genetic-plan-methods.lisp.

Generic Function: evolve (thing)

Create new generations until a termination condition is reached.

Package

geco.

Source

generics.lisp.

Methods
Method: evolve ((self ecosystem))
Source

ecosystem-methods.lisp.

Generic Reader: g2b-map (object)
Package

geco.

Methods
Reader Method: g2b-map ((gray-code-translation gray-code-translation))

automatically generated reader method

Source

classes.lisp.

Target Slot

g2b-map.

Generic Writer: (setf g2b-map) (object)
Package

geco.

Methods
Writer Method: (setf g2b-map) ((gray-code-translation gray-code-translation))

automatically generated writer method

Source

classes.lisp.

Target Slot

g2b-map.

Generic Reader: generation-limit (object)
Generic Writer: (setf generation-limit) (object)
Package

geco.

Methods
Reader Method: generation-limit ((genetic-plan genetic-plan))
Writer Method: (setf generation-limit) ((genetic-plan genetic-plan))

If non-nil, it should be an integer, the final evaluation number.

Source

classes.lisp.

Target Slot

generation-limit.

Generic Reader: generation-number (object)
Package

geco.

Methods
Reader Method: generation-number ((ecosystem ecosystem))

automatically generated reader method

Source

classes.lisp.

Target Slot

generation-number.

Generic Writer: (setf generation-number) (object)
Package

geco.

Methods
Writer Method: (setf generation-number) ((ecosystem ecosystem))

automatically generated writer method

Source

classes.lisp.

Target Slot

generation-number.

Generic Reader: genotype (object)
Package

geco.

Methods
Reader Method: genotype ((organism organism))

automatically generated reader method

Source

classes.lisp.

Target Slot

genotype.

Generic Writer: (setf genotype) (object)
Package

geco.

Methods
Writer Method: (setf genotype) ((organism organism))

automatically generated writer method

Source

classes.lisp.

Target Slot

genotype.

Generic Function: genotype-printable-form (self)
Package

geco.

Methods
Method: genotype-printable-form ((self organism))
Source

organism-methods.lisp.

Generic Function: gray2bin (self gray)
Package

geco.

Methods
Method: gray2bin ((self gray-code-translation) gray)
Source

chromosome-methods.lisp.

Generic Function: hamming-distance (c1 c2)
Package

geco.

Methods
Method: hamming-distance ((c1 chromosome) (c2 chromosome))
Source

chromosome-methods.lisp.

Generic Reader: loci (object)
Package

geco.

Methods
Reader Method: loci ((chromosome chromosome))

automatically generated reader method

Source

classes.lisp.

Target Slot

loci.

Generic Writer: (setf loci) (object)
Package

geco.

Methods
Writer Method: (setf loci) ((chromosome chromosome))

automatically generated writer method

Source

classes.lisp.

Target Slot

loci.

Generic Function: loci-printable-form (self)
Package

geco.

Methods
Method: loci-printable-form ((self chromosome))
Source

chromosome-methods.lisp.

Generic Function: locus (self index)
Package

geco.

Methods
Method: locus ((self chromosome) index)
Source

chromosome-methods.lisp.

Generic Function: (setf locus) (self index)
Package

geco.

Methods
Method: (setf locus) ((self chromosome) index)
Source

chromosome-methods.lisp.

Generic Function: locus-arity (chromosome locus-index)

Returns the number of allele values which may be used at this locus of this chromosome.

Package

geco.

Source

generics.lisp.

Methods
Method: locus-arity ((self binary-chromosome) locus-index)
Source

chromosome-methods.lisp.

Generic Function: locus-printable-form (self locus-index)
Package

geco.

Methods
Method: locus-printable-form ((self chromosome) locus-index)

Returns a character which represents the value of the allele at the indicated locus of the chromosome.

Source

chromosome-methods.lisp.

Generic Function: make-chromosome (organism chromosome-class &key size random)

Returns an instance of chromosome-class which will be a part of organsm. The chromosome’s size
is specified by the keyword size, and the chromosome’s allele’s will be initialized to random values if the keyword random has a non-nil value.

Package

geco.

Source

generics.lisp.

Methods
Method: make-chromosome ((org organism) chromosome-class &key size random)
Source

organism-methods.lisp.

Generic Function: make-chromosomes (organism &key random)

Returns a list instances of the appropriate subclasses of chromosome-class for organsm. The
chromosome’s sizes are the default size for each instance, and the chromosome’s allele’s will be initialized to random values if the keyword random has a non-nil value.

Package

geco.

Source

generics.lisp.

Methods
Method: make-chromosomes ((self organism) &key random)
Source

organism-methods.lisp.

Generic Function: make-genetic-plan (ecosystem genetic-plan-class)

Returns an instance of genetic-plan-class which will be used by ecosystem.

Package

geco.

Source

generics.lisp.

Methods
Method: make-genetic-plan ((ecosystem ecosystem) plan-class)
Source

ecosystem-methods.lisp.

Generic Function: make-loci-vector (chromosome size &key random &allow-other-keys)

Returns the object (usually a vector) which will contain the loci for the chromosome.
If random is non-nil, the loci are initialized to random alleles.

Package

geco.

Source

generics.lisp.

Methods
Method: make-loci-vector ((self binary-chromosome) size &key &allow-other-keys)
Source

chromosome-methods.lisp.

Method: make-loci-vector :around ((self chromosome) size &key random)
Source

chromosome-methods.lisp.

Method: make-loci-vector ((self chromosome) size &key &allow-other-keys)
Source

chromosome-methods.lisp.

Generic Function: make-organism (population &key random no-chromosomes)

Returns an instance of organism-class, or the appropriate subclass, for population.
The organisms chromosomes will be initialized to random values if the keyword random has a non-nil value.

Package

geco.

Source

generics.lisp.

Methods
Method: make-organism ((pop population) &key random no-chromosomes)
Source

population-methods.lisp.

Generic Function: make-organisms (population &key random)

Creates all the organisms for the specified population, storing them in the organisms vector.
The organism instances are created using make-organism, using the value of the random keyword argument. The organisms chromosomes will be initialized to random values if the keyword random has a non-nil value. The value returned by this function is not defined.

Package

geco.

Source

generics.lisp.

Methods
Method: make-organisms ((pop population) &key random)
Source

population-methods.lisp.

Generic Function: make-organisms-vector (population size)

Returns the object (usually a vector) which will contain the organisms for the population.

Package

geco.

Source

generics.lisp.

Methods
Method: make-organisms-vector ((self population) size)
Source

population-methods.lisp.

Generic Function: make-population (ecosystem population-class &key size random)

Returns an instance of population-class which will be a part of ecosystem. If size is specified, the population’s organism vector and organisms will be created.

Package

geco.

Source

generics.lisp.

Methods
Method: make-population ((ecosystem ecosystem) pop-class &key size random)
Source

ecosystem-methods.lisp.

Generic Function: make-population-statistics (population)

Returns an instance of (possibly a subclass of) population-statistics which will be used for population.

Package

geco.

Source

generics.lisp.

Methods
Method: make-population-statistics ((pop population))
Source

population-methods.lisp.

Generic Reader: max-organism (object)
Package

geco.

Methods
Reader Method: max-organism ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

max-organism.

Generic Writer: (setf max-organism) (object)
Package

geco.

Methods
Writer Method: (setf max-organism) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

max-organism.

Generic Reader: max-score (object)
Package

geco.

Methods
Reader Method: max-score ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

max-score.

Generic Writer: (setf max-score) (object)
Package

geco.

Methods
Writer Method: (setf max-score) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

max-score.

Generic Function: maximizing-p (pop)
Package

geco.

Methods
Method: maximizing-p ((pop minimizing-score-mixin))
Source

population-methods.lisp.

Method: maximizing-p ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Reader: min-organism (object)
Package

geco.

Methods
Reader Method: min-organism ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

min-organism.

Generic Writer: (setf min-organism) (object)
Package

geco.

Methods
Writer Method: (setf min-organism) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

min-organism.

Generic Reader: min-score (object)
Package

geco.

Methods
Reader Method: min-score ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

min-score.

Generic Writer: (setf min-score) (object)
Package

geco.

Methods
Writer Method: (setf min-score) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

min-score.

Generic Function: minimizing-p (pop)
Package

geco.

Methods
Method: minimizing-p ((pop minimizing-score-mixin))
Source

population-methods.lisp.

Method: minimizing-p ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Function: mutate-chromosome (self locus-index)
Package

geco.

Methods
Method: mutate-chromosome ((self chromosome) locus-index)
Source

chromosome-methods.lisp.

Generic Function: mutate-organism (self &key chromosome-index chromosome locus-index)
Package

geco.

Methods
Method: mutate-organism ((self organism) &key chromosome-index chromosome locus-index)

Mutate a random locus on an organism

Source

organism-methods.lisp.

Generic Function: normalize-score (thing plan)

Normalize the score for a population or organism, according to the genetic plan plan, and revise the population statistics if necessary.

Package

geco.

Source

generics.lisp.

Methods
Method: normalize-score ((pop population) (plan genetic-plan))

Normalize all the score values for each organism in the population, according to the genetic plan, and update the population-statistics with normalized values
(using compute-normalized-statistics).

Source

population-methods.lisp.

Method: normalize-score ((self organism) (plan genetic-plan))
Source

organism-methods.lisp.

Generic Reader: normalized-score (object)
Package

geco.

Methods
Reader Method: normalized-score ((organism organism))

automatically generated reader method

Source

classes.lisp.

Target Slot

normalized-score.

Generic Writer: (setf normalized-score) (object)
Package

geco.

Methods
Writer Method: (setf normalized-score) ((organism organism))

automatically generated writer method

Source

classes.lisp.

Target Slot

normalized-score.

Generic Reader: number-of-bits (object)
Package

geco.

Methods
Reader Method: number-of-bits ((gray-code-translation gray-code-translation))

automatically generated reader method

Source

classes.lisp.

Target Slot

number-of-bits.

Generic Writer: (setf number-of-bits) (object)
Package

geco.

Methods
Writer Method: (setf number-of-bits) ((gray-code-translation gray-code-translation))

automatically generated writer method

Source

classes.lisp.

Target Slot

number-of-bits.

Generic Reader: organism (object)
Package

geco.

Methods
Reader Method: organism ((chromosome chromosome))

automatically generated reader method

Source

classes.lisp.

Target Slot

organism.

Generic Writer: (setf organism) (object)
Package

geco.

Methods
Writer Method: (setf organism) ((chromosome chromosome))

automatically generated writer method

Source

classes.lisp.

Target Slot

organism.

Generic Function: organism-class (population)

Returns the class of organisms which are expected in the population. Typically this is a class allocated slot on the instantiated class.

Package

geco.

Source

generics.lisp.

Generic Reader: organisms (object)
Package

geco.

Methods
Reader Method: organisms ((population population))

automatically generated reader method

Source

classes.lisp.

Target Slot

organisms.

Generic Writer: (setf organisms) (object)
Package

geco.

Methods
Writer Method: (setf organisms) ((population population))

automatically generated writer method

Source

classes.lisp.

Target Slot

organisms.

Generic Reader: phenotype (object)
Package

geco.

Methods
Reader Method: phenotype ((organism-phenotype-mixin organism-phenotype-mixin))

automatically generated reader method

Source

classes.lisp.

Target Slot

phenotype.

Generic Writer: (setf phenotype) (object)
Package

geco.

Methods
Writer Method: (setf phenotype) ((organism-phenotype-mixin organism-phenotype-mixin))

automatically generated writer method

Source

classes.lisp.

Target Slot

phenotype.

Generic Function: pick-random-allele (self locus-index)
Package

geco.

Methods
Method: pick-random-allele ((self chromosome) locus-index)

Returns a random allele for the locus.

Source

chromosome-methods.lisp.

Generic Function: pick-random-alleles (self)
Package

geco.

Methods
Method: pick-random-alleles ((self sequence-chromosome))
Source

chromosome-methods.lisp.

Method: pick-random-alleles ((self chromosome))
Source

chromosome-methods.lisp.

Generic Function: pick-random-chromosome (self)
Package

geco.

Methods
Method: pick-random-chromosome ((self organism))
Source

organism-methods.lisp.

Generic Function: pick-random-chromosome-index (self)
Package

geco.

Methods
Method: pick-random-chromosome-index ((self organism))
Source

organism-methods.lisp.

Generic Function: pick-random-locus-index (self)
Package

geco.

Methods
Method: pick-random-locus-index ((self chromosome))

Returns a random locus index into the chromosome.

Source

chromosome-methods.lisp.

Generic Function: pick-random-organism (p)
Package

geco.

Methods
Method: pick-random-organism ((p population))

Returns a random organism from the population.

Source

selection-methods.lisp.

Generic Function: pick-random-organism-index (p)
Package

geco.

Methods
Method: pick-random-organism-index ((p population))

Returns the index number of a random organism from the population.

Source

selection-methods.lisp.

Generic Function: pick-some-random-organism-indices (p number-to-pick)
Package

geco.

Methods
Method: pick-some-random-organism-indices ((p population) number-to-pick)

Returns number-to-pick random organism indices for the population.

Source

selection-methods.lisp.

Generic Reader: plan (object)
Package

geco.

Methods
Reader Method: plan ((ecosystem ecosystem))

automatically generated reader method

Source

classes.lisp.

Target Slot

plan.

Generic Writer: (setf plan) (object)
Package

geco.

Methods
Writer Method: (setf plan) ((ecosystem ecosystem))

automatically generated writer method

Source

classes.lisp.

Target Slot

plan.

Generic Function: pmx-cross-chromosomes (parent1 parent2 child1 child2 &key locus-index1 locus-index2 allele-test)
Package

geco.

Methods
Method: pmx-cross-chromosomes ((parent1 sequence-chromosome) (parent2 sequence-chromosome) (child1 sequence-chromosome) (child2 sequence-chromosome) &key locus-index1 locus-index2 allele-test)
Source

chromosome-methods.lisp.

Generic Function: pmx-cross-organisms (parent1 parent2 child1 child2 &key allele-test chromosome-index parent1-chromosome locus-index1 locus-index2)
Package

geco.

Methods
Method: pmx-cross-organisms ((parent1 organism) (parent2 organism) (child1 organism) (child2 organism) &key allele-test chromosome-index parent1-chromosome locus-index1 locus-index2)
Source

organism-methods.lisp.

Generic Reader: population (object)
Package

geco.

Methods
Reader Method: population ((organism organism))

automatically generated reader method

Source

classes.lisp.

Target Slot

population.

Reader Method: population ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

population.

Reader Method: population ((ecosystem ecosystem))

automatically generated reader method

Source

classes.lisp.

Target Slot

population.

Generic Writer: (setf population) (object)
Package

geco.

Methods
Writer Method: (setf population) ((organism organism))

automatically generated writer method

Source

classes.lisp.

Target Slot

population.

Writer Method: (setf population) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

population.

Writer Method: (setf population) ((ecosystem ecosystem))

automatically generated writer method

Source

classes.lisp.

Target Slot

population.

Generic Function: population-statistics-class (population)

Returns the class of the population-statistics instance to be used with the population.

Package

geco.

Source

generics.lisp.

Methods
Method: population-statistics-class ((pop population))
Source

population-methods.lisp.

Generic Function: printable-allele-values (chromosome locus-index)

Returns a vector of characters which represents the possible values of the allele at the indicated locus of the chromosome.

Package

geco.

Source

generics.lisp.

Methods
Method: printable-allele-values ((self binary-chromosome) locus-index)
Source

chromosome-methods.lisp.

Generic Function: r3-cross-chromosomes (parent1 parent2 child1 child2 &key allele-test)
Package

geco.

Methods
Method: r3-cross-chromosomes ((parent1 sequence-chromosome) (parent2 sequence-chromosome) (child1 sequence-chromosome) (child2 sequence-chromosome) &key allele-test)

Random, Respectful Recombination (R3) crossover operator. Based on forma analysis work of Nicholas J. Radcliffe.

Source

chromosome-methods.lisp.

Generic Function: r3-cross-organisms (parent1 parent2 child1 child2 &key allele-test chromosome-index)
Package

geco.

Methods
Method: r3-cross-organisms ((parent1 organism) (parent2 organism) (child1 organism) (child2 organism) &key allele-test chromosome-index)
Source

organism-methods.lisp.

Generic Function: randomize-chromosomes (self)
Package

geco.

Methods
Method: randomize-chromosomes ((self organism))
Source

organism-methods.lisp.

Generic Function: ranking-preselect (pop &key multiplier max)
Package

geco.

Methods
Method: ranking-preselect ((pop population) &key multiplier max)

Prepare and return a function of no arguments which will select random organisms from the population, weighted by score, using a ranking technique developed by Baker.

Source

selection-methods.lisp.

Generic Function: regenerate (genetic-plan thing)

Returns a new, regenerated thing. Default methods are provided for ecosystems and populations.

Package

geco.

Source

generics.lisp.

Methods
Method: regenerate ((plan genetic-plan) (old-pop generational-population))

A rather dumb default method, which should be replaced by one that creates a new population from the previous one, using genetic operators, e.g., selection, mutation, and crossover.

Source

genetic-plan-methods.lisp.

Method: regenerate ((plan genetic-plan) (ecosys ecosystem))
Source

genetic-plan-methods.lisp.

Generic Function: roulette-pick-random-organism (pop)
Package

geco.

Methods
Method: roulette-pick-random-organism ((pop population))

Select a random organism from the population, weighted by score, using the roulette wheel approach, as used in DeJong’s R1; also known as Brindle’s stochastic sampling with replacement.

Source

selection-methods.lisp.

Generic Function: roulette-pick-random-organism-index (pop)
Package

geco.

Methods
Method: roulette-pick-random-organism-index ((pop population))

Select a random organism number from the population, weighted by score, using the roulette wheel approach, as used in DeJong’s R1; also known as Brindle’s stochastic sampling with replacement.

Source

selection-methods.lisp.

Generic Reader: score (object)
Package

geco.

Methods
Reader Method: score ((organism organism))

automatically generated reader method

Source

classes.lisp.

Target Slot

score.

Generic Writer: (setf score) (object)
Package

geco.

Methods
Writer Method: (setf score) ((organism organism))

automatically generated writer method

Source

classes.lisp.

Target Slot

score.

Generic Function: scramble-alleles (self)
Package

geco.

Methods
Method: scramble-alleles ((self chromosome))
Source

chromosome-methods.lisp.

Generic Function: size (thing)

Returns the size the thing. Typically this is a class allocated slot on the instantiated class.

Package

geco.

Source

generics.lisp.

Methods
Method: size ((self chromosome))
Source

chromosome-methods.lisp.

Reader Method: size ((population population))

automatically generated reader method

Source

classes.lisp.

Target Slot

size.

Generic Writer: (setf size) (object)
Package

geco.

Methods
Writer Method: (setf size) ((population population))

automatically generated writer method

Source

classes.lisp.

Target Slot

size.

Generic Reader: statistics (object)
Package

geco.

Methods
Reader Method: statistics ((population population))

automatically generated reader method

Source

classes.lisp.

Target Slot

statistics.

Generic Writer: (setf statistics) (object)
Package

geco.

Methods
Writer Method: (setf statistics) ((population population))

automatically generated writer method

Source

classes.lisp.

Target Slot

statistics.

Generic Function: stochastic-remainder-preselect (pop &key multiplier)
Package

geco.

Methods
Method: stochastic-remainder-preselect ((pop population) &key multiplier)

Prepare and return a function of no arguments which will select random organisms from the population, weighted by score, using a technique referred to by Brindle as stochastic remainder selection without replacement.

Source

selection-methods.lisp.

Generic Reader: sum-normalized-score (object)
Package

geco.

Methods
Reader Method: sum-normalized-score ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

sum-normalized-score.

Generic Writer: (setf sum-normalized-score) (object)
Package

geco.

Methods
Writer Method: (setf sum-normalized-score) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

sum-normalized-score.

Generic Reader: sum-score (object)
Package

geco.

Methods
Reader Method: sum-score ((population-statistics population-statistics))

automatically generated reader method

Source

classes.lisp.

Target Slot

sum-score.

Generic Writer: (setf sum-score) (object)
Package

geco.

Methods
Writer Method: (setf sum-score) ((population-statistics population-statistics))

automatically generated writer method

Source

classes.lisp.

Target Slot

sum-score.

Generic Function: swap-alleles (self &key chromosome locus-index locus-index2)
Package

geco.

Methods
Method: swap-alleles ((self organism) &key chromosome locus-index locus-index2)
Source

organism-methods.lisp.

Method: swap-alleles ((self chromosome) &key locus-index locus-index2)
Source

chromosome-methods.lisp.

Generic Function: tournament-select-organism (p tournament-size)
Package

geco.

Methods
Method: tournament-select-organism ((p population) tournament-size)

Pick tournament-size organisms from the population at random, and returns the best one.

Source

selection-methods.lisp.

Generic Function: uniform-cross-chromosomes (parent1 parent2 child1 child2 &key bias)
Package

geco.

Methods
Method: uniform-cross-chromosomes ((parent1 chromosome) (parent2 chromosome) (child1 chromosome) (child2 chromosome) &key bias)

Uniform crossover of chromosomes between two parents, with optional bias in (0.0:1.0]. Default bias is 0.5; larger bias indicates larger number of crossed alleles.

Source

chromosome-methods.lisp.

Generic Function: uniform-cross-organisms (parent1 parent2 child1 child2 &key chromosome-index bias)
Package

geco.

Methods
Method: uniform-cross-organisms ((parent1 organism) (parent2 organism) (child1 organism) (child2 organism) &key chromosome-index bias)

Uniform crossover of random chromosomes between two organisms.

Source

organism-methods.lisp.

Generic Function: worst-organism (pop)
Package

geco.

Methods
Method: worst-organism ((pop minimizing-score-mixin))
Source

population-methods.lisp.

Method: worst-organism ((pop maximizing-score-mixin))
Source

population-methods.lisp.

Generic Function: worst-organism-accessor (pop)
Package

geco.

Methods
Method: worst-organism-accessor ((pop maximizing-score-mixin))
Source

population-methods.lisp.


6.1.3 Standalone methods

Method: print-object ((self population-statistics) stream)
Source

pop-stats-methods.lisp.

Method: print-object ((self organism) stream)
Source

organism-methods.lisp.

Method: print-object ((self chromosome) stream)
Source

chromosome-methods.lisp.

Method: shared-initialize :after ((self population-statistics) slot-names &rest initargs)
Source

pop-stats-methods.lisp.

Method: shared-initialize :after ((self ecosystem) slot-names &rest initargs &key plan-class pop-class pop-size generation-limit evaluation-limit)
Source

ecosystem-methods.lisp.

Method: shared-initialize :after ((organism organism) slot-names &rest initargs &key random no-chromosomes)
Source

organism-methods.lisp.

Method: shared-initialize :after ((self gray-code-translation) slot-names &rest initargs &key number-of-bits number-of-bits-supplied-p)
Source

chromosome-methods.lisp.

Method: shared-initialize :after ((self chromosome) slot-names &rest initargs &key size organism random)
Source

chromosome-methods.lisp.

Method: shared-initialize :after ((pop population) slot-names &rest initargs &key random)
Source

population-methods.lisp.


6.1.4 Classes

Class: binary-chromosome
Package

geco.

Source

classes.lisp.

Direct superclasses

chromosome.

Direct methods
Class: chromosome
Package

geco.

Source

classes.lisp.

Direct subclasses
Direct methods
Direct slots
Slot: organism
Type

(or geco:organism null)

Initform

(quote nil)

Initargs

:organism

Readers

organism.

Writers

(setf organism).

Slot: loci
Type

array

Initargs

:loci

Readers

loci.

Writers

(setf loci).

Class: ecosystem
Package

geco.

Source

classes.lisp.

Direct methods
Direct slots
Slot: plan
Type

geco:genetic-plan

Readers

plan.

Writers

(setf plan).

Slot: population
Type

geco:population

Readers

population.

Writers

(setf population).

Slot: generation-number
Type

integer

Initform

0

Readers

generation-number.

Writers

(setf generation-number).

Slot: evaluation-number
Type

integer

Initform

0

Readers

evaluation-number.

Writers

(setf evaluation-number).

Class: generational-population
Package

geco.

Source

classes.lisp.

Direct superclasses

population.

Direct methods

regenerate.

Class: genetic-plan
Package

geco.

Source

classes.lisp.

Direct methods
Direct slots
Slot: ecosystem
Type

geco:ecosystem

Initargs

:ecosystem

Readers

ecosystem.

Writers

(setf ecosystem).

Slot: generation-limit

If non-nil, it should be an integer, the final evaluation number.

Type

(or integer null)

Initargs

:generation-limit

Readers

generation-limit.

Writers

(setf generation-limit).

Slot: evaluation-limit

If non-nil, it should be an integer, the final generation number.

Type

(or integer null)

Initargs

:evaluation-limit

Readers

evaluation-limit.

Writers

(setf evaluation-limit).

Class: gray-code-translation
Package

geco.

Source

classes.lisp.

Direct methods
Direct slots
Slot: number-of-bits
Type

fixnum

Initargs

:number-of-bits

Readers

number-of-bits.

Writers

(setf number-of-bits).

Slot: b2g-map
Type

(array bit (* *))

Readers

b2g-map.

Writers

(setf b2g-map).

Slot: g2b-map
Type

(array bit (* *))

Readers

g2b-map.

Writers

(setf g2b-map).

Class: maximizing-score-mixin

Class to mix with population classes whose organism’s score is better when larger. An organisms score represents fitness or benefit.

Package

geco.

Source

classes.lisp.

Direct methods
Class: minimizing-score-mixin

Class to mix with population classes whose organism’s score is better when smaller. An organisms score represents a cost or penalty.

Package

geco.

Source

classes.lisp.

Direct methods
Class: organism
Package

geco.

Source

classes.lisp.

Direct methods
Direct slots
Slot: population
Type

(or geco:population null)

Initform

(quote nil)

Initargs

:population

Readers

population.

Writers

(setf population).

Slot: genotype
Type

list

Initform

(quote nil)

Initargs

:genotype

Readers

genotype.

Writers

(setf genotype).

Slot: score
Initform

(quote nil)

Initargs

:score

Readers

score.

Writers

(setf score).

Slot: normalized-score
Initform

(quote nil)

Initargs

:normalized-score

Readers

normalized-score.

Writers

(setf normalized-score).

Class: organism-phenotype-mixin
Package

geco.

Source

classes.lisp.

Direct methods
Direct slots
Slot: phenotype
Initargs

:phenotype

Readers

phenotype.

Writers

(setf phenotype).

Class: population
Package

geco.

Source

classes.lisp.

Direct subclasses

generational-population.

Direct methods
Direct slots
Slot: ecosystem
Type

geco:ecosystem

Initargs

:ecosystem

Readers

ecosystem.

Writers

(setf ecosystem).

Slot: organisms
Type

vector

Readers

organisms.

Writers

(setf organisms).

Slot: size
Type

(or fixnum null)

Initargs

:size

Readers

size.

Writers

(setf size).

Slot: statistics
Type

geco:population-statistics

Initargs

:statistics

Readers

statistics.

Writers

(setf statistics).

Class: population-statistics
Package

geco.

Source

classes.lisp.

Direct methods
Direct slots
Slot: population
Type

geco:population

Initargs

:population

Readers

population.

Writers

(setf population).

Slot: sum-score
Type

number

Initargs

:sum-score

Readers

sum-score.

Writers

(setf sum-score).

Slot: avg-score
Type

number

Initargs

:avg-score

Readers

avg-score.

Writers

(setf avg-score).

Slot: max-score
Type

number

Initargs

:max-score

Readers

max-score.

Writers

(setf max-score).

Slot: min-score
Type

number

Initargs

:min-score

Readers

min-score.

Writers

(setf min-score).

Slot: max-organism
Type

geco:organism

Initargs

:max-organism

Readers

max-organism.

Writers

(setf max-organism).

Slot: min-organism
Type

geco:organism

Initargs

:min-organism

Readers

min-organism.

Writers

(setf min-organism).

Slot: sum-normalized-score
Initargs

:sum-normalized-score

Readers

sum-normalized-score.

Writers

(setf sum-normalized-score).

Slot: avg-normalized-score
Initargs

:avg-normalized-score

Readers

avg-normalized-score.

Writers

(setf avg-normalized-score).

Class: sequence-chromosome
Package

geco.

Source

classes.lisp.

Direct superclasses

chromosome.

Direct methods

6.2 Internals


6.2.1 Special variables

Special Variable: *dbg-flags*

Either a list of flags controlling debugging code, or T for globally on, or NIL for globally off.

Package

geco.

Source

dbg.lisp.


6.2.2 Ordinary functions

Function: geco-random-state ()
Package

geco.

Source

random.lisp.

Function: set-geco-random-state (new-state)
Package

geco.

Source

random.lisp.


Appendix A Indexes


A.1 Concepts


A.2 Functions

Jump to:   (   2  
A   B   C   D   E   F   G   H   L   M   N   O   P   R   S   T   U   W  
Index Entry  Section

(
(setf avg-normalized-score): Public generic functions
(setf avg-normalized-score): Public generic functions
(setf avg-score): Public generic functions
(setf avg-score): Public generic functions
(setf b2g-map): Public generic functions
(setf b2g-map): Public generic functions
(setf ecosystem): Public generic functions
(setf ecosystem): Public generic functions
(setf ecosystem): Public generic functions
(setf evaluation-limit): Public generic functions
(setf evaluation-limit): Public generic functions
(setf evaluation-number): Public generic functions
(setf evaluation-number): Public generic functions
(setf g2b-map): Public generic functions
(setf g2b-map): Public generic functions
(setf generation-limit): Public generic functions
(setf generation-limit): Public generic functions
(setf generation-number): Public generic functions
(setf generation-number): Public generic functions
(setf genotype): Public generic functions
(setf genotype): Public generic functions
(setf loci): Public generic functions
(setf loci): Public generic functions
(setf locus): Public generic functions
(setf locus): Public generic functions
(setf max-organism): Public generic functions
(setf max-organism): Public generic functions
(setf max-score): Public generic functions
(setf max-score): Public generic functions
(setf min-organism): Public generic functions
(setf min-organism): Public generic functions
(setf min-score): Public generic functions
(setf min-score): Public generic functions
(setf normalized-score): Public generic functions
(setf normalized-score): Public generic functions
(setf number-of-bits): Public generic functions
(setf number-of-bits): Public generic functions
(setf organism): Public generic functions
(setf organism): Public generic functions
(setf organisms): Public generic functions
(setf organisms): Public generic functions
(setf phenotype): Public generic functions
(setf phenotype): Public generic functions
(setf plan): Public generic functions
(setf plan): Public generic functions
(setf population): Public generic functions
(setf population): Public generic functions
(setf population): Public generic functions
(setf population): Public generic functions
(setf score): Public generic functions
(setf score): Public generic functions
(setf size): Public generic functions
(setf size): Public generic functions
(setf statistics): Public generic functions
(setf statistics): Public generic functions
(setf sum-normalized-score): Public generic functions
(setf sum-normalized-score): Public generic functions
(setf sum-score): Public generic functions
(setf sum-score): Public generic functions

2
2x-cross-chromosomes: Public generic functions
2x-cross-chromosomes: Public generic functions
2x-cross-organisms: Public generic functions
2x-cross-organisms: Public generic functions

A
allele-code-to-value: Public generic functions
allele-code-to-value: Public generic functions
allele-code-to-value: Public generic functions
allele-values: Public generic functions
allele-values: Public generic functions
as-good-as-test: Public generic functions
as-good-as-test: Public generic functions
as-good-as-test: Public generic functions
avg-normalized-score: Public generic functions
avg-normalized-score: Public generic functions
avg-score: Public generic functions
avg-score: Public generic functions

B
b2g-map: Public generic functions
b2g-map: Public generic functions
best-organism: Public generic functions
best-organism: Public generic functions
best-organism: Public generic functions
best-organism-accessor: Public generic functions
best-organism-accessor: Public generic functions
better-than-test: Public generic functions
better-than-test: Public generic functions
better-than-test: Public generic functions
bin2gray: Public generic functions
bin2gray: Public generic functions

C
chromosome-classes: Public generic functions
compute-binary-allele-statistics: Public generic functions
compute-binary-allele-statistics: Public generic functions
compute-normalized-statistics: Public generic functions
compute-normalized-statistics: Public generic functions
compute-statistics: Public generic functions
compute-statistics: Public generic functions
compute-statistics: Public generic functions
converged-p: Public generic functions
converged-p: Public generic functions
convergence-fraction: Public generic functions
convergence-fraction: Public generic functions
convergence-fraction: Public generic functions
convergence-threshold-margin: Public generic functions
convergence-threshold-margin: Public generic functions
convergence-threshold-margin: Public generic functions
copy-chromosome: Public generic functions
copy-chromosome: Public generic functions
copy-chromosome-with-score: Public generic functions
copy-organism: Public generic functions
copy-organism: Public generic functions
copy-organism-with-score: Public generic functions
copy-organism-with-score: Public generic functions
count-allele-codes: Public generic functions
count-allele-codes: Public generic functions
cross-chromosomes: Public generic functions
cross-chromosomes: Public generic functions
cross-organisms: Public generic functions
cross-organisms: Public generic functions

D
dbg: Public ordinary functions
dbg-p: Public ordinary functions
dbg?: Public ordinary functions
dbgo: Public ordinary functions
decode: Public generic functions
decode-binary-loci-value: Public generic functions
decode-binary-loci-value: Public generic functions

E
ecosystem: Public generic functions
ecosystem: Public generic functions
ecosystem: Public generic functions
eidetic: Public generic functions
eidetic: Public generic functions
eidetic: Public generic functions
evaluate: Public generic functions
evaluate: Public generic functions
evaluate: Public generic functions
evaluate: Public generic functions
evaluate: Public generic functions
evaluation-limit: Public generic functions
evaluation-limit: Public generic functions
evaluation-number: Public generic functions
evaluation-number: Public generic functions
evolution-termination-p: Public generic functions
evolution-termination-p: Public generic functions
evolve: Public generic functions
evolve: Public generic functions

F
Function, dbg: Public ordinary functions
Function, dbg-p: Public ordinary functions
Function, dbg?: Public ordinary functions
Function, dbgo: Public ordinary functions
Function, geco-random-float: Public ordinary functions
Function, geco-random-integer: Public ordinary functions
Function, geco-random-state: Private ordinary functions
Function, roulette-pick-random-weight-index: Public ordinary functions
Function, set-geco-random-state: Private ordinary functions
Function, undbg: Public ordinary functions

G
g2b-map: Public generic functions
g2b-map: Public generic functions
geco-random-float: Public ordinary functions
geco-random-integer: Public ordinary functions
geco-random-state: Private ordinary functions
generation-limit: Public generic functions
generation-limit: Public generic functions
generation-number: Public generic functions
generation-number: Public generic functions
Generic Function, (setf avg-normalized-score): Public generic functions
Generic Function, (setf avg-score): Public generic functions
Generic Function, (setf b2g-map): Public generic functions
Generic Function, (setf ecosystem): Public generic functions
Generic Function, (setf evaluation-limit): Public generic functions
Generic Function, (setf evaluation-number): Public generic functions
Generic Function, (setf g2b-map): Public generic functions
Generic Function, (setf generation-limit): Public generic functions
Generic Function, (setf generation-number): Public generic functions
Generic Function, (setf genotype): Public generic functions
Generic Function, (setf loci): Public generic functions
Generic Function, (setf locus): Public generic functions
Generic Function, (setf max-organism): Public generic functions
Generic Function, (setf max-score): Public generic functions
Generic Function, (setf min-organism): Public generic functions
Generic Function, (setf min-score): Public generic functions
Generic Function, (setf normalized-score): Public generic functions
Generic Function, (setf number-of-bits): Public generic functions
Generic Function, (setf organism): Public generic functions
Generic Function, (setf organisms): Public generic functions
Generic Function, (setf phenotype): Public generic functions
Generic Function, (setf plan): Public generic functions
Generic Function, (setf population): Public generic functions
Generic Function, (setf score): Public generic functions
Generic Function, (setf size): Public generic functions
Generic Function, (setf statistics): Public generic functions
Generic Function, (setf sum-normalized-score): Public generic functions
Generic Function, (setf sum-score): Public generic functions
Generic Function, 2x-cross-chromosomes: Public generic functions
Generic Function, 2x-cross-organisms: Public generic functions
Generic Function, allele-code-to-value: Public generic functions
Generic Function, allele-values: Public generic functions
Generic Function, as-good-as-test: Public generic functions
Generic Function, avg-normalized-score: Public generic functions
Generic Function, avg-score: Public generic functions
Generic Function, b2g-map: Public generic functions
Generic Function, best-organism: Public generic functions
Generic Function, best-organism-accessor: Public generic functions
Generic Function, better-than-test: Public generic functions
Generic Function, bin2gray: Public generic functions
Generic Function, chromosome-classes: Public generic functions
Generic Function, compute-binary-allele-statistics: Public generic functions
Generic Function, compute-normalized-statistics: Public generic functions
Generic Function, compute-statistics: Public generic functions
Generic Function, converged-p: Public generic functions
Generic Function, convergence-fraction: Public generic functions
Generic Function, convergence-threshold-margin: Public generic functions
Generic Function, copy-chromosome: Public generic functions
Generic Function, copy-chromosome-with-score: Public generic functions
Generic Function, copy-organism: Public generic functions
Generic Function, copy-organism-with-score: Public generic functions
Generic Function, count-allele-codes: Public generic functions
Generic Function, cross-chromosomes: Public generic functions
Generic Function, cross-organisms: Public generic functions
Generic Function, decode: Public generic functions
Generic Function, decode-binary-loci-value: Public generic functions
Generic Function, ecosystem: Public generic functions
Generic Function, eidetic: Public generic functions
Generic Function, evaluate: Public generic functions
Generic Function, evaluation-limit: Public generic functions
Generic Function, evaluation-number: Public generic functions
Generic Function, evolution-termination-p: Public generic functions
Generic Function, evolve: Public generic functions
Generic Function, g2b-map: Public generic functions
Generic Function, generation-limit: Public generic functions
Generic Function, generation-number: Public generic functions
Generic Function, genotype: Public generic functions
Generic Function, genotype-printable-form: Public generic functions
Generic Function, gray2bin: Public generic functions
Generic Function, hamming-distance: Public generic functions
Generic Function, loci: Public generic functions
Generic Function, loci-printable-form: Public generic functions
Generic Function, locus: Public generic functions
Generic Function, locus-arity: Public generic functions
Generic Function, locus-printable-form: Public generic functions
Generic Function, make-chromosome: Public generic functions
Generic Function, make-chromosomes: Public generic functions
Generic Function, make-genetic-plan: Public generic functions
Generic Function, make-loci-vector: Public generic functions
Generic Function, make-organism: Public generic functions
Generic Function, make-organisms: Public generic functions
Generic Function, make-organisms-vector: Public generic functions
Generic Function, make-population: Public generic functions
Generic Function, make-population-statistics: Public generic functions
Generic Function, max-organism: Public generic functions
Generic Function, max-score: Public generic functions
Generic Function, maximizing-p: Public generic functions
Generic Function, min-organism: Public generic functions
Generic Function, min-score: Public generic functions
Generic Function, minimizing-p: Public generic functions
Generic Function, mutate-chromosome: Public generic functions
Generic Function, mutate-organism: Public generic functions
Generic Function, normalize-score: Public generic functions
Generic Function, normalized-score: Public generic functions
Generic Function, number-of-bits: Public generic functions
Generic Function, organism: Public generic functions
Generic Function, organism-class: Public generic functions
Generic Function, organisms: Public generic functions
Generic Function, phenotype: Public generic functions
Generic Function, pick-random-allele: Public generic functions
Generic Function, pick-random-alleles: Public generic functions
Generic Function, pick-random-chromosome: Public generic functions
Generic Function, pick-random-chromosome-index: Public generic functions
Generic Function, pick-random-locus-index: Public generic functions
Generic Function, pick-random-organism: Public generic functions
Generic Function, pick-random-organism-index: Public generic functions
Generic Function, pick-some-random-organism-indices: Public generic functions
Generic Function, plan: Public generic functions
Generic Function, pmx-cross-chromosomes: Public generic functions
Generic Function, pmx-cross-organisms: Public generic functions
Generic Function, population: Public generic functions
Generic Function, population-statistics-class: Public generic functions
Generic Function, printable-allele-values: Public generic functions
Generic Function, r3-cross-chromosomes: Public generic functions
Generic Function, r3-cross-organisms: Public generic functions
Generic Function, randomize-chromosomes: Public generic functions
Generic Function, ranking-preselect: Public generic functions
Generic Function, regenerate: Public generic functions
Generic Function, roulette-pick-random-organism: Public generic functions
Generic Function, roulette-pick-random-organism-index: Public generic functions
Generic Function, score: Public generic functions
Generic Function, scramble-alleles: Public generic functions
Generic Function, size: Public generic functions
Generic Function, statistics: Public generic functions
Generic Function, stochastic-remainder-preselect: Public generic functions
Generic Function, sum-normalized-score: Public generic functions
Generic Function, sum-score: Public generic functions
Generic Function, swap-alleles: Public generic functions
Generic Function, tournament-select-organism: Public generic functions
Generic Function, uniform-cross-chromosomes: Public generic functions
Generic Function, uniform-cross-organisms: Public generic functions
Generic Function, worst-organism: Public generic functions
Generic Function, worst-organism-accessor: Public generic functions
genotype: Public generic functions
genotype: Public generic functions
genotype-printable-form: Public generic functions
genotype-printable-form: Public generic functions
gray2bin: Public generic functions
gray2bin: Public generic functions

H
hamming-distance: Public generic functions
hamming-distance: Public generic functions

L
loci: Public generic functions
loci: Public generic functions
loci-printable-form: Public generic functions
loci-printable-form: Public generic functions
locus: Public generic functions
locus: Public generic functions
locus-arity: Public generic functions
locus-arity: Public generic functions
locus-printable-form: Public generic functions
locus-printable-form: Public generic functions

M
make-chromosome: Public generic functions
make-chromosome: Public generic functions
make-chromosomes: Public generic functions
make-chromosomes: Public generic functions
make-genetic-plan: Public generic functions
make-genetic-plan: Public generic functions
make-loci-vector: Public generic functions
make-loci-vector: Public generic functions
make-loci-vector: Public generic functions
make-loci-vector: Public generic functions
make-organism: Public generic functions
make-organism: Public generic functions
make-organisms: Public generic functions
make-organisms: Public generic functions
make-organisms-vector: Public generic functions
make-organisms-vector: Public generic functions
make-population: Public generic functions
make-population: Public generic functions
make-population-statistics: Public generic functions
make-population-statistics: Public generic functions
max-organism: Public generic functions
max-organism: Public generic functions
max-score: Public generic functions
max-score: Public generic functions
maximizing-p: Public generic functions
maximizing-p: Public generic functions
maximizing-p: Public generic functions
Method, (setf avg-normalized-score): Public generic functions
Method, (setf avg-score): Public generic functions
Method, (setf b2g-map): Public generic functions
Method, (setf ecosystem): Public generic functions
Method, (setf ecosystem): Public generic functions
Method, (setf evaluation-limit): Public generic functions
Method, (setf evaluation-number): Public generic functions
Method, (setf g2b-map): Public generic functions
Method, (setf generation-limit): Public generic functions
Method, (setf generation-number): Public generic functions
Method, (setf genotype): Public generic functions
Method, (setf loci): Public generic functions
Method, (setf locus): Public generic functions
Method, (setf max-organism): Public generic functions
Method, (setf max-score): Public generic functions
Method, (setf min-organism): Public generic functions
Method, (setf min-score): Public generic functions
Method, (setf normalized-score): Public generic functions
Method, (setf number-of-bits): Public generic functions
Method, (setf organism): Public generic functions
Method, (setf organisms): Public generic functions
Method, (setf phenotype): Public generic functions
Method, (setf plan): Public generic functions
Method, (setf population): Public generic functions
Method, (setf population): Public generic functions
Method, (setf population): Public generic functions
Method, (setf score): Public generic functions
Method, (setf size): Public generic functions
Method, (setf statistics): Public generic functions
Method, (setf sum-normalized-score): Public generic functions
Method, (setf sum-score): Public generic functions
Method, 2x-cross-chromosomes: Public generic functions
Method, 2x-cross-organisms: Public generic functions
Method, allele-code-to-value: Public generic functions
Method, allele-code-to-value: Public generic functions
Method, allele-values: Public generic functions
Method, as-good-as-test: Public generic functions
Method, as-good-as-test: Public generic functions
Method, avg-normalized-score: Public generic functions
Method, avg-score: Public generic functions
Method, b2g-map: Public generic functions
Method, best-organism: Public generic functions
Method, best-organism: Public generic functions
Method, best-organism-accessor: Public generic functions
Method, better-than-test: Public generic functions
Method, better-than-test: Public generic functions
Method, bin2gray: Public generic functions
Method, compute-binary-allele-statistics: Public generic functions
Method, compute-normalized-statistics: Public generic functions
Method, compute-statistics: Public generic functions
Method, compute-statistics: Public generic functions
Method, converged-p: Public generic functions
Method, convergence-fraction: Public generic functions
Method, convergence-fraction: Public generic functions
Method, convergence-threshold-margin: Public generic functions
Method, convergence-threshold-margin: Public generic functions
Method, copy-chromosome: Public generic functions
Method, copy-organism: Public generic functions
Method, copy-organism-with-score: Public generic functions
Method, count-allele-codes: Public generic functions
Method, cross-chromosomes: Public generic functions
Method, cross-organisms: Public generic functions
Method, decode-binary-loci-value: Public generic functions
Method, ecosystem: Public generic functions
Method, ecosystem: Public generic functions
Method, eidetic: Public generic functions
Method, eidetic: Public generic functions
Method, evaluate: Public generic functions
Method, evaluate: Public generic functions
Method, evaluate: Public generic functions
Method, evaluate: Public generic functions
Method, evaluation-limit: Public generic functions
Method, evaluation-number: Public generic functions
Method, evolution-termination-p: Public generic functions
Method, evolve: Public generic functions
Method, g2b-map: Public generic functions
Method, generation-limit: Public generic functions
Method, generation-number: Public generic functions
Method, genotype: Public generic functions
Method, genotype-printable-form: Public generic functions
Method, gray2bin: Public generic functions
Method, hamming-distance: Public generic functions
Method, loci: Public generic functions
Method, loci-printable-form: Public generic functions
Method, locus: Public generic functions
Method, locus-arity: Public generic functions
Method, locus-printable-form: Public generic functions
Method, make-chromosome: Public generic functions
Method, make-chromosomes: Public generic functions
Method, make-genetic-plan: Public generic functions
Method, make-loci-vector: Public generic functions
Method, make-loci-vector: Public generic functions
Method, make-loci-vector: Public generic functions
Method, make-organism: Public generic functions
Method, make-organisms: Public generic functions
Method, make-organisms-vector: Public generic functions
Method, make-population: Public generic functions
Method, make-population-statistics: Public generic functions
Method, max-organism: Public generic functions
Method, max-score: Public generic functions
Method, maximizing-p: Public generic functions
Method, maximizing-p: Public generic functions
Method, min-organism: Public generic functions
Method, min-score: Public generic functions
Method, minimizing-p: Public generic functions
Method, minimizing-p: Public generic functions
Method, mutate-chromosome: Public generic functions
Method, mutate-organism: Public generic functions
Method, normalize-score: Public generic functions
Method, normalize-score: Public generic functions
Method, normalized-score: Public generic functions
Method, number-of-bits: Public generic functions
Method, organism: Public generic functions
Method, organisms: Public generic functions
Method, phenotype: Public generic functions
Method, pick-random-allele: Public generic functions
Method, pick-random-alleles: Public generic functions
Method, pick-random-alleles: Public generic functions
Method, pick-random-chromosome: Public generic functions
Method, pick-random-chromosome-index: Public generic functions
Method, pick-random-locus-index: Public generic functions
Method, pick-random-organism: Public generic functions
Method, pick-random-organism-index: Public generic functions
Method, pick-some-random-organism-indices: Public generic functions
Method, plan: Public generic functions
Method, pmx-cross-chromosomes: Public generic functions
Method, pmx-cross-organisms: Public generic functions
Method, population: Public generic functions
Method, population: Public generic functions
Method, population: Public generic functions
Method, population-statistics-class: Public generic functions
Method, print-object: Public standalone methods
Method, print-object: Public standalone methods
Method, print-object: Public standalone methods
Method, printable-allele-values: Public generic functions
Method, r3-cross-chromosomes: Public generic functions
Method, r3-cross-organisms: Public generic functions
Method, randomize-chromosomes: Public generic functions
Method, ranking-preselect: Public generic functions
Method, regenerate: Public generic functions
Method, regenerate: Public generic functions
Method, roulette-pick-random-organism: Public generic functions
Method, roulette-pick-random-organism-index: Public generic functions
Method, score: Public generic functions
Method, scramble-alleles: Public generic functions
Method, shared-initialize: Public standalone methods
Method, shared-initialize: Public standalone methods
Method, shared-initialize: Public standalone methods
Method, shared-initialize: Public standalone methods
Method, shared-initialize: Public standalone methods
Method, shared-initialize: Public standalone methods
Method, size: Public generic functions
Method, size: Public generic functions
Method, statistics: Public generic functions
Method, stochastic-remainder-preselect: Public generic functions
Method, sum-normalized-score: Public generic functions
Method, sum-score: Public generic functions
Method, swap-alleles: Public generic functions
Method, swap-alleles: Public generic functions
Method, tournament-select-organism: Public generic functions
Method, uniform-cross-chromosomes: Public generic functions
Method, uniform-cross-organisms: Public generic functions
Method, worst-organism: Public generic functions
Method, worst-organism: Public generic functions
Method, worst-organism-accessor: Public generic functions
min-organism: Public generic functions
min-organism: Public generic functions
min-score: Public generic functions
min-score: Public generic functions
minimizing-p: Public generic functions
minimizing-p: Public generic functions
minimizing-p: Public generic functions
mutate-chromosome: Public generic functions
mutate-chromosome: Public generic functions
mutate-organism: Public generic functions
mutate-organism: Public generic functions

N
normalize-score: Public generic functions
normalize-score: Public generic functions
normalize-score: Public generic functions
normalized-score: Public generic functions
normalized-score: Public generic functions
number-of-bits: Public generic functions
number-of-bits: Public generic functions

O
organism: Public generic functions
organism: Public generic functions
organism-class: Public generic functions
organisms: Public generic functions
organisms: Public generic functions

P
phenotype: Public generic functions
phenotype: Public generic functions
pick-random-allele: Public generic functions
pick-random-allele: Public generic functions
pick-random-alleles: Public generic functions
pick-random-alleles: Public generic functions
pick-random-alleles: Public generic functions
pick-random-chromosome: Public generic functions
pick-random-chromosome: Public generic functions
pick-random-chromosome-index: Public generic functions
pick-random-chromosome-index: Public generic functions
pick-random-locus-index: Public generic functions
pick-random-locus-index: Public generic functions
pick-random-organism: Public generic functions
pick-random-organism: Public generic functions
pick-random-organism-index: Public generic functions
pick-random-organism-index: Public generic functions
pick-some-random-organism-indices: Public generic functions
pick-some-random-organism-indices: Public generic functions
plan: Public generic functions
plan: Public generic functions
pmx-cross-chromosomes: Public generic functions
pmx-cross-chromosomes: Public generic functions
pmx-cross-organisms: Public generic functions
pmx-cross-organisms: Public generic functions
population: Public generic functions
population: Public generic functions
population: Public generic functions
population: Public generic functions
population-statistics-class: Public generic functions
population-statistics-class: Public generic functions
print-object: Public standalone methods
print-object: Public standalone methods
print-object: Public standalone methods
printable-allele-values: Public generic functions
printable-allele-values: Public generic functions

R
r3-cross-chromosomes: Public generic functions
r3-cross-chromosomes: Public generic functions
r3-cross-organisms: Public generic functions
r3-cross-organisms: Public generic functions
randomize-chromosomes: Public generic functions
randomize-chromosomes: Public generic functions
ranking-preselect: Public generic functions
ranking-preselect: Public generic functions
regenerate: Public generic functions
regenerate: Public generic functions
regenerate: Public generic functions
roulette-pick-random-organism: Public generic functions
roulette-pick-random-organism: Public generic functions
roulette-pick-random-organism-index: Public generic functions
roulette-pick-random-organism-index: Public generic functions
roulette-pick-random-weight-index: Public ordinary functions

S
score: Public generic functions
score: Public generic functions
scramble-alleles: Public generic functions
scramble-alleles: Public generic functions
set-geco-random-state: Private ordinary functions
shared-initialize: Public standalone methods
shared-initialize: Public standalone methods
shared-initialize: Public standalone methods
shared-initialize: Public standalone methods
shared-initialize: Public standalone methods
shared-initialize: Public standalone methods
size: Public generic functions
size: Public generic functions
size: Public generic functions
statistics: Public generic functions
statistics: Public generic functions
stochastic-remainder-preselect: Public generic functions
stochastic-remainder-preselect: Public generic functions
sum-normalized-score: Public generic functions
sum-normalized-score: Public generic functions
sum-score: Public generic functions
sum-score: Public generic functions
swap-alleles: Public generic functions
swap-alleles: Public generic functions
swap-alleles: Public generic functions

T
tournament-select-organism: Public generic functions
tournament-select-organism: Public generic functions

U
undbg: Public ordinary functions
uniform-cross-chromosomes: Public generic functions
uniform-cross-chromosomes: Public generic functions
uniform-cross-organisms: Public generic functions
uniform-cross-organisms: Public generic functions

W
worst-organism: Public generic functions
worst-organism: Public generic functions
worst-organism: Public generic functions
worst-organism-accessor: Public generic functions
worst-organism-accessor: Public generic functions


A.3 Variables

Jump to:   *  
A   B   E   G   L   M   N   O   P   S  
Index Entry  Section

*
*dbg-flags*: Private special variables

A
avg-normalized-score: Public classes
avg-score: Public classes

B
b2g-map: Public classes

E
ecosystem: Public classes
ecosystem: Public classes
evaluation-limit: Public classes
evaluation-number: Public classes

G
g2b-map: Public classes
generation-limit: Public classes
generation-number: Public classes
genotype: Public classes

L
loci: Public classes

M
max-organism: Public classes
max-score: Public classes
min-organism: Public classes
min-score: Public classes

N
normalized-score: Public classes
number-of-bits: Public classes

O
organism: Public classes
organisms: Public classes

P
phenotype: Public classes
plan: Public classes
population: Public classes
population: Public classes
population: Public classes

S
score: Public classes
size: Public classes
Slot, avg-normalized-score: Public classes
Slot, avg-score: Public classes
Slot, b2g-map: Public classes
Slot, ecosystem: Public classes
Slot, ecosystem: Public classes
Slot, evaluation-limit: Public classes
Slot, evaluation-number: Public classes
Slot, g2b-map: Public classes
Slot, generation-limit: Public classes
Slot, generation-number: Public classes
Slot, genotype: Public classes
Slot, loci: Public classes
Slot, max-organism: Public classes
Slot, max-score: Public classes
Slot, min-organism: Public classes
Slot, min-score: Public classes
Slot, normalized-score: Public classes
Slot, number-of-bits: Public classes
Slot, organism: Public classes
Slot, organisms: Public classes
Slot, phenotype: Public classes
Slot, plan: Public classes
Slot, population: Public classes
Slot, population: Public classes
Slot, population: Public classes
Slot, score: Public classes
Slot, size: Public classes
Slot, statistics: Public classes
Slot, sum-normalized-score: Public classes
Slot, sum-score: Public classes
Special Variable, *dbg-flags*: Private special variables
statistics: Public classes
sum-normalized-score: Public classes
sum-score: Public classes


A.4 Data types

Jump to:   B   C   D   E   F   G   M   O   P   R   S   U  
Index Entry  Section

B
binary-chromosome: Public classes

C
chromosome: Public classes
chromosome-methods.lisp: The geco/methods/chromosome-methods․lisp file
Class, binary-chromosome: Public classes
Class, chromosome: Public classes
Class, ecosystem: Public classes
Class, generational-population: Public classes
Class, genetic-plan: Public classes
Class, gray-code-translation: Public classes
Class, maximizing-score-mixin: Public classes
Class, minimizing-score-mixin: Public classes
Class, organism: Public classes
Class, organism-phenotype-mixin: Public classes
Class, population: Public classes
Class, population-statistics: Public classes
Class, sequence-chromosome: Public classes
classes.lisp: The geco/definitions/classes․lisp file

D
dbg.lisp: The geco/utilities/dbg․lisp file
definitions: The geco/definitions module

E
ecosystem: Public classes
ecosystem-methods.lisp: The geco/methods/ecosystem-methods․lisp file

F
File, chromosome-methods.lisp: The geco/methods/chromosome-methods․lisp file
File, classes.lisp: The geco/definitions/classes․lisp file
File, dbg.lisp: The geco/utilities/dbg․lisp file
File, ecosystem-methods.lisp: The geco/methods/ecosystem-methods․lisp file
File, geco.asd: The geco/geco․asd file
File, generics.lisp: The geco/definitions/generics․lisp file
File, genetic-plan-methods.lisp: The geco/methods/genetic-plan-methods․lisp file
File, organism-methods.lisp: The geco/methods/organism-methods․lisp file
File, packages.lisp: The geco/packages․lisp file
File, pop-stats-methods.lisp: The geco/methods/pop-stats-methods․lisp file
File, population-methods.lisp: The geco/methods/population-methods․lisp file
File, random.lisp: The geco/utilities/random․lisp file
File, selection-methods.lisp: The geco/methods/selection-methods․lisp file

G
geco: The geco system
geco: The geco package
geco-user: The geco-user package
geco.asd: The geco/geco․asd file
generational-population: Public classes
generics.lisp: The geco/definitions/generics․lisp file
genetic-plan: Public classes
genetic-plan-methods.lisp: The geco/methods/genetic-plan-methods․lisp file
gray-code-translation: Public classes

M
maximizing-score-mixin: Public classes
methods: The geco/methods module
minimizing-score-mixin: Public classes
Module, definitions: The geco/definitions module
Module, methods: The geco/methods module
Module, utilities: The geco/utilities module

O
organism: Public classes
organism-methods.lisp: The geco/methods/organism-methods․lisp file
organism-phenotype-mixin: Public classes

P
Package, geco: The geco package
Package, geco-user: The geco-user package
packages.lisp: The geco/packages․lisp file
pop-stats-methods.lisp: The geco/methods/pop-stats-methods․lisp file
population: Public classes
population-methods.lisp: The geco/methods/population-methods․lisp file
population-statistics: Public classes

R
random.lisp: The geco/utilities/random․lisp file

S
selection-methods.lisp: The geco/methods/selection-methods․lisp file
sequence-chromosome: Public classes
System, geco: The geco system

U
utilities: The geco/utilities module