The geco Reference Manual

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The geco Reference Manual

This is the geco Reference Manual, version 2.1, generated automatically by Declt version 3.0 "Montgomery Scott" on Mon Apr 19 16:08:18 2021 GMT+0.


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1 Introduction

GECO

Genetic Evolution through Combination of Objects (GECO), version 2.1.1

GECO is an extensible, object-oriented framework for prototyping genetic algorithms in Common Lisp. GECO makes extensive use of CLOS, the Common Lisp Object System, to implement its functionality. The abstractions provided by the classes have been chosen with the intent both of being easily understandable to anyone familiar with the paradigm of genetic algorithms, and of providing the algorithm developer with the ability to customize all aspects of its operation. It comes with extensive documentation, in the form of a two PDF files (see below), and some simple examples are also provided to illustrate its intended use.

The official release is available from https://github.com/gpwwjr/GECO Among the files included in the official release are: README.md Basic information about the software (this file) CHANGES.txt Which gives a summary of the version history, including information about changes in each release COPYING.LIB-2.0 A copy of the GNU LIBRARY GENERAL PUBLIC LICENSE, Version 2, June 1991 All the source code, including the TeX source for the documentation GECO-pdf.tgz Unix-compressed documentation This archive includes: - geco.pdf, a normal printable PDF file - geco-hyperlinked.pdf, a hyperlinked version of geco.pdf, which is handy for online reading, but not as nice for printing

Copyright (C) 1992,1993,2020,2021 George P. W. Williams, Jr.

This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Library General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
Library General Public License for more details.

You should have received a copy of the GNU Library General Public
License along with this library; if not, write to the Free
Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

Author: George P. W. Williams, Jr. 1334 Columbus City Rd. Scottsboro, AL 35769-9014 george.p.williams@pobox.com

This is an updated version as of 2020 (the original version has been long-neglected; it hasn't been updated since 1993). The current version has been updated to use the ASDF system definition/build system, and the files have all been converted to use unix line endings (line-feeds; previous versions used old the old MacOS convention of carriage-returns). I'm also now providing the documentation in PDF format (instead of PostScript in the earlier versions).

Bug reports, improvements, and feature requests should be sent to the author at the contact information above. I will try to respond to them. Ports to other lisps are also welcome.

I have gone to a lot of effort to make GECO portable among CLtL2 compliant Common Lisps. I tested the previous versions on several different lisp implemenations (MCL 2.0, ACL 4.1, and LCL 4.1). This version has been tested using Clozure CL 1.12 (macOS 10.15.7), and Steel Bank Common Lisp 2.0.11 (Ubuntu 20.04 Linux).

TO USE THIS SOFTWARE


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2 Systems

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


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2.1 geco

Author

George P. W. Williams, Jr

Contact

george.p.williams@pobox.com

License

GPL 2.0

Description

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

Version

2.1

Source

geco.asd (file)

Components

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3 Modules

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


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3.1 geco/definitions

Dependency

packages.lisp (file)

Parent

geco (system)

Location

definitions/

Components

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3.2 geco/utilities

Dependency

packages.lisp (file)

Parent

geco (system)

Location

utilities/

Components

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3.3 geco/methods

Dependencies
Parent

geco (system)

Location

methods/

Components

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4 Files

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


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4.1 Lisp


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4.1.1 geco.asd

Location

geco.asd

Systems

geco (system)


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4.1.2 geco/packages.lisp

Parent

geco (system)

Location

packages.lisp

Packages

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4.1.3 geco/definitions/generics.lisp

Parent

definitions (module)

Location

definitions/generics.lisp

Exported Definitions

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4.1.4 geco/definitions/classes.lisp

Parent

definitions (module)

Location

definitions/classes.lisp

Exported Definitions

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4.1.5 geco/utilities/dbg.lisp

Parent

utilities (module)

Location

utilities/dbg.lisp

Exported Definitions
Internal Definitions

*dbg-flags* (special variable)


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4.1.6 geco/utilities/random.lisp

Parent

utilities (module)

Location

utilities/random.lisp

Exported Definitions
Internal Definitions

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4.1.7 geco/methods/chromosome-methods.lisp

Parent

methods (module)

Location

methods/chromosome-methods.lisp

Exported Definitions

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4.1.8 geco/methods/organism-methods.lisp

Parent

methods (module)

Location

methods/organism-methods.lisp

Exported Definitions

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4.1.9 geco/methods/selection-methods.lisp

Parent

methods (module)

Location

methods/selection-methods.lisp

Exported Definitions

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

Parent

methods (module)

Location

methods/pop-stats-methods.lisp

Exported Definitions

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4.1.11 geco/methods/population-methods.lisp

Parent

methods (module)

Location

methods/population-methods.lisp

Exported Definitions

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

Parent

methods (module)

Location

methods/genetic-plan-methods.lisp

Exported Definitions

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4.1.13 geco/methods/ecosystem-methods.lisp

Parent

methods (module)

Location

methods/ecosystem-methods.lisp

Exported Definitions

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5 Packages

Packages are listed by definition order.


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5.1 geco

Source

packages.lisp (file)

Nickname

ga

Use List

common-lisp

Used By List

geco-user

Exported Definitions
Internal Definitions

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5.2 geco-user

Source

packages.lisp (file)

Nickname

gu

Use List

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6 Definitions

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


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6.1 Exported definitions


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6.1.1 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 (file)

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 (file)

Function: dbg? ()

Tell me what debugging flags are active.

Package

geco

Source

dbg.lisp (file)

Function: dbgo FMT-STRING &rest FMT-ARGS
Package

geco

Source

dbg.lisp (file)

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 (file)

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 (file)

Function: roulette-pick-random-weight-index WEIGHTS-TABLE &key INVERT-P &aux SIZE

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 (file)

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 (file)


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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 &aux N TEST

[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 (file)

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 (file)

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 (file)

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 (file)

Method: allele-code-to-value (SELF chromosome) LOCUS-INDEX ALLELE-CODE
Source

chromosome-methods.lisp (file)

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 (file)

Methods
Method: allele-values (SELF binary-chromosome) LOCUS-INDEX
Source

chromosome-methods.lisp (file)

Generic Function: as-good-as-test POP
Package

geco

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

population-methods.lisp (file)

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

population-methods.lisp (file)

Generic Function: avg-normalized-score OBJECT
Generic Function: (setf avg-normalized-score) NEW-VALUE OBJECT
Package

geco

Methods
Method: avg-normalized-score (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf avg-normalized-score) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: avg-score OBJECT
Generic Function: (setf avg-score) NEW-VALUE OBJECT
Package

geco

Methods
Method: avg-score (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf avg-score) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: b2g-map OBJECT
Generic Function: (setf b2g-map) NEW-VALUE OBJECT
Package

geco

Methods
Method: b2g-map (GRAY-CODE-TRANSLATION gray-code-translation)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf b2g-map) NEW-VALUE (GRAY-CODE-TRANSLATION gray-code-translation)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: best-organism POP
Package

geco

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

population-methods.lisp (file)

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

population-methods.lisp (file)

Generic Function: best-organism-accessor POP
Package

geco

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

population-methods.lisp (file)

Generic Function: better-than-test POP
Package

geco

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

population-methods.lisp (file)

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

population-methods.lisp (file)

Generic Function: bin2gray SELF BIN
Package

geco

Methods
Method: bin2gray (SELF gray-code-translation) BIN &aux GRAY BIT B2G NUMBITS NUMBITS-1 II JJ
Source

chromosome-methods.lisp (file)

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 (file)

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 (file)

Generic Function: compute-normalized-statistics SELF
Package

geco

Methods
Method: compute-normalized-statistics (SELF population-statistics) &aux MIN MAX
Source

pop-stats-methods.lisp (file)

Generic Function: compute-statistics THING

Compute the statistics for the relevent thing.

Package

geco

Source

generics.lisp (file)

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 (file)

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

pop-stats-methods.lisp (file)

Generic Function: converged-p POPULATION

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

Package

geco

Source

generics.lisp (file)

Methods
Method: converged-p (POP population) &aux POP-SIZE ORGANISMS STATS THRESHOLD PASSING-COUNT AS-GOOD-AS-TEST

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 (file)

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 (file)

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

population-methods.lisp (file)

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

population-methods.lisp (file)

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 (file)

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

population-methods.lisp (file)

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

population-methods.lisp (file)

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 (file)

Methods
Method: copy-chromosome (SELF chromosome) OWNER-ORGANISM
Source

chromosome-methods.lisp (file)

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 (file)

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 (file)

Methods
Method: copy-organism (SELF organism) &key NEW-POPULATION &aux NEW-SELF RESULT
Source

organism-methods.lisp (file)

Generic Function: copy-organism-with-score SELF &key NEW-POPULATION
Package

geco

Methods
Method: copy-organism-with-score (SELF organism) &key NEW-POPULATION &aux NEW-SELF
Source

organism-methods.lisp (file)

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 (file)

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 (file)

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 (file)

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 (file)

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 (file)

Generic Function: ecosystem OBJECT
Generic Function: (setf ecosystem) NEW-VALUE OBJECT
Package

geco

Methods
Method: ecosystem (POPULATION population)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf ecosystem) NEW-VALUE (POPULATION population)

automatically generated writer method

Source

classes.lisp (file)

Method: ecosystem (GENETIC-PLAN genetic-plan)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf ecosystem) NEW-VALUE (GENETIC-PLAN genetic-plan)

automatically generated writer method

Source

classes.lisp (file)

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 (file)

Methods
Method: eidetic (ORG1 organism) (ORG2 organism) &aux GENES-1 GENES-2

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

Source

organism-methods.lisp (file)

Method: eidetic (CHR1 chromosome) (CHR2 chromosome) &aux SIZE1

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

Source

chromosome-methods.lisp (file)

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 (file)

Methods
Method: evaluate (SELF ecosystem) (PLAN genetic-plan)
Source

ecosystem-methods.lisp (file)

Method: evaluate (POP population) (PLAN genetic-plan) &aux ORGS
Source

population-methods.lisp (file)

Method: evaluate (SELF organism) (PLAN genetic-plan) after
Source

organism-methods.lisp (file)

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

organism-methods.lisp (file)

Generic Function: evaluation-limit OBJECT
Generic Function: (setf evaluation-limit) NEW-VALUE OBJECT
Package

geco

Methods
Method: evaluation-limit (GENETIC-PLAN genetic-plan)
Method: (setf evaluation-limit) NEW-VALUE (GENETIC-PLAN genetic-plan)

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

Source

classes.lisp (file)

Generic Function: evaluation-number OBJECT
Generic Function: (setf evaluation-number) NEW-VALUE OBJECT
Package

geco

Methods
Method: evaluation-number (ECOSYSTEM ecosystem)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf evaluation-number) NEW-VALUE (ECOSYSTEM ecosystem)

automatically generated writer method

Source

classes.lisp (file)

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 (file)

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

genetic-plan-methods.lisp (file)

Generic Function: evolve THING

Create new generations until a termination condition is reached.

Package

geco

Source

generics.lisp (file)

Methods
Method: evolve (SELF ecosystem)
Source

ecosystem-methods.lisp (file)

Generic Function: g2b-map OBJECT
Generic Function: (setf g2b-map) NEW-VALUE OBJECT
Package

geco

Methods
Method: g2b-map (GRAY-CODE-TRANSLATION gray-code-translation)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf g2b-map) NEW-VALUE (GRAY-CODE-TRANSLATION gray-code-translation)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: generation-limit OBJECT
Generic Function: (setf generation-limit) NEW-VALUE OBJECT
Package

geco

Methods
Method: generation-limit (GENETIC-PLAN genetic-plan)
Method: (setf generation-limit) NEW-VALUE (GENETIC-PLAN genetic-plan)

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

Source

classes.lisp (file)

Generic Function: generation-number OBJECT
Generic Function: (setf generation-number) NEW-VALUE OBJECT
Package

geco

Methods
Method: generation-number (ECOSYSTEM ecosystem)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf generation-number) NEW-VALUE (ECOSYSTEM ecosystem)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: genotype OBJECT
Generic Function: (setf genotype) NEW-VALUE OBJECT
Package

geco

Methods
Method: genotype (ORGANISM organism)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf genotype) NEW-VALUE (ORGANISM organism)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: genotype-printable-form SELF
Package

geco

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

organism-methods.lisp (file)

Generic Function: gray2bin SELF GRAY
Package

geco

Methods
Method: gray2bin (SELF gray-code-translation) GRAY &aux BIN BIT G2B NUMBITS NUMBITS-1 II JJ
Source

chromosome-methods.lisp (file)

Generic Function: hamming-distance C1 C2
Package

geco

Methods
Method: hamming-distance (C1 chromosome) (C2 chromosome) &aux DISTANCE
Source

chromosome-methods.lisp (file)

Generic Function: loci OBJECT
Generic Function: (setf loci) NEW-VALUE OBJECT
Package

geco

Methods
Method: loci (CHROMOSOME chromosome)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf loci) NEW-VALUE (CHROMOSOME chromosome)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: loci-printable-form SELF
Package

geco

Methods
Method: loci-printable-form (SELF chromosome) &aux S
Source

chromosome-methods.lisp (file)

Generic Function: locus SELF INDEX
Generic Function: (setf locus) NEW-VALUE SELF INDEX
Package

geco

Methods
Method: locus (SELF chromosome) INDEX
Method: (setf locus) NEW-VALUE (SELF chromosome) INDEX
Source

chromosome-methods.lisp (file)

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 (file)

Methods
Method: locus-arity (SELF binary-chromosome) LOCUS-INDEX
Source

chromosome-methods.lisp (file)

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 (file)

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 (file)

Methods
Method: make-chromosome (ORG organism) CHROMOSOME-CLASS &key SIZE RANDOM
Source

organism-methods.lisp (file)

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 (file)

Methods
Method: make-chromosomes (SELF organism) &key RANDOM &aux RESULT
Source

organism-methods.lisp (file)

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 (file)

Methods
Method: make-genetic-plan (ECOSYSTEM ecosystem) PLAN-CLASS
Source

ecosystem-methods.lisp (file)

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 (file)

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

chromosome-methods.lisp (file)

Method: make-loci-vector (SELF chromosome) SIZE &key RANDOM around
Source

chromosome-methods.lisp (file)

Method: make-loci-vector (SELF chromosome) SIZE &key &allow-other-keys
Source

chromosome-methods.lisp (file)

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 (file)

Methods
Method: make-organism (POP population) &key RANDOM NO-CHROMOSOMES
Source

population-methods.lisp (file)

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 (file)

Methods
Method: make-organisms (POP population) &key RANDOM &aux ORGANISMS
Source

population-methods.lisp (file)

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 (file)

Methods
Method: make-organisms-vector (SELF population) SIZE
Source

population-methods.lisp (file)

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 (file)

Methods
Method: make-population (ECOSYSTEM ecosystem) POP-CLASS &key SIZE RANDOM
Source

ecosystem-methods.lisp (file)

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 (file)

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

population-methods.lisp (file)

Generic Function: max-organism OBJECT
Generic Function: (setf max-organism) NEW-VALUE OBJECT
Package

geco

Methods
Method: max-organism (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf max-organism) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: max-score OBJECT
Generic Function: (setf max-score) NEW-VALUE OBJECT
Package

geco

Methods
Method: max-score (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf max-score) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: maximizing-p POP
Package

geco

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

population-methods.lisp (file)

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

population-methods.lisp (file)

Generic Function: min-organism OBJECT
Generic Function: (setf min-organism) NEW-VALUE OBJECT
Package

geco

Methods
Method: min-organism (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf min-organism) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: min-score OBJECT
Generic Function: (setf min-score) NEW-VALUE OBJECT
Package

geco

Methods
Method: min-score (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf min-score) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: minimizing-p POP
Package

geco

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

population-methods.lisp (file)

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

population-methods.lisp (file)

Generic Function: mutate-chromosome SELF LOCUS-INDEX
Package

geco

Methods
Method: mutate-chromosome (SELF chromosome) LOCUS-INDEX
Source

chromosome-methods.lisp (file)

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 (file)

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 (file)

Methods
Method: normalize-score (POP population) (PLAN genetic-plan) &aux ORGS STATS

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 (file)

Method: normalize-score (SELF organism) (PLAN genetic-plan) &aux STATS
Source

organism-methods.lisp (file)

Generic Function: normalized-score OBJECT
Generic Function: (setf normalized-score) NEW-VALUE OBJECT
Package

geco

Methods
Method: normalized-score (ORGANISM organism)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf normalized-score) NEW-VALUE (ORGANISM organism)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: number-of-bits OBJECT
Generic Function: (setf number-of-bits) NEW-VALUE OBJECT
Package

geco

Methods
Method: number-of-bits (GRAY-CODE-TRANSLATION gray-code-translation)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf number-of-bits) NEW-VALUE (GRAY-CODE-TRANSLATION gray-code-translation)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: organism OBJECT
Generic Function: (setf organism) NEW-VALUE OBJECT
Package

geco

Methods
Method: organism (CHROMOSOME chromosome)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf organism) NEW-VALUE (CHROMOSOME chromosome)

automatically generated writer method

Source

classes.lisp (file)

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 (file)

Generic Function: organisms OBJECT
Generic Function: (setf organisms) NEW-VALUE OBJECT
Package

geco

Methods
Method: organisms (POPULATION population)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf organisms) NEW-VALUE (POPULATION population)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: phenotype OBJECT
Generic Function: (setf phenotype) NEW-VALUE OBJECT
Package

geco

Methods
Method: phenotype (ORGANISM-PHENOTYPE-MIXIN organism-phenotype-mixin)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf phenotype) NEW-VALUE (ORGANISM-PHENOTYPE-MIXIN organism-phenotype-mixin)

automatically generated writer method

Source

classes.lisp (file)

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 (file)

Generic Function: pick-random-alleles SELF
Package

geco

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

chromosome-methods.lisp (file)

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

chromosome-methods.lisp (file)

Generic Function: pick-random-chromosome SELF
Package

geco

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

organism-methods.lisp (file)

Generic Function: pick-random-chromosome-index SELF
Package

geco

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

organism-methods.lisp (file)

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 (file)

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 (file)

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 (file)

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 &aux POP-SIZE

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

Source

selection-methods.lisp (file)

Generic Function: plan OBJECT
Generic Function: (setf plan) NEW-VALUE OBJECT
Package

geco

Methods
Method: plan (ECOSYSTEM ecosystem)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf plan) NEW-VALUE (ECOSYSTEM ecosystem)

automatically generated writer method

Source

classes.lisp (file)

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 &aux N TEST-INDEX2
Source

chromosome-methods.lisp (file)

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 (file)

Generic Function: population OBJECT
Generic Function: (setf population) NEW-VALUE OBJECT
Package

geco

Methods
Method: population (ORGANISM organism)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf population) NEW-VALUE (ORGANISM organism)

automatically generated writer method

Source

classes.lisp (file)

Method: population (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf population) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

Method: population (ECOSYSTEM ecosystem)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf population) NEW-VALUE (ECOSYSTEM ecosystem)

automatically generated writer method

Source

classes.lisp (file)

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 (file)

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

population-methods.lisp (file)

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 (file)

Methods
Method: printable-allele-values (SELF binary-chromosome) LOCUS-INDEX
Source

chromosome-methods.lisp (file)

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 &aux N MISMATCHED-ALLELES1 MISMATCHED-ALLELES2 MISMATCHED-LOCI MISMATCHED-COUNT

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

Source

chromosome-methods.lisp (file)

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 &aux PARENT1-CHROMOSOME
Source

organism-methods.lisp (file)

Generic Function: randomize-chromosomes SELF
Package

geco

Methods
Method: randomize-chromosomes (SELF organism)
Source

organism-methods.lisp (file)

Generic Function: ranking-preselect POP &key MULTIPLIER MAX
Package

geco

Methods
Method: ranking-preselect (POP population) &key MULTIPLIER MAX &aux MIN POP-SIZE INVERT-P

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 (file)

Generic Function: regenerate GENETIC-PLAN THING

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

Package

geco

Source

generics.lisp (file)

Methods
Method: regenerate (PLAN genetic-plan) (OLD-POP generational-population) &aux POP-SIZE NEW-POP NEW-ORGANISMS

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 (file)

Method: regenerate (PLAN genetic-plan) (ECOSYS ecosystem)
Source

genetic-plan-methods.lisp (file)

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 (file)

Generic Function: roulette-pick-random-organism-index POP
Package

geco

Methods
Method: roulette-pick-random-organism-index (POP population) &aux INVERT-P

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 (file)

Generic Function: score OBJECT
Generic Function: (setf score) NEW-VALUE OBJECT
Package

geco

Methods
Method: score (ORGANISM organism)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf score) NEW-VALUE (ORGANISM organism)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: scramble-alleles SELF
Package

geco

Methods
Method: scramble-alleles (SELF chromosome) &aux LOCI ALLELES
Source

chromosome-methods.lisp (file)

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 (file)

Writer

(setf size) (generic function)

Methods
Method: size (SELF chromosome)
Source

chromosome-methods.lisp (file)

Method: size (POPULATION population)

automatically generated reader method

Source

classes.lisp (file)

Generic Function: (setf size) NEW-VALUE OBJECT
Package

geco

Reader

size (generic function)

Methods
Method: (setf size) NEW-VALUE (POPULATION population)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: statistics OBJECT
Generic Function: (setf statistics) NEW-VALUE OBJECT
Package

geco

Methods
Method: statistics (POPULATION population)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf statistics) NEW-VALUE (POPULATION population)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: stochastic-remainder-preselect POP &key MULTIPLIER
Package

geco

Methods
Method: stochastic-remainder-preselect (POP population) &key MULTIPLIER &aux POP-SIZE INVERT-P

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 (file)

Generic Function: sum-normalized-score OBJECT
Generic Function: (setf sum-normalized-score) NEW-VALUE OBJECT
Package

geco

Methods
Method: sum-normalized-score (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf sum-normalized-score) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

Generic Function: sum-score OBJECT
Generic Function: (setf sum-score) NEW-VALUE OBJECT
Package

geco

Methods
Method: sum-score (POPULATION-STATISTICS population-statistics)

automatically generated reader method

Source

classes.lisp (file)

Method: (setf sum-score) NEW-VALUE (POPULATION-STATISTICS population-statistics)

automatically generated writer method

Source

classes.lisp (file)

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 (file)

Method: swap-alleles (SELF chromosome) &key LOCUS-INDEX LOCUS-INDEX2
Source

chromosome-methods.lisp (file)

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 (file)

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 (file)

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 &aux PARENT1-CHROMOSOME

Uniform crossover of random chromosomes between two organisms.

Source

organism-methods.lisp (file)

Generic Function: worst-organism POP
Package

geco

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

population-methods.lisp (file)

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

population-methods.lisp (file)

Generic Function: worst-organism-accessor POP
Package

geco

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

population-methods.lisp (file)


Previous: , Up: Exported definitions   [Contents][Index]

6.1.3 Classes

Class: binary-chromosome ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

chromosome (class)

Direct methods
Class: chromosome ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

standard-object (class)

Direct subclasses
Direct methods
Direct slots
Slot: organism
Type

(or geco:organism null)

Initargs

:organism

Initform

(quote nil)

Readers

organism (generic function)

Writers

(setf organism) (generic function)

Slot: loci
Type

array

Initargs

:loci

Readers

loci (generic function)

Writers

(setf loci) (generic function)

Class: ecosystem ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: plan
Type

geco:genetic-plan

Readers

plan (generic function)

Writers

(setf plan) (generic function)

Slot: population
Type

geco:population

Readers

population (generic function)

Writers

(setf population) (generic function)

Slot: generation-number
Type

integer

Initform

0

Readers

generation-number (generic function)

Writers

(setf generation-number) (generic function)

Slot: evaluation-number
Type

integer

Initform

0

Readers

evaluation-number (generic function)

Writers

(setf evaluation-number) (generic function)

Class: generational-population ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

population (class)

Direct methods

regenerate (method)

Class: genetic-plan ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: ecosystem
Type

geco:ecosystem

Initargs

:ecosystem

Readers

ecosystem (generic function)

Writers

(setf ecosystem) (generic function)

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 (generic function)

Writers

(setf generation-limit) (generic function)

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 (generic function)

Writers

(setf evaluation-limit) (generic function)

Class: gray-code-translation ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

standard-object (class)

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

fixnum

Initargs

:number-of-bits

Readers

number-of-bits (generic function)

Writers

(setf number-of-bits) (generic function)

Slot: b2g-map
Type

(array bit (* *))

Readers

b2g-map (generic function)

Writers

(setf b2g-map) (generic function)

Slot: g2b-map
Type

(array bit (* *))

Readers

g2b-map (generic function)

Writers

(setf g2b-map) (generic function)

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 (file)

Direct superclasses

standard-object (class)

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 (file)

Direct superclasses

standard-object (class)

Direct methods
Class: organism ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: population
Type

(or geco:population null)

Initargs

:population

Initform

(quote nil)

Readers

population (generic function)

Writers

(setf population) (generic function)

Slot: genotype
Type

list

Initargs

:genotype

Initform

(quote nil)

Readers

genotype (generic function)

Writers

(setf genotype) (generic function)

Slot: score
Initargs

:score

Initform

(quote nil)

Readers

score (generic function)

Writers

(setf score) (generic function)

Slot: normalized-score
Initargs

:normalized-score

Initform

(quote nil)

Readers

normalized-score (generic function)

Writers

(setf normalized-score) (generic function)

Class: organism-phenotype-mixin ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: phenotype
Initargs

:phenotype

Readers

phenotype (generic function)

Writers

(setf phenotype) (generic function)

Class: population ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

standard-object (class)

Direct subclasses

generational-population (class)

Direct methods
Direct slots
Slot: ecosystem
Type

geco:ecosystem

Initargs

:ecosystem

Readers

ecosystem (generic function)

Writers

(setf ecosystem) (generic function)

Slot: organisms
Type

vector

Readers

organisms (generic function)

Writers

(setf organisms) (generic function)

Slot: size
Type

(or fixnum null)

Initargs

:size

Readers

size (generic function)

Writers

(setf size) (generic function)

Slot: statistics
Type

geco:population-statistics

Initargs

:statistics

Readers

statistics (generic function)

Writers

(setf statistics) (generic function)

Class: population-statistics ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

standard-object (class)

Direct methods
Direct slots
Slot: population
Type

geco:population

Initargs

:population

Readers

population (generic function)

Writers

(setf population) (generic function)

Slot: sum-score
Type

number

Initargs

:sum-score

Readers

sum-score (generic function)

Writers

(setf sum-score) (generic function)

Slot: avg-score
Type

number

Initargs

:avg-score

Readers

avg-score (generic function)

Writers

(setf avg-score) (generic function)

Slot: max-score
Type

number

Initargs

:max-score

Readers

max-score (generic function)

Writers

(setf max-score) (generic function)

Slot: min-score
Type

number

Initargs

:min-score

Readers

min-score (generic function)

Writers

(setf min-score) (generic function)

Slot: max-organism
Type

geco:organism

Initargs

:max-organism

Readers

max-organism (generic function)

Writers

(setf max-organism) (generic function)

Slot: min-organism
Type

geco:organism

Initargs

:min-organism

Readers

min-organism (generic function)

Writers

(setf min-organism) (generic function)

Slot: sum-normalized-score
Initargs

:sum-normalized-score

Readers

sum-normalized-score (generic function)

Writers

(setf sum-normalized-score) (generic function)

Slot: avg-normalized-score
Initargs

:avg-normalized-score

Readers

avg-normalized-score (generic function)

Writers

(setf avg-normalized-score) (generic function)

Class: sequence-chromosome ()
Package

geco

Source

classes.lisp (file)

Direct superclasses

chromosome (class)

Direct methods

Previous: , Up: Definitions   [Contents][Index]

6.2 Internal definitions


Next: , Previous: , Up: Internal definitions   [Contents][Index]

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 (file)


Previous: , Up: Internal definitions   [Contents][Index]

6.2.2 Functions

Function: geco-random-state ()
Package

geco

Source

random.lisp (file)

Function: set-geco-random-state NEW-STATE
Package

geco

Source

random.lisp (file)


Previous: , Up: Top   [Contents][Index]

Appendix A Indexes


Next: , Previous: , Up: Indexes   [Contents][Index]

A.1 Concepts

Jump to:   F   G   L   M  
Index Entry  Section

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

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

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

M
Module, geco/definitions: The geco/definitions module
Module, geco/methods: The geco/methods module
Module, geco/utilities: The geco/utilities module

Jump to:   F   G   L   M  

Next: , Previous: , Up: Indexes   [Contents][Index]

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

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

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

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

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

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

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

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

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

H
hamming-distance: Exported generic functions
hamming-distance: Exported generic functions

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

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

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

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

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

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

S
score: Exported generic functions
score: Exported generic functions
scramble-alleles: Exported generic functions
scramble-alleles: Exported generic functions
set-geco-random-state: Internal functions
size: Exported generic functions
size: Exported generic functions
size: Exported generic functions
statistics: Exported generic functions
statistics: Exported generic functions
stochastic-remainder-preselect: Exported generic functions
stochastic-remainder-preselect: Exported generic functions
sum-normalized-score: Exported generic functions
sum-normalized-score: Exported generic functions
sum-score: Exported generic functions
sum-score: Exported generic functions
swap-alleles: Exported generic functions
swap-alleles: Exported generic functions
swap-alleles: Exported generic functions

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

U
undbg: Exported functions
uniform-cross-chromosomes: Exported generic functions
uniform-cross-chromosomes: Exported generic functions
uniform-cross-organisms: Exported generic functions
uniform-cross-organisms: Exported generic functions

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

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A.3 Variables

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Index Entry  Section

*
*dbg-flags*: Internal special variables

A
avg-normalized-score: Exported classes
avg-score: Exported classes

B
b2g-map: Exported classes

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

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

L
loci: Exported classes

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

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

O
organism: Exported classes
organisms: Exported classes

P
phenotype: Exported classes
plan: Exported classes
population: Exported classes
population: Exported classes
population: Exported classes

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

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A.4 Data types

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Index Entry  Section

B
binary-chromosome: Exported classes

C
chromosome: Exported classes
Class, binary-chromosome: Exported classes
Class, chromosome: Exported classes
Class, ecosystem: Exported classes
Class, generational-population: Exported classes
Class, genetic-plan: Exported classes
Class, gray-code-translation: Exported classes
Class, maximizing-score-mixin: Exported classes
Class, minimizing-score-mixin: Exported classes
Class, organism: Exported classes
Class, organism-phenotype-mixin: Exported classes
Class, population: Exported classes
Class, population-statistics: Exported classes
Class, sequence-chromosome: Exported classes

E
ecosystem: Exported classes

G
geco: The geco system
geco: The geco package
geco-user: The geco-user package
generational-population: Exported classes
genetic-plan: Exported classes
gray-code-translation: Exported classes

M
maximizing-score-mixin: Exported classes
minimizing-score-mixin: Exported classes

O
organism: Exported classes
organism-phenotype-mixin: Exported classes

P
Package, geco: The geco package
Package, geco-user: The geco-user package
population: Exported classes
population-statistics: Exported classes

S
sequence-chromosome: Exported classes
System, geco: The geco system

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