rgp: R genetic programming framework

RGP is a simple modular Genetic Programming (GP) system build in pure R. In addition to general GP tasks, the system supports Symbolic Regression by GP through the familiar R model formula interface. GP individuals are represented as R expressions, an (optional) type system enables domain-specific function sets containing functions of diverse domain- and range types. A basic set of genetic operators for variation (mutation and crossover) and selection is provided.

AuthorOliver Flasch, Olaf Mersmann, Thomas Bartz-Beielstein, Joerg Stork, Martin Zaefferer
Date of publication2014-08-08 14:05:23
MaintainerOliver Flasch <oliver.flasch@fh-koeln.de>
LicenseGPL-2
Version0.4-1
http://rsymbolic.org/projects/show/rgp

View on CRAN

Man pages

arity: Determine the number of arguments of a function

arity.primitive: Determine the number of arguments of a primitive function

booleanFunctionManipulation: Tools for manipulating boolean functions

breeding: Breeding of GP individuals

buildingBlocks: Support for GP buidling blocks

buildingBlockTags: Building block tags

customDist: A 'dist' function that supports custom metrics

dataDrivenGeneticProgramming: Data-driven untyped standard genetic programming

defaultGPFunctionAndConstantSets: Default function- and constant factory sets for Genetic...

do.call.ignore.unused.arguments: A variant of do.call that ignores unused arguments

embedDataFrame: Embed columns in a data frame

evolutionRestartConditions: Evolution restart conditions

evolutionRestartStrategies: Evolution restart strategies

evolutionStopConditions: Evolution stop conditions

exprChildrenOrEmptyList: Return the Children of an Expression or the Empty List if...

expressionComplexityMeasures: Complexity measures for R functions and expressions

expressionComposing: Functions for decomposing and recombining R expressions

expressionCounts: Upper bounds for expression tree search space sizes

expressionCrossover: Random crossover (recombination) of functions and expressions

expressionMutation: Random mutation of functions and expressions

expressionNames: Functions for handling R symbols / names

expressionSimilarityMeasures: Similarity and Distance Measures for R Functions and...

expressionTransformation: Common higher-order functions for transforming R expressions

exprLabel: Return the "label" at the Root Node of an Expression Tree

exprToPlotmathExpr: Convert any expression to an expression that is plottable by...

extractAttributes: Extract a given attribute of all objects in a list and tag...

formatSeconds: Format time and data values into human-readable character...

funcToPlotmathExpr: Convert a function to an expression plottable by plotmath

geneticProgramming: Standard typed and untyped genetic programming

gpIndividualVisualization: Visualization of functions and expressions as trees

gridDesign: Create a regular grid design matrix

individualAnalysis: Functions for analysing GP individuals

inversePermutation: Calculate the inverse of a permutation

is.sType: Check if an object is an sType

iterate: Repeatedly apply a function

joinElites: Join elite lists

latinHypercubeDesign: Create a latin hypercube design (LHD)

lispLists: Functions for Lisp-like list processing

listSplittingAndGrouping: Splitting and grouping of lists

mae: Mean absolute error (MAE)

makeAgeFitnessComplexityParetoGpSearchHeuristic: Age Fitness Complexity Pareto GP Search Heuristic for RGP

makeArchiveBasedParetoTournamentSearchHeuristic: Archive-based Pareto Tournament Search Heuristic for RGP

makeClosure: Create a new R closure given a function body expression and...

makeCommaEvolutionStrategySearchHeuristic: Comma Evolution Strategy Search Heuristic for RGP

makeFunctionFitnessFunction: Create a fitness function from a reference function of one...

makeNaryFunctionFitnessFunction: Create a fitness function from a n-ary reference function

makeRegressionFitnessFunction: Create a fitness function for symbolic regression

makeSeSymbolicFitnessFunction: Create a fitness function based on symbolic squared error...

makeTinyGpSearchHeuristic: Tiny GP Search Heuristic for RGP

mse: Mean squared error (MSE)

multiNicheGeneticProgramming: Cluster-based multi-niche genetic programming

multiNicheSymbolicRegression: Symbolic regression via multi-niche standard genetic...

new.alist: Create a new function argument list from a list or vector of...

new.function: Create a new function stub

nmse: Normalized mean squared error (NMSE)

nondeterministicRanking: Create a nondeterministic ranking

normalize: Normalize a vector into the interval [0, 1]

normalizedDesign: Create a normalized design matrix

orderByParetoMeasure: Rearrange points via an arbitrary Pareto-based ranking

paretoFrontKneeIndex: Find the knee of a two dimensional pareto front

paretoSorting: Rearrange points via Pareto-based rankings

plotFunction3d: Plot a 2D function as a 3D surface

plotFunctions: Show an overlayed plot of multiple functions

plotParetoFront: Plot a GP Pareto Front

plotPopulationFitnessComplexity: Fitness/Complexity plot for populations

popfitness: Calculate the fitness value of each individual in a...

populationClustering: Clustering Populations for Niching

populationCreation: Classes for populations of individuals represented as...

predict.symbolicRegressionModel: Predict method for symbolic regression models

print.sType: Prints a sType and returns it invisible.

randelt: Choose a random element from a list or vector

randomExpressionChilds: Select random childs or subtrees of an expression

randomExpressionCreation: Creates an R expression by random growth

randomExpressionCreationTyped: Creates an R expression by random growth respecting type...

randomFunctionCreation: Creates an R function with a random expression as its body

randomFunctionCreationTyped: Creates a well-typed R function with a random expression as...

randterminalTyped: Create a random terminal node

rangeTypeOfType: Return the range type if t is a function type, otherwise just...

rgp-package: The RGP package

rgpTestingAndBenchmarking: Utility functions for testing and benchmarking the RGP system

r_mae: R version of Mean absolute error (MAE)

rmse: Root mean squared error (RMSE)

rsquared: Coefficient of determination (R^2)

r_sse: R version of Sum squared error (SSE)

r_ssse: R version of Scaled sum squared error (sSSE)

safeGPfunctions: Some simple arithmetic and logic functions for use in GP...

searchSpaceDefinition: Functions for defining the search space for Genetic...

selectionFunctions: GP selection functions

seSymbolic: Symbolic squared error (SE)

seSymbolicFunction: Symbolic squared error function (SE)

smse: Scaled mean squared error (SMSE)

sortBy: Sort a vector or list by the result of applying a function

sortByRange: Tabulate a list of functions or input variables by the range...

sortByRanking: Sort a vector or list via a given ranking

sortByType: Tabulate a list of functions or input variables by their...

sortingAlgorithms: Sorting algorithms for vectors and lists

sse: Sum squared error (SSE)

ssse: Scaled sum squared error (sSSE)

sTypeConstructors: Type constructors for types in the Rsymbolic type system

sTypeInference: Inference of sTypes

subDataFrame: Select a continuous subframe of a data frame

summary.geneticProgrammingResult: Summary reports of genetic programming run result objects

symbolicRegression: Symbolic regression via untyped standard genetic programming

tabulateFunction: Tabulate an n-ary function

variablePresenceMaps: Variable Presence Maps

Files in this package

rgp
rgp/inst
rgp/inst/unittests
rgp/inst/unittests/runner.r
rgp/inst/unittests/runit-gp.r
rgp/inst/doc
rgp/inst/doc/rgp_introduction.R
rgp/inst/doc/rgp_introduction.pdf
rgp/inst/doc/rgp_introduction.Rnw
rgp/src
rgp/src/unification.c
rgp/src/initialization.c
rgp/src/linear_gp_genotype.c
rgp/src/mutation.h
rgp/src/sexp_utils.c
rgp/src/complexity.h
rgp/src/unification.h
rgp/src/eval_vectorized.c
rgp/src/list_utils.h
rgp/src/initialization.h
rgp/src/complexity.c
rgp/src/eval_vectorized.h
rgp/src/mutation.c
rgp/src/crossover.h
rgp/src/list_utils.c
rgp/src/error_measures.c
rgp/src/random_utils.h
rgp/src/evaluate_language_expression.h
rgp/src/random_utils.c
rgp/src/linear_gp_genotype.h
rgp/src/sexp_utils.h
rgp/src/crossover.c
rgp/NAMESPACE
rgp/demo
rgp/demo/00Index
rgp/demo/demo1sine.r
rgp/R
rgp/R/stypes.r
rgp/R/plot_utils.r
rgp/R/recombination.r
rgp/R/niching.r
rgp/R/search_space.r
rgp/R/test_utils.r
rgp/R/creation.r
rgp/R/population.r
rgp/R/expression_utils.r
rgp/R/building_blocks.r
rgp/R/complexity.r
rgp/R/data_driven_gp.r
rgp/R/similarity.r
rgp/R/breeding.r
rgp/R/design_of_experiments.r
rgp/R/data_utils.r
rgp/R/search_heuristics.r
rgp/R/symbolic_regression.r
rgp/R/selection.r
rgp/R/individual.r
rgp/R/list_utils.r
rgp/R/evolution.r
rgp/R/time_utils.r
rgp/R/fitness.r
rgp/R/function_utils.r
rgp/R/mutation.r
rgp/R/pareto_utils.r
rgp/R/rgp.r
rgp/vignettes
rgp/vignettes/tufte-common.def
rgp/vignettes/Makefile
rgp/vignettes/figures
rgp/vignettes/figures/rgpui.png
rgp/vignettes/figures/weierstrass_ensemble.pdf
rgp/vignettes/figures/logo_spotseven.pdf
rgp/vignettes/figures/best_versus_true_sine.pdf
rgp/vignettes/figures/example_ensemble.pdf
rgp/vignettes/figures/do_arith_trig_1.pdf
rgp/vignettes/figures/logo_rgp.pdf
rgp/vignettes/rgp_introduction-013.pdf
rgp/vignettes/rgp_introduction.Rnw
rgp/vignettes/tufte-handout.cls
rgp/vignettes/rgp_introduction.bib
rgp/MD5
rgp/build
rgp/build/vignette.rds
rgp/DESCRIPTION
rgp/ChangeLog
rgp/man
rgp/man/orderByParetoMeasure.Rd rgp/man/summary.geneticProgrammingResult.Rd rgp/man/seSymbolic.Rd rgp/man/makeSeSymbolicFitnessFunction.Rd rgp/man/new.function.Rd rgp/man/makeTinyGpSearchHeuristic.Rd rgp/man/exprLabel.Rd rgp/man/do.call.ignore.unused.arguments.Rd rgp/man/sortingAlgorithms.Rd rgp/man/makeCommaEvolutionStrategySearchHeuristic.Rd rgp/man/rgpTestingAndBenchmarking.Rd rgp/man/subDataFrame.Rd rgp/man/rmse.Rd rgp/man/arity.primitive.Rd rgp/man/r_sse.Rd rgp/man/multiNicheSymbolicRegression.Rd rgp/man/tabulateFunction.Rd rgp/man/dataDrivenGeneticProgramming.Rd rgp/man/populationCreation.Rd rgp/man/expressionCrossover.Rd rgp/man/plotParetoFront.Rd rgp/man/exprToPlotmathExpr.Rd rgp/man/gpIndividualVisualization.Rd rgp/man/expressionSimilarityMeasures.Rd rgp/man/expressionTransformation.Rd rgp/man/randomExpressionChilds.Rd rgp/man/new.alist.Rd rgp/man/populationClustering.Rd rgp/man/mae.Rd rgp/man/randterminalTyped.Rd rgp/man/paretoSorting.Rd rgp/man/randomFunctionCreationTyped.Rd rgp/man/exprChildrenOrEmptyList.Rd rgp/man/formatSeconds.Rd rgp/man/individualAnalysis.Rd rgp/man/gridDesign.Rd rgp/man/expressionNames.Rd rgp/man/randelt.Rd rgp/man/normalizedDesign.Rd rgp/man/latinHypercubeDesign.Rd rgp/man/funcToPlotmathExpr.Rd rgp/man/r_mae.Rd rgp/man/expressionCounts.Rd rgp/man/defaultGPFunctionAndConstantSets.Rd rgp/man/randomExpressionCreation.Rd rgp/man/variablePresenceMaps.Rd rgp/man/expressionComposing.Rd rgp/man/makeFunctionFitnessFunction.Rd rgp/man/selectionFunctions.Rd rgp/man/smse.Rd rgp/man/sortByRanking.Rd rgp/man/searchSpaceDefinition.Rd rgp/man/is.sType.Rd rgp/man/buildingBlockTags.Rd rgp/man/makeAgeFitnessComplexityParetoGpSearchHeuristic.Rd rgp/man/symbolicRegression.Rd rgp/man/extractAttributes.Rd rgp/man/r_ssse.Rd rgp/man/inversePermutation.Rd rgp/man/sse.Rd rgp/man/iterate.Rd rgp/man/randomExpressionCreationTyped.Rd rgp/man/ssse.Rd rgp/man/seSymbolicFunction.Rd rgp/man/listSplittingAndGrouping.Rd rgp/man/evolutionRestartStrategies.Rd rgp/man/joinElites.Rd rgp/man/nondeterministicRanking.Rd rgp/man/randomFunctionCreation.Rd rgp/man/plotFunction3d.Rd rgp/man/paretoFrontKneeIndex.Rd rgp/man/expressionComplexityMeasures.Rd rgp/man/evolutionStopConditions.Rd rgp/man/sTypeConstructors.Rd rgp/man/makeNaryFunctionFitnessFunction.Rd rgp/man/customDist.Rd rgp/man/nmse.Rd rgp/man/normalize.Rd rgp/man/buildingBlocks.Rd rgp/man/multiNicheGeneticProgramming.Rd rgp/man/mse.Rd rgp/man/rangeTypeOfType.Rd rgp/man/arity.Rd rgp/man/plotFunctions.Rd rgp/man/makeRegressionFitnessFunction.Rd rgp/man/sortByType.Rd rgp/man/evolutionRestartConditions.Rd rgp/man/booleanFunctionManipulation.Rd rgp/man/embedDataFrame.Rd rgp/man/rgp-package.Rd rgp/man/popfitness.Rd rgp/man/geneticProgramming.Rd rgp/man/plotPopulationFitnessComplexity.Rd rgp/man/predict.symbolicRegressionModel.Rd rgp/man/lispLists.Rd rgp/man/rsquared.Rd rgp/man/expressionMutation.Rd rgp/man/sortBy.Rd rgp/man/safeGPfunctions.Rd rgp/man/sTypeInference.Rd rgp/man/sortByRange.Rd rgp/man/breeding.Rd rgp/man/makeClosure.Rd rgp/man/print.sType.Rd rgp/man/makeArchiveBasedParetoTournamentSearchHeuristic.Rd

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