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.

Author
Oliver Flasch, Olaf Mersmann, Thomas Bartz-Beielstein, Joerg Stork, Martin Zaefferer
Date of publication
2014-08-08 14:05:23
Maintainer
Oliver Flasch <oliver.flasch@fh-koeln.de>
License
GPL-2
Version
0.4-1
URLs

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