GeneticAlg.int: Genetic Algorithm with Integer Chromosomes
In gramEvol: Grammatical Evolution for R

Description Usage Arguments Details Value References See Also Examples

Uses genetic algorithm to find the minima of a given cost function. It evolves chromosomes with limited-range integers as codons.

GeneticAlg.int(genomeLen, codonMin, codonMax, 
    genomeMin = rep.int(codonMin, genomeLen), 
    genomeMax = rep.int(codonMax, genomeLen), 
    suggestions = NULL, popSize = 50, 
    iterations = 100, terminationCost = NA, 
    mutationChance = 1/(genomeLen+1), elitism = floor(popSize/10), 
    geneCrossoverPoints = NULL,
    monitorFunc = NULL, evalFunc, allowrepeat = TRUE, 
    showSettings = FALSE, verbose = FALSE, plapply = lapply)

`genomeLen`	Number of integers (i.e, codons) in chromosome.
`codonMin`	Minimum integer value range for all codons.
`codonMax`	Maximum integer value range for all codons.
`genomeMin`	A vector of length `genomeLen` containing fine-grained control over each codon's minimum. Overrides `codonMin`.
`genomeMax`	A vector of length `genomeLen` containing fine-grained control over each codon's maximum. Overrides `codonMax`.
`suggestions`	A list of suggested chromosomes to be used in the initial population. Alternatively, an m-by-n matrix, where m is the number of suggestions and n is the chromosome length.
`popSize`	Size of the population.
`iterations`	Number of generations to evolve the population.
`terminationCost`	Target cost. If the best chromosome's cost reaches this value the algorithm terminates.
`mutationChance`	The chance of a codon being mutated. It must be between 0 and 1.
`geneCrossoverPoints`	Codon groupings (genes) to be considered while crossover occurs. If given, odd and even codon groups are exchanged between parents. Otherwise random points are selected and a classic single-point crossover is performed.
`elitism`	Number of top ranking chromosomes that are directly transfered to next generation without going through evolutionary operations.
`monitorFunc`	A function that is called at each generation. Can be used to monitor evolution of population.
`evalFunc`	The cost function.
`allowrepeat`	Allows or forbids repeated integers in the chromosome.
`showSettings`	Enables printing GA settings.
`verbose`	Enables verbose debugging info.
`plapply`	`lapply` function used for mapping chromosomes to cost function. See details for parallelization tips.

GeneticAlg.int implements evolutionary algorithms with chromosomes created from integer values in the range of codonMin to codonMax. genomeMin and genomeMax allow fine-grained control of range for individual codons. It first creates an initial population, using suggested inputs suggestions and randomly generated chromosomes. Cost of each chromosome is evaluated using the cost function evalFunc. If one of the chromosomes reaches terminationCost, the algorithm terminates; Otherwise evolutionary operators including selection, cross-over and mutation are applied to the population to create a new generation. This iteration is continued until the required cost is reached or the number of generations exceeds iterations.

At each generation, the supplied monitorFunc is called with a list similar to GeneticAlg.int returning value as its argument.

The evalFunc receives integer sequences and must return a numeric value. The goal of optimization would be to find a chromosome which minimizes this value.

To parallelize cost function evaluation, set plapply to a parallelized lapply, such as mclapply from package parallel. In functions that do not handle data dependencies such as parLapply, variables and functions required for correct execution of evalFunc must be exported to worker nodes before invoking GeneticAlg.int.

A list containing information about settings, population, and the best chromosome.

`settings$genomeMin`	Minimum of each codon.
`Settings$genomeMax`	Maximum of each codon.
`settings$popSize`	Size of the population.
`settings$elitism`	Number of elite individuals.
`settings$iterations`	Number of maximum generations.
`settings$suggestions`	Suggested chromosomes.
`settings$mutationChance`	Mutation chance.
`settings$geneCrossoverPoints`	Cross-over points.
`population$population`	The genomic data of the current population.
`population$evaluations`	Cost of the latest generation.
`population$best`	Historical cost of the best chromosomes.
`population$mean`	Historical mean cost of population.
`population$currentIteration`	Number of generations evolved until now.
`best$genome`	The best chromosome.
`best$cost`	The cost of the best chromosome.

This function is partially inspired by genalg package by Egon Willighagen. See https://cran.r-project.org/package=genalg.

GrammaticalEvolution, EvolutionStrategy.int

# define the evaluate function
evalfunc <- function(l) {
    # maximize the odd indices and minimize the even indices
    # no repeated values are allowed
    odd <- seq(1, 20, 2)
    even <- seq(2, 20, 2)
    err <- sum(l[even]) - sum(l[odd]);

    stopifnot(!any(duplicated(l))) # no duplication allowed

    return (err)
}

monitorFunc <- function(result) {
    cat("Best of gen: ", min(result$best$cost), "\n")
}

x <- GeneticAlg.int(genomeLen = 20, codonMin = 0, codonMax = 20,
                allowrepeat = FALSE, terminationCost = -110,
                monitorFunc = monitorFunc, evalFunc = evalfunc)

print(x)

best.result <- x$best$genome
print("Odds:")
print(sort(best.result[seq(1, 20, 2)]))
print("Evens:")
print(sort(best.result[seq(2, 20, 2)]))