genAlg {gaselect}

Genetic algorithm for variable subset selection

Description

A genetic algorithm to find "good" variable subsets based on internal PLS evaluation or a user specified evaluation function

Usage

genAlg(y, X, control, evaluator = evaluatorPLS(), seed)

Arguments

y

The numeric response vector of length n

X

A n x p numeric matrix with all p covariates

control

Options for controlling the genetic algorithm. See genAlgControl for details.

evaluator

The evaluator used to evaluate the fitness of a variable subset. See evaluatorPLS, evaluatorLM or evaluatorUserFunction for details.

seed

Integer with the seed for the random number generator or NULL to automatically seed the RNG

Details

The GA generates an initial "population" of populationSize chromosomes where each initial chromosome has a random number of randomly selected variables. The fitness of every chromosome is evaluated by the specified evaluator. The default built-in PLS evaluator (see evaluatorPLS) is the preferred evaluator. Chromosomes with higher fitness have higher probability of mating with another chromosome. populationSize / 2 couples each create 2 children. The children are created by randomly mixing the parents' variables. These children make up the new generation and are again selected for mating based on their fitness. A total of numGenerations generations are built this way. The algorithm returns the last generation as well as the best elitism chromosomes from all generations.

Value

An object of type GenAlg

Examples

ctrl <- genAlgControl(populationSize = 100, numGenerations = 15, minVariables = 5,
    maxVariables = 12, verbosity = 1)

evaluatorSRCV <- evaluatorPLS(numReplications = 2, innerSegments = 7, testSetSize = 0.4,
    numThreads = 1)

evaluatorRDCV <- evaluatorPLS(numReplications = 2, innerSegments = 5, outerSegments = 3,
    numThreads = 1)

# Generate demo-data
set.seed(12345)
X <- matrix(rnorm(10000, sd = 1:5), ncol = 50, byrow = TRUE)
y <- drop(-1.2 + rowSums(X[, seq(1, 43, length = 8)]) + rnorm(nrow(X), 1.5));

resultSRCV <- genAlg(y, X, control = ctrl, evaluator = evaluatorSRCV, seed = 123)
resultRDCV <- genAlg(y, X, control = ctrl, evaluator = evaluatorRDCV, seed = 123)

subsets(resultSRCV, 1:5)
subsets(resultRDCV, 1:5)