cross_validation: bootstrap_blocked_cross_validation

In bbuchsbaum/rMVPA: Multivoxel Pattern Analysis in R

bootstrap_blocked_cross_validation

Description

Bootstrap Blocked Cross-Validation Specification

This function constructs a cross-validation specification using a predefined blocking variable.

This function constructs a cross-validation specification using a predefined blocking variable, dividing each block into a specified number of folds.

This function constructs a cross-validation specification that uses a user-supplied set of training and test indices.

Usage

bootstrap_blocked_cross_validation(block_var, nreps = 10, weights = NULL)

blocked_cross_validation(block_var)

sequential_blocked_cross_validation(block_var, nfolds = 2, nreps = 4)

custom_cross_validation(sample_set)

Arguments

block_var	An integer vector indicating the cross-validation blocks. Each block is indicated by a unique integer.
nreps	The number of repetitions for the cross-validation procedure.
weights	A numeric vector of the same length as 'block_var', representing the weights for each sample. Higher weights indicate that observations will be sampled more often. If not provided, all samples are treated as equally likely.
nfolds	The number of folds to divide each sequence of trials within a block.
sample_set	A list of training and test sample indices. Each element of the list must be a named list with two elements: "train" and "test".

Details

This function constructs a cross-validation specification using a predefined blocking variable and creates bootstrap resamples within the blocks.

The function first checks if the provided weights are non-negative and normalizes them to sum to 1. It then constructs a list containing the block variable, number of folds, block indices, number of repetitions, and weights. The output list is assigned the class '"bootstrap_blocked_cross_validation"', '"cross_validation"', and '"list"'.

The function constructs a list containing the block variable, number of folds, and block indices. The output list is assigned the class '"blocked_cross_validation"', '"cross_validation"', and '"list"'.

The function constructs a list containing the block variable, number of folds, number of repetitions, and block indices. The output list is assigned the class '"sequential_blocked_cross_validation"', '"cross_validation"', and '"list"'.

The custom_cross_validation class allows users to define their own cross-validation structure by providing a set of training and test indices. This can be useful in situations where the standard cross-validation methods (e.g., k-fold, leave-one-out) do not adequately represent the desired validation structure.

The function constructs a list containing the sample set and the number of folds, derived from the length of the sample set. The output list is assigned the class '"custom_cross_validation"', '"cross_validation"', and '"list"'.

Value

A list containing the cross-validation specification, with class attributes "bootstrap_blocked_cross_validation", "cross_validation", and "list".

A list containing the cross-validation specification, with class attributes "blocked_cross_validation", "cross_validation", and "list".

A list containing the cross-validation specification, with class attributes "sequential_blocked_cross_validation", "cross_validation", and "list".

A list containing the custom cross-validation specification, with class attributes "custom_cross_validation", "cross_validation", and "list".

Examples

block_var <- rep(1:5, each=50)
weights <- runif(length(block_var))
weights[1] = 0
cval <- bootstrap_blocked_cross_validation(block_var, weights=weights)
X <- matrix(rnorm(length(block_var) * 10), length(block_var), 10)
y <- rep(letters[1:5], length.out=length(block_var))

sam <- crossval_samples(cval, as.data.frame(X), y)
block_var <- rep(1:5, each=50)
cval <- blocked_cross_validation(block_var)
X <- matrix(rnorm(length(block_var) * 10), length(block_var), 10)
y <- rep(letters[1:5], length.out=length(block_var))

sam <- crossval_samples(cval, as.data.frame(X), y)
block_var <- rep(1:5, each=50)
nfolds <- 2
nreps <- 4
cval <- sequential_blocked_cross_validation(block_var, nfolds, nreps)
X <- matrix(rnorm(length(block_var) * 10), length(block_var), 10)
y <- rep(letters[1:5], length.out=length(block_var))

sam <- crossval_samples(cval, as.data.frame(X), y)
sample_set <- list(
  list(train = 1:80, test = 81:100),
  list(train = 1:60, test = 61:100),
  list(train = 1:40, test = 41:100)
)
cval <- custom_cross_validation(sample_set)
X <- matrix(rnorm(100 * 10), 100, 10)
y <- rep(letters[1:4], length.out=100)

sam <- crossval_samples(cval, as.data.frame(X), y)

bbuchsbaum/rMVPA documentation built on April 28, 2024, 6:30 a.m.