mccTest: MCC test

In powerPLS: Power Analysis for PLS Classification

MCC test

Description

Performs permutation-based test based on Matthews Correlation Coefficient

Usage

mccTest(X, Y, nperm = 200, A, randomization = FALSE,
Y.prob = FALSE, eps = 0.01, scaling = 'auto-scaling',
post.transformation = TRUE, cross.validation = FALSE, seed = 123, ...)

Arguments

X	data matrix where columns represent the p variables and rows the n observations.
Y	data matrix where columns represent the two classes and rows the n observations.
nperm	number of permutations. Default to 200.
A	number of score components
randomization	Boolean value. Default to FALSE. If TRUE the permutation p-value is computed
Y.prob	Boolean value. Default FALSE. IF TRUE Y is a probability vector
eps	Default 0.01. eps is used when Y.prob = FALSE to transform Y in a probability vector
scaling	Type of scaling, one of c('auto-scaling', 'pareto-scaling', 'mean-centering'). Default 'auto-scaling'.
post.transformation	Boolean value. TRUE if you want to apply post transformation. Default TRUE
cross.validation	Boolean value. Default FALSE. TRUE if you want to compute the observed test statistic by nested cross-validation
seed	Seed value
...	additional arguments related to cross.validation. See repeatedCV_test

Value

List with the following objects:

pv

raw p-value. It equals NA if randomization = FALSE

pv_adj

adjusted p-value. It equals NA if randomization = FALSE

test

estimated test statistic

Author(s)

Angela Andreella

References

For the general framework of power analysis for PLS-based methods see:

Andreella, A., Fino, L., Scarpa, B., & Stocchero, M. (2024). Towards a power analysis for PLS-based methods. arXiv preprint https://arxiv.org/abs/2403.10289.

See Also

Other test statistics implemented: AUCTest, scoreTest, dQ2Test, sensitivityTest,AUCTest, R2Test, specificityTest, FMTest.

Examples

datas <- simulatePilotData(nvar = 30, clus.size = c(15,15),m = 6,nvar_rel = 5,A = 1)
out <- mccTest(X = datas$X, Y = datas$Y, A = 1)
out

powerPLS documentation built on April 4, 2025, 1:57 a.m.