epPCA.inference.battery {InPosition}

epPCA.inference.battery: Inference tests for Principal Component Analysis (PCA) via InPosition.

Description

Principal Component Analysis (PCA) and a battery of inference tests via InPosition. The battery includes permutation and bootstrap tests.

Usage

epPCA.inference.battery(DATA, scale = TRUE, center = TRUE, DESIGN = NULL, 
	make_design_nominal = TRUE, graphs = TRUE, k = 0, 
	test.iters = 100, constrained = FALSE, critical.value = 2)

Arguments

DATA

original data to perform a PCA on.

scale

a boolean, vector, or string. See expo.scale for details.

center

a boolean, vector, or string. See expo.scale for details.

DESIGN

a design matrix to indicate if rows belong to groups.

make_design_nominal

a boolean. If TRUE (default), DESIGN is a vector that indicates groups (and will be dummy-coded). If FALSE, DESIGN is a dummy-coded matrix.

graphs

a boolean. If TRUE (default), graphs and plots are provided (via epGraphs)

k

number of components to return.

test.iters

number of iterations

constrained

a boolean. If a DESIGN matrix is used, this will constrain bootstrap resampling to be within groups.

critical.value

numeric. A value, analogous to a z- or t-score to be used to determine significance (via bootstrap ratio).

Details

epPCA.inference.battery performs principal components analysis and inference tests on a data matrix.

If the expected time to compute the results (based on test.iters) exceeds 1 minute, you will be asked (via command line) if you want to continue.

Value

Returns two lists ($Fixed.Data and $Inference.Data). For $Fixed.Data, see epPCA, corePCA for details on the descriptive (fixed-effects) results.

$Inference.Data returns:

components

Permutation tests of components. p-values ($p.vals) and distributions of eigenvalues ($eigs.perm) for each component

fj.boots

Bootstrap tests of measures (columns). See boot.ratio.test output details.

Author(s)

Derek Beaton and Hervé Abdi.

See Also

epPCA, epGPCA, epGPCA.inference.battery

Examples

	data(words)
	pca.words.res <- epPCA.inference.battery(words$data)