epPCA.inference.battery: epPCA.inference.battery: Inference tests for Principal...

In InPosition: Inference Tests for ExPosition

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

Examples

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

InPosition documentation built on April 15, 2025, 9:07 a.m.