epGPCA.inference.battery: epGPCA.inference.battery: Inference tests for Generalized...

In InPosition: Inference Tests for ExPosition

Description

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

Usage

epGPCA.inference.battery(DATA, scale = TRUE, center = TRUE, DESIGN = NULL, 
	make_design_nominal = TRUE, masses = NULL, weights = NULL, 
	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.
masses	a diagonal matrix or column-vector of masses for the row items.
weights	a diagonal matrix or column-vector of weights for the column items.
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

epGPCA.inference.battery performs generalized 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 epGPCA, 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

epGPCA, epPCA, epPCA.inference.battery

Examples

	#this is for ExPosition's iris data
	data(ep.iris)
	data<-ep.iris$data
	design<-ep.iris$design
	gpca.iris.res <- epGPCA.inference.battery(data,DESIGN=design,make_design_nominal=FALSE)

InPosition documentation built on May 2, 2019, 7:59 a.m.