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

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)

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).

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.

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.

Examples

Run this code

# NOT RUN {
	#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)
# }

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