tepBADA.inference.battery: Barycentric Discriminant Analysis Inference Battery

In TInPosition: Inference Tests for TExPosition

Description

Barycentric Discriminant Analysis (BADA) Inference Battery via TInPosition.

Usage

tepBADA.inference.battery(DATA, scale = TRUE, center = TRUE, DESIGN = NULL, 
	make_design_nominal = TRUE, 
	group.masses = NULL, weights = NULL, 
	graphs = TRUE, k = 0, 
	test.iters = 100, critical.value = 2)

Arguments

DATA	original data to perform a BADA 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. Required for BADA.
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.
group.masses	a diagonal matrix or column-vector of masses for the groups.
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
critical.value	numeric. A value, analogous to a z- or t-score to be used to determine significance (via bootstrap ratio).

Details

tepBADA.inference.battery performs barycentric discriminant analysis and inference tests on based on data and (row) design matrices.

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 tepBADA and corePCA for details on the descriptive (fixed-effects) results.

$Inference.Data returns:

omni	Permutation tests of components. p-values ($p.val) and distributions of total inertia ($inertia.perm)
r2	Permutation tests of R-squared value. p-values ($p.val) and distributions of R2s ($r2.perm)
components	Permutation tests of components. p-values ($p.vals) and distributions of eigenvalues ($eigs.perm) for each component
boot.data	Bootstrap tests for $fi and $fj. Contains distributions. See also boot.ratio.test output details.
loo.data	Leave one out cross-validation tests. Includes assignments ($loo.assign), factor scores ($loo.fii), LOO and fixed confusion matrices ($loo.confuse, $fixed.confuse), and accuracy ($loo.acc, $fixed.acc)

Author(s)

Derek Beaton, Jenny Rieck, Hervé Abdi

Examples

	data(bada.wine)
	data<-bada.wine$data
	design <- bada.wine$design
	bada.res <- 
		tepBADA.inference.battery(data,scale=FALSE,DESIGN=design,
			make_design_nominal=FALSE,test.iters=50)

TInPosition documentation built on May 2, 2019, 3:46 p.m.