epCA.inference.battery: epCA.inference.battery: Inference tests for Correspondence...
In InPosition: Inference Tests for ExPosition

Description Usage Arguments Details Value Author(s) See Also Examples

Correspondence Analysis (CA) and a battery of inference tests via InPosition. The battery includes permutation and bootstrap tests.

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epCA.inference.battery(DATA, DESIGN = NULL, make_design_nominal = TRUE, 
	masses = NULL, weights = NULL, hellinger = FALSE, symmetric = TRUE, 
	graphs = TRUE, k = 0, test.iters = 100, critical.value = 2)

`DATA`	original data to perform a CA on.
`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 it
`hellinger`	a boolean. If FALSE (default), Chi-square distance will be used. If TRUE, Hellinger distance will be used.
`symmetric`	a boolean. If TRUE (default) symmetric factor scores for rows and columns are computed. If FALSE, the simplex (column-based) will be returned.
`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).

epCA.inference.battery performs correspondence 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.

Returns two lists ($Fixed.Data and $Inference.Data). For $Fixed.Data, see epCA, coreCA 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.
`omni`	Permutation tests of components. p-values ($p.val) and distributions of total inertia ($inertia.perm)

Derek Beaton, Joseph Dunlop, and Hervé Abdi.

epCA, epMCA, epMCA.inference.battery, caChiTest

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	##warning: this example takes a while to compute. This is why it is reduced.
	data(authors)
	ca.authors.res <- epCA.inference.battery(authors$ca$data/100)

Loading required package: prettyGraphs
Loading required package: ExPosition
[1] "It is estimated that your iterations will take 0.49 minutes."
[1] "R is not in interactive() mode. Resample-based tests will be conducted. Please take note of the progress bar."
================================================================================dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")