epGPCA.inference.battery
epGPCA.inference.battery: Inference tests for Generalized Principal Component Analysis (PCA) via InPosition.
Generalized Principal Component Analysis (PCA) and a battery of inference tests via InPosition. The battery includes permutation and bootstrap tests.
- Keywords
- Bootstrap, multivariate, Permutation
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.scalefor details.- center
a boolean, vector, or string. See
expo.scalefor 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.
$Inference.Data returns:
Permutation tests of components. p-values ($p.vals) and distributions of eigenvalues ($eigs.perm) for each component
Bootstrap tests of measures (columns). See boot.ratio.test output details.
See Also
Examples
# NOT RUN {
#this is for ExPosition's iris data
data(ep.iris)
data<-ep.iris$data
design<-ep.iris$design
gpca.iris.res <- epGPCA.inference.battery(data,DESIGN=design,make_design_nominal=FALSE)
# }