View source: R/adaptivegpca-package.R
gpcaFullFamily | R Documentation |
Creates a sequence of gPCA data representations. One end of the sequence (r = 0) doesn't do any regularization according to the variable structure (and so is just standard PCA), and the other (r = 1) does a maximal amount of regularization according to the variable structure.
gpcaFullFamily(X, Q, weights = rep(1, nrow(X)), k = 2, rvec = (0:100)/100, findReflections = TRUE, returnLong = FALSE, sampledata = NULL, variabledata = NULL)
X |
A data matrix of size n \times p. |
Q |
A p \times p similarity matrix defining an inner
product on the rows of |
weights |
A vector of weights for the rows of |
k |
The number of components to compute for each ordination. |
rvec |
The values of r for which to make the ordinations. |
findReflections |
Whether or not flip the axes so as to make
neighboring ordinations as close as possible. If |
returnLong |
Return a long data frame with the samples/variables instead of a list of data frames. |
sampledata |
Extra sample data to be included along with the sample scores. |
variabledata |
Extra variable data to be included along with the variable loadings. |
A list containing elements for the sample points
(locationList
), the species points (speciesList
), and
the variance fractions (varsList
). Each element is itself a
list of data frames (location/species points) or of vectors (for
the variances).
data(AntibioticSmall) out.ff = gpcaFullFamily(AntibioticSmall$X, AntibioticSmall$Q, k = 2)
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