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adaptiveGPCA (version 0.1.3)

Adaptive Generalized PCA

Description

Implements adaptive gPCA, as described in: Fukuyama, J. (2017) . The package also includes functionality for applying the method to 'phyloseq' objects so that the method can be easily applied to microbiome data and a 'shiny' app for interactive visualization.

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Version

Install

install.packages('adaptiveGPCA')

Monthly Downloads

448

Version

0.1.3

License

AGPL-3

Maintainer

Julia Fukuyama

Last Published

December 8th, 2022

Functions in adaptiveGPCA (0.1.3)

processPhyloseq

Make the input matrices for adaptive gPCA
plot.adaptivegpca

Plot an adaptivegpca object
print.adaptivegpca

Print an adaptivegpca object
sigma2OfR

Value of \(\sigma^2\) that maximizes the likelihood for a given value of \(r\)
likelihoodR

The likelihood at a given value of \(r\) and the maximizing \(\sigma\) for that value of \(r\).
likelihood_two_params

Likelihood of data in two-parameter model
likelihood

The likelihood at a given value of \(r\) and \(\sigma\)
visualizeFullFamily

Shiny gadget for adaptive gPCA
varianceOnEvecs

Variance along eigenvectors of Q
gradSigma2OfR

Derivative of \(\sigma^2\)
adaptivegpca

Adaptive gPCA
findReflection

Find reflection
estimateComponents

Estimate parameters in hierarchical model
AntibioticPhyloseq

Antibiotic time course experiment.
gpca

gPCA
adaptiveGPCA-package

adaptiveGPCA: A package for structured dimensionality reduction
AntibioticSmall

A subset of the antibiotic data
gradLik

Derivative of the likelihood
gpcaEvecs

gPCA using pre-computed eidendecomposition
estimateComponents2

Estimate variance components
gpcaFullFamily

Make a sequence of ordinations
normalizeMatrix

Normalizes a matrix.
check_phyloseq

Check compatibility of agpca and phyloseq objects
inspectTaxonomy

Shiny gadget for tree/taxonomy inspection
check_axes

Check that the axes specified are valid