adaptiveGPCA0.1.3 package

adaptiveGPCA: A package for structured dimensionality reduction

Adaptive gPCA

Check that the axes specified are valid

Check compatibility of agpca and phyloseq objects

Estimate parameters in hierarchical model

Estimate variance components

Find reflection

gPCA

gPCA using pre-computed eidendecomposition

Make a sequence of ordinations

Derivative of the likelihood

Derivative of $\sigma^2$

Shiny gadget for tree/taxonomy inspection

The likelihood at a given value of $r$ and $\sigma$

Likelihood of data in two-parameter model

The likelihood at a given value of $r$ and the maximizing $\sigma$ for...

Normalizes a matrix.

Plot an adaptivegpca object

Print an adaptivegpca object

Make the input matrices for adaptive gPCA

Value of $\sigma^2$ that maximizes the likelihood for a given value of...

Variance along eigenvectors of Q

Shiny gadget for adaptive gPCA