Man pages for jfukuyama/adaptiveGPCA
Adaptive Generalized PCA
| adaptivegpca | Adaptive gPCA |
| adaptiveGPCA-package | adaptiveGPCA: A package for structured dimensionality... |
| AntibioticPhyloseq | Antibiotic time course experiment. |
| AntibioticSmall | A subset of the antibiotic data |
| check_axes | Check that the axes specified are valid |
| check_phyloseq | Check compatibility of agpca and phyloseq objects |
| estimateComponents | Estimate parameters in hierarchical model |
| estimateComponents2 | Estimate variance components |
| findReflection | Find reflection |
| gpca | gPCA |
| gpcaEvecs | gPCA using pre-computed eidendecomposition |
| gpcaFullFamily | Make a sequence of ordinations |
| gradLik | Derivative of the likelihood |
| gradSigma2OfR | Derivative of sigma^2 |
| inspectTaxonomy | Shiny gadget for tree/taxonomy inspection |
| likelihood | The likelihood at a given value of r and sigma |
| likelihoodR | The likelihood at a given value of r and the maximizing sigma... |
| likelihood_two_params | Likelihood of data in two-parameter model |
| normalizeMatrix | Normalizes a matrix. |
| plot.adaptivegpca | Plot an adaptivegpca object |
| print.adaptivegpca | Print an adaptivegpca object |
| processPhyloseq | Make the input matrices for adaptive gPCA |
| sigma2OfR | Value of sigma^2 that maximizes the likelihood for a given... |
| varianceOnEvecs | Variance along eigenvectors of Q |
| visualizeFullFamily | Shiny gadget for adaptive gPCA |
