adaptiveGPCA is an R package for dimensionality reduction when the variables measured are related to each other.
The primary use case so far has been in microbiome data.
In that case, the variables measured are bacterial species and they are related to each other by a phylogenetic tree.
It can also be used to provide a “guided tour” of the data, an example of which can be seen here.
The package is available on CRAN, and can be installed using
install.packages("adaptiveGPCA")
treeDA is an R package for sparse, tree-based discriminant analysis for microbiome data.
The package is available on CRAN, and can be installed using
install.packages("treeDA")
phyloseqGraphTest is an R package implementing a permutational version of the Friedman-Rafsky test. It is designed to work with a phyloseq object describing a microbiome experiment, and allows for testing based on minimum spanning trees, k-nearest neighbor graphs, or distance threshold graphs with any of the many distances implemented in phyloseq.
The package is available on CRAN and can be installed using
install.packages("phyloseqGraphTest")
