readme.md
In jfukuyama/treeDA: Tree-Based Discriminant Analysis

treeDA Package

This package performs a version of sparse discriminant analysis which takes into account the tree structure of the variables. It is intended for use in microbiome data analysis, but in principle it could be used in any situation in which the analyst has a number of classes to be separated and a tree structure to the predictor variables.

The package is available on CRAN and can be installed using

install.packages("treeDA")

and then loaded with

library("treeDA")

Since treeDA was intended to be used to analyze microbiome data, it depends on phyloseq, which is a bioconductor package and might need to be installed separately. Installation of phyloseq is described on the bioconductor website, and is accomplished with the following commands in R:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")

The main functions in the package are treeda, which fits a model with a given sparsity level, and treedacv, which performs cross-validation to choose the sparsity level. There is also a function to plot the leaf coefficients obtained from the model aligned to the tree (plot_coefficients). A full vignette showing an analysis of microbiome data is available in the vignettes directory, or by clicking here.