Statistical Object Oriented Data Analysis of RDP-based Taxonomic trees from Human Microbiome Data: Modeling, Visualization, and Two-Group Comparison

Documentation for package ‘HMPTrees’ version 1.1

checkTreeValidity	Check Validity of an RDP-Based Taxonomic Tree
compareTwoDataSets	Likelihood-Ratio-Test Statistics to Compare the Distribution of 2 Sets of RDP-Based Taxonomic Trees
createAndPlot	Create and Plot a Tree from a Data Set
createTrees	Create a Tree Object
displayLegend	Displays Tree Plot Legend
formatData	Formats a Data Set
generateTree	Generate Test Trees
getMLEandLoglike	Get MLE and Log Likelihood of a Data Set
mergeDataSets	Merge Multiple Data Sets
plotTree	Plots a Tree Object
plotTreeDataMDS	Plot an MDS Plot of a Group of Trees
saliva	Saliva Data Set
stool	Stool Data Set
throat	Throat Data Set
transformHMPtoHMPTree	Transform data from HMP to HMPTrees
transformHMPTreetoHMP	Transform data from HMPTrees to HMP
trimToTaxaLevel	Trim a Tree to a Given Level