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HMPTrees (version 1.4)

Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data

Description

Tools to model, compare, and visualize populations of taxonomic tree objects.

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Version

Install

install.packages('HMPTrees')

Monthly Downloads

186

Version

1.4

License

Apache License (== 2.0)

Maintainer

Berkley Shands

Last Published

July 5th, 2017

Functions in HMPTrees (1.4)

generateTree

Generate Test Trees
getMLEandLoglike

Get MLE and Log Likelihood of a Data Set
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
HMPTrees-internal

Internal Functions
HMPTrees-package

Object Oriented Data Analysis of Taxonomic Trees
mergeDataSets

Merge Multiple Data Sets
pairedCompareTwoDataSets

Likelihood-Ratio-Test Statistics to Compare the Distribution of 2 Paired Sets of RDP-Based Taxonomic Trees
throat

Throat Data Set
trimToTaxaLevel

Trim a Tree to a Given Level
displayLegend

Displays Tree Plot Legend
formatData

Formats a Data Set
saliva

Saliva Data Set
stool

Stool Data Set
createAndPlot

Create and Plot a Tree from a Data Set
createTrees

Create a Tree Object
plotTree

Plots a Tree Object
plotTreeDataMDS

Plot an MDS Plot of a Group of Trees