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

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

Author
Patricio S. La Rosa, Elena Deych, Berkley Shands, William D. Shannon
Date of publication
2016-01-19 23:53:07
Maintainer
Berkley Shands <rpackages@biorankings.com>
License
Apache License (== 2.0)
Version
1.3

View on CRAN

Man pages

checkTreeValidity
Check Validity of an RDP-Based Taxonomic Tree
compareTwoDataSets
Likelihood-Ratio-Test Statistics to Compare the Distribution...
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
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...
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

Files in this package

HMPTrees
HMPTrees/inst
HMPTrees/inst/doc
HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.Rnw
HMPTrees/inst/doc/Creating-Data-From-RDP-Tutorial.pdf
HMPTrees/NAMESPACE
HMPTrees/NEWS
HMPTrees/data
HMPTrees/data/saliva.rda
HMPTrees/data/throat.rda
HMPTrees/data/stool.rda
HMPTrees/R
HMPTrees/R/getBranchSizes.R
HMPTrees/R/traverseTreeHelp.R
HMPTrees/R/createTrees.R
HMPTrees/R/transformHMPtoHMPTree.R
HMPTrees/R/pairedCompareTwoDataSets.R
HMPTrees/R/getTaxaDepth.R
HMPTrees/R/plotTree.R
HMPTrees/R/trimToTaxaLevel.R
HMPTrees/R/subsetData.R
HMPTrees/R/traverseTree.R
HMPTrees/R/createAndPlot.R
HMPTrees/R/buildTree.R
HMPTrees/R/transformHMPTreetoHMP.R
HMPTrees/R/generateTree.R
HMPTrees/R/displayLegend.R
HMPTrees/R/plotTreeDataMDS.R
HMPTrees/R/mergeDataSets.R
HMPTrees/R/removeUnclass.R
HMPTrees/R/formatData.R
HMPTrees/R/getMLEandLoglike.R
HMPTrees/R/checkTreeValidity.R
HMPTrees/R/compareTwoDataSets.R
HMPTrees/R/checkTreeValidHelp.R
HMPTrees/vignettes
HMPTrees/vignettes/Creating-Data-From-RDP-Tutorial.Rnw
HMPTrees/MD5
HMPTrees/build
HMPTrees/build/vignette.rds
HMPTrees/DESCRIPTION
HMPTrees/man
HMPTrees/man/HMPTrees-internal.Rd
HMPTrees/man/displayLegend.Rd
HMPTrees/man/transformHMPtoHMPTree.Rd
HMPTrees/man/transformHMPTreetoHMP.Rd
HMPTrees/man/trimToTaxaLevel.Rd
HMPTrees/man/pairedCompareTwoDataSets.Rd
HMPTrees/man/generateTree.Rd
HMPTrees/man/plotTree.Rd
HMPTrees/man/checkTreeValidity.Rd
HMPTrees/man/createAndPlot.Rd
HMPTrees/man/throat.Rd
HMPTrees/man/stool.Rd
HMPTrees/man/formatData.Rd
HMPTrees/man/compareTwoDataSets.Rd
HMPTrees/man/mergeDataSets.Rd
HMPTrees/man/HMPTrees-package.Rd
HMPTrees/man/getMLEandLoglike.Rd
HMPTrees/man/saliva.Rd
HMPTrees/man/plotTreeDataMDS.Rd
HMPTrees/man/createTrees.Rd