Package: HMPTrees 1.4
Berkley Shands
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.
Authors:
HMPTrees_1.4.tar.gz
HMPTrees_1.4.tar.gz(r-4.5-noble)HMPTrees_1.4.tar.gz(r-4.4-noble)
HMPTrees_1.4.tgz(r-4.4-emscripten)HMPTrees_1.4.tgz(r-4.3-emscripten)
HMPTrees.pdf |HMPTrees.html✨
HMPTrees/json (API)
NEWS
# Install 'HMPTrees' in R: |
install.packages('HMPTrees', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 7 years agofrom:fab611dd1d. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 29 2024 |
R-4.5-linux | OK | Nov 29 2024 |
Exports:buildTreecheckTreeValidHelpcheckTreeValiditycompareTwoDataSetscreateAndPlotcreateTreesdisplayLegendformatDatagenerateTreegetBranchSizesgetMLEandLoglikegetTaxaDepthmergeDataSetspairedCompareTwoDataSetsplotTreeplotTreeDataMDSremoveUnclasssubsetDatatransformHMPtoHMPTreetransformHMPTreetoHMPtraverseTreetraverseTreeHelptrimToTaxaLevel
Dependencies:apebitopscaToolscliclustercodetoolscolorspacedigestdirmultdoParallelfansifarverforeachggplot2gluegplotsgtablegtoolsHMPisobanditeratorsKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepermutepillarpkgconfigR6RColorBrewerRcpprlangrpartrpart.plotscalestibbleutf8vctrsveganviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Object Oriented Data Analysis of Taxonomic Trees | HMPTrees-package HMPTrees |
Check Validity of an RDP-Based Taxonomic Tree | checkTreeValidity |
Likelihood-Ratio-Test Statistics to Compare the Distribution of 2 Sets of RDP-Based Taxonomic Trees | compareTwoDataSets |
Create and Plot a Tree from a Data Set | createAndPlot |
Create a Tree Object | createTrees |
Displays Tree Plot Legend | displayLegend |
Formats a Data Set | formatData |
Generate Test Trees | generateTree |
Get MLE and Log Likelihood of a Data Set | getMLEandLoglike |
Merge Multiple Data Sets | mergeDataSets |
Likelihood-Ratio-Test Statistics to Compare the Distribution of 2 Paired Sets of RDP-Based Taxonomic Trees | pairedCompareTwoDataSets |
Plots a Tree Object | plotTree |
Plot an MDS Plot of a Group of Trees | plotTreeDataMDS |
Saliva Data Set | saliva |
Stool Data Set | stool |
Throat Data Set | throat |
Trim a Tree to a Given Level | trimToTaxaLevel |