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 | Oct 30 2024 |
| R-4.5-linux | OK | Oct 30 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 |