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.


News

CHANGES IN HMPTrees VERSION 1.5

CHANGES

  • Changed the getMLEandLoglike function to return additional values and use weightCols instead of weight

  • Tidied up some code, comments and variable names

  • Rewrote how trees are created

  • Changed mergeDataSets to not calculate MLEs by default

  • Changed generateTrees arguments to allow for different number of reads per sample

  • transformHMPTreetoHMP and transformHMPtoHMPTree are now internal functions since they don't really do much more than transposing data frames

  • Stopped using 'samples' in several functions to select which trees to use. Just pass in only the trees to use.

  • Simplified plotTreeDataMDS's arguments some

CHANGES IN HMPTrees VERSION 1.4

CHANGES

  • Changed buildTree to not set anything greater than 1 to 1

  • Added drop=FALSE to several functions to prevent single samples from crashing

  • Made pi base::pi so it wouldn't have conflict

CHANGES IN HMPTrees VERSION 1.3

CHANGES

  • Added a function to compare paired data sets

CHANGES IN HMPTrees VERSION 1.2

CHANGES

  • Changed every function to expect the taxa to be listed as the rownames, rather than the first column

  • Changed the parallel computing in the compareTwoDataSets functions to work on any OS and use the doParallel package

  • Changed the plotTreeDataMDS and mergeDataSets functions to accommodate any number of data sets

  • Added more functionality/options to the plotTreeDataMDS function

  • Changed the generateTree function

  • Changed several functions to allow the use of splits besides a '.' in the taxa names

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("HMPTrees")

1.4 by Berkley Shands, 4 years ago


Browse source code at https://github.com/cran/HMPTrees


Authors: Patricio S. La Rosa , Elena Deych , Berkley Shands , William D. Shannon


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


Apache License (== 2.0) license


Imports ape, HMP, dirmult, doParallel, foreach, parallel, stats, graphics


See at CRAN