PhILR

Overview

PhILR = Phylogenetic Isometric Log-Ratio Transform. This R package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota/genome survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

Installation

If you don't already have the devtools package installed, run:

install.packages('devtools')

The development version is maintained on GitHub, try:

devtools::install_github('jsilve24/philr')

Alternatively, download and decompress package and then run:

source('http://bioconductor.org/biocLite.R')
devtools::install_local(‘x’)  # replace x with path to decompressed package

Documentation

Each exported function in the package has been documented and we have also written an introductory vignette that is accessible by calling

vignette('philr-intro', package='philr')

Authors and Contributors

Justin Silverman (@jsilve24), Duke University