philr

A phylogenetic transform for analysis of compositional microbiome data

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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 survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

Authors

Justin Silverman, Duke University

Citation

Justin D Silverman, Alex D Washburne, Sayan Mukherjee, Lawrence A David. A phylogenetic transform enhances analysis of compositional microbiota data. eLife 2017;6:e21887

License

All source code freely availale under GPL-3 License.

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')

Installation

The release version of philr is maintained on Bioconductor

## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("philr")

The development version is maintained on GitHub and can be downloaded as follows:

## install.packages('devtools') # if devtools not installed
devtools::install_github('jsilve24/philr')

Alternatively, download and decompress package and then run:

## install.packages('devtools') # if devtools not installed
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
devtools::install_local(‘x’)  # replace x with path to decompressed package

Bugs/Feature requests

I appreciate bug reports and feature requests. Please post to the github issue tracker here.