DOI: 10.18129/B9.bioc.philr    

This is the development version of philr; for the stable release version, see philr.

Phylogenetic partitioning based ILR transform for metagenomics data

Bioconductor version: Development (3.8)

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This 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.

Author: Justin Silverman

Maintainer: Justin Silverman <jsilve24 at>

Citation (from within R, enter citation("philr")):


To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
BiocManager::install("philr", version = "devel")


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Introduction to PhILR
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biocViews Metagenomics, Microbiome, Sequencing, Software
Version 1.7.1
In Bioconductor since BioC 3.4 (R-3.3) (2 years)
License GPL-3
Imports ape, phangorn, tidyr, ggplot2, ggtree
Suggests testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr
Depends On Me
Imports Me
Suggests Me
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