# philr
*A phylogenetic transform for analysis of compositional microbiome data*
***
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](https://elifesciences.org/content/6/e21887)
## License ##
All source code freely availale under [GPL-3 License](https://www.gnu.org/licenses/gpl-3.0.en.html).
## Documentation ##
Each exported function in the package has been documented and we have also written an introductory vignette that is accessible by calling
``` r
vignette('philr-intro', package='philr')
```
## Installation ##
The release version of philr is maintained on [Bioconductor](http://bioconductor.org/packages/philr/)
``` r
## 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:
``` r
## install.packages('devtools') # if devtools not installed
devtools::install_github('jsilve24/philr')
```
Alternatively, download and decompress package and then run:
```r
## 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](https://github.com/jsilve24/philr/issues).
