DESCRIPTION

Package: philr
Type: Package
Title: Phylogenetic partitioning based ILR transform for metagenomics data
Version: 1.31.1
Date: 2024-10-15
Authors@R:
    c(person("Justin", "Silverman", role=c("aut", "cre"),
                     email = "jsilve24@gmail.com"),
      person(given = "Leo", family = "Lahti", role = c("ctb"),
             comment = c(ORCID = "0000-0001-5537-637X")))
Description: 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.
License: GPL-3
RoxygenNote: 7.3.2
Imports:
    ape,
    phangorn,
    tidyr,
    ggplot2,
    ggtree,
    methods
Suggests:
    testthat,
    knitr,
    ecodist,
    rmarkdown,
    BiocStyle,
    phyloseq,
    SummarizedExperiment,
    TreeSummarizedExperiment,    
    glmnet,
    dplyr,
    mia
VignetteBuilder: knitr
biocViews: ImmunoOncology, Sequencing, Microbiome, Metagenomics, Software
URL: https://github.com/jsilve24/philr 
BugReports: https://github.com/jsilve24/philr/issues