DESCRIPTION

Package: propr
Title: An R package to calculate proportionality and other measures for compositional data
Version: 5.1.5
URL: https://github.com/tpq/propr
BugReports: https://github.com/tpq/propr/issues
Authors@R: c(
    person("Thomas", "Quinn", email = "contacttomquinn@gmail.com", role = c("aut", "cre")),
    person("Suzanne", "Jin", email = "suzanne.jin.yao@gmail.com", role = "aut"),
    person("Ionas", "Erb", email = "ionas.erb@crg.eu", role = "aut"),
    person("David", "Lovell", email = "david.lovell@qut.edu.au", role = "aut"),
    person("Anders", "Bilgrau", email = "anders.ellern.bilgrau@gmail.com", role = "ctb"),
    person("Greg", "Gloor", email = "ggloor@uwo.ca", role = "ctb"),
    person("Ryan", "Moore", email = "rmm1047@gmail.com", role = "ctb")
    )
Description: The bioinformatic evaluation of gene co-expression often begins with
    correlation-based analyses. However, conventional correlation measures lack validity 
    when applied to compositional data, including count data generated by next-generation
    sequencing. Here we implemented valid alternatives for measuring association between 
    vectors of compositional data. These include several metrics for proportionality, such as 
    phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and 
    rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. It also implements a
    regularized version of logratio partial correlations [Jin et al (2023) <DOI:10.57645/20.8080.02.8>]. 
    Moreover, this package implements several metrics for 
    differential proportionality [Erb et al (2017) <DOI:10.1101/134536>].
License: GPL-2
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.3.2
Encoding: UTF-8
Depends:
    methods,
    R (>= 3.2.2)
Imports:
    corpcor,
    ppcor,
    Rcpp,
    stats
Suggests:
    ALDEx2,
    fastcluster,
    knitr,
    limma,
    parallel,
    rmarkdown,
    testthat (>= 3.0.0),
    vegan
LinkingTo:
    Rcpp
Config/testthat/edition: 3