Package: IFAA
Title: Robust Inference for Absolute Abundance in Microbiome Analysis
Version: 1.15.0
Authors@R: c(person(given = "Quran",
           family = "Wu",
           role = c("aut"),
           email = "wuquran@ufl.edu"),
           person(given = "Zhigang",
           family = "Li",
           role = c("aut", "cre"),
           email = "lzg2151@gmail.com")
           )
Description: This package offers a robust approach to make inference on
        the association of covariates with the absolute abundance (AA)
        of microbiome in an ecosystem. It can be also directly applied
        to relative abundance (RA) data to make inference on AA because
        the ratio of two RA is equal to the ratio of their AA. This
        algorithm can estimate and test the associations of interest
        while adjusting for potential confounders. The estimates of
        this method have easy interpretation like a typical regression
        analysis. High-dimensional covariates are handled with
        regularization and it is implemented by parallel computing.
        False discovery rate is automatically controlled by this
        approach. Zeros do not need to be imputed by a positive value
        for the analysis. The IFAA package also offers the 'MZILN'
        function for estimating and testing associations of abundance
        ratios with covariates.
License: GPL-2
Encoding: UTF-8
URL: https://pubmed.ncbi.nlm.nih.gov/35241863/,
        https://pubmed.ncbi.nlm.nih.gov/30923584/,
        https://github.com/quranwu/IFAA
BugReports: https://github.com/quranwu/IFAA/issues
RoxygenNote: 7.3.1
Depends: R (>= 4.2.0),
Imports: mathjaxr, doRNG, foreach (>= 1.4.3), Matrix (>= 1.4-0), HDCI
        (>= 1.0-2), parallel (>= 3.3.0), doParallel (>= 1.0.11),
        parallelly , glmnet, stats, utils, SummarizedExperiment,
        stringr, S4Vectors, DescTools, MatrixExtra, methods
biocViews: Software, Technology, Sequencing, Microbiome, Regression
RdMacros: mathjaxr
Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-05-30 07:56:40 UTC; root
Config/pak/sysreqs: cmake make libicu-dev libuv1-dev libssl-dev
        libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:59:29 UTC
RemoteUrl: https://github.com/bioc/IFAA
RemoteRef: HEAD
RemoteSha: ca971399a54408343cea32ff027f36f1fcf3b39e
Author: Quran Wu [aut],
  Zhigang Li [aut, cre]
Maintainer: Zhigang Li <lzg2151@gmail.com>