Package: MAI
Type: Package
Title: Mechanism-Aware Imputation
Version: 1.19.0
Authors@R: 
  c(person(given = "Jonathan",
           family = "Dekermanjian",
           role = c("aut", "cre"),
           email = "Jonathan.Dekermanjian@CUAnschutz.edu"),
    person(given = "Elin",
           family = "Shaddox",
           role = c("aut"),
           email = "Elin.Shaddox@CUAnschutz.edu"),
    person(given = "Debmalya",
           family = "Nandy",
           role = c("aut"),
           email = "Debmalya.Nandy@CUAnschutz.edu"),
   person(given = "Debashis",
           family = "Ghosh",
           role = c("aut"),
           email = "Debashis.Ghosh@CUAnschutz.edu"),
   person(given = "Katerina",
           family = "Kechris",
           role = c("aut"),
           email = "Katerina.Kechris@CUAnschutz.edu"))
Description: A two-step approach to imputing missing data in
        metabolomics. Step 1 uses a random forest classifier to
        classify missing values as either Missing Completely at
        Random/Missing At Random (MCAR/MAR) or Missing Not At Random
        (MNAR). MCAR/MAR are combined because it is often difficult to
        distinguish these two missing types in metabolomics data. Step
        2 imputes the missing values based on the classified missing
        mechanisms, using the appropriate imputation algorithms.
        Imputation algorithms tested and available for MCAR/MAR include
        Bayesian Principal Component Analysis (BPCA), Multiple
        Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and
        Random Forest. Imputation algorithms tested and available for
        MNAR include nsKNN and a single imputation approach for
        imputation of metabolites where left-censoring is present.
License: GPL-3
Encoding: UTF-8
Imports: caret, parallel, doParallel, foreach, e1071, future.apply,
        future, missForest, pcaMethods, tidyverse, stats, utils,
        methods, SummarizedExperiment, S4Vectors
biocViews: Software, Metabolomics, StatisticalMethod, Classification
Suggests: knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://github.com/KechrisLab/MAI
BugReports: https://github.com/KechrisLab/MAI/issues
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev make libharfbuzz-dev libicu-dev libjpeg-dev
        libpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev
        libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:56:39 UTC
RemoteUrl: https://github.com/bioc/MAI
RemoteRef: HEAD
RemoteSha: 0c453ca746f4889fb13990f9fed0218232665d92
NeedsCompilation: no
Packaged: 2026-07-04 06:33:09 UTC; root
Author: Jonathan Dekermanjian [aut, cre],
  Elin Shaddox [aut],
  Debmalya Nandy [aut],
  Debashis Ghosh [aut],
  Katerina Kechris [aut]
Maintainer: Jonathan Dekermanjian <Jonathan.Dekermanjian@CUAnschutz.edu>
Depends: R (>= 3.5.0)