Package: LUCIDus
Title: LUCID with Multiple Omics Data
Version: 3.2.1
Authors@R: c(
    person("Qiran", "Jia", , "qiranjia@usc.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0790-5967")),
    person(given = "Yinqi", family = "Zhao", 
           email = "yinqiz@usc.edu", 
           role = "aut",
           comment = c(ORCID = "0000-0003-2413-732X")),
    person(given = "David", family = "Conti", 
           email = "dconti@usc.med.edu", role = "ths",
           comment = c(ORCID = "0000-0002-2941-7833")),
    person(given = "Jesse", family = "Goodrich", 
           role = "ctb",
           comment = c(ORCID = "0000-0001-6615-0472"))
  )
Description: Implements Latent Unknown Clusters By Integrating Multi-omics Data
    (LUCID; Peng (2019) <doi:10.1093/bioinformatics/btz667>) for integrative
    clustering with exposures, multi-omics data, and health outcomes.
    Supports three integration strategies: early, parallel, and serial.
    Provides model fitting and tuning, lasso-type regularization for exposure
    and omics feature selection, handling of missing data, including both
    sporadic and complete-case patterns, prediction, and g-computation for
    estimating causal effects of exposures, bootstrap inference for
    uncertainty estimation, and S3 summary and plot methods. For the
    multi-omics integration framework, see Jia (2024)
    <https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf>.
    For the missing-data imputation mechanism, see Jia (2024)
    <doi:10.1093/bioadv/vbae123>.
Depends: R (>= 3.6.0)
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
LazyData: true
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, plotly, mix, visdat
Config/testthat/edition: 3
VignetteBuilder: knitr
Imports: mclust, nnet, boot, jsonlite, networkD3, progress, stats,
        utils, glasso, glmnet, ggplot2, grDevices
URL:
        https://journal.r-project.org/articles/RJ-2024-012/RJ-2024-012.pdf,
        https://doi.org/10.1093/bioadv/vbae123
NeedsCompilation: no
Packaged: 2026-09-02 02:14:40 UTC; qiranjia19961112
Author: Qiran Jia [aut, cre] (ORCID: <https://orcid.org/0000-0002-0790-5967>),
  Yinqi Zhao [aut] (ORCID: <https://orcid.org/0000-0003-2413-732X>),
  David Conti [ths] (ORCID: <https://orcid.org/0000-0002-2941-7833>),
  Jesse Goodrich [ctb] (ORCID: <https://orcid.org/0000-0001-6615-0472>)
Maintainer: Qiran Jia <qiranjia@usc.edu>
Repository: CRAN
Date/Publication: 2026-09-02 17:10:14 UTC
Built: R 4.6.0; ; 2026-09-02 17:58:47 UTC; unix
