Package: plmmr
Title: Penalized Linear Mixed Models for Correlated Data
Version: 4.3.0.3
Authors@R: c(
    person("Tabitha K.", "Peter", , "tabitha.peter15@gmail.com", role = "aut",
           comment = c(ORCID = "0009-0005-2524-4751")),
    person("Anna C.", "Reisetter", , "anna-reisetter@uiowa.edu", role = "aut",
           comment = c(ORCID = "0000-0001-8332-4585")),
    person("Yujing", "Lu", role = "aut"),
    person("Oscar A.", "Rysavy", , "oscar-rysavy@uiowa.edu", role = "aut",
           comment = c(ORCID = "0000-0002-1019-5724")),
    person("Patrick J.", "Breheny", , "patrick-breheny@uiowa.edu", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-0650-1119"))
  )
Description: Fits penalized linear mixed models that correct for
        unobserved confounding factors. 'plmmr' infers and corrects for
        the presence of unobserved confounding effects such as
        population stratification and environmental heterogeneity. It
        then fits a linear model via penalized maximum likelihood.
        Originally designed for the multivariate analysis of single
        nucleotide polymorphisms (SNPs) measured in a genome-wide
        association study (GWAS), 'plmmr' eliminates the need for
        subpopulation-specific analyses and post-analysis p-value
        adjustments. Functions for the appropriate processing of
        'PLINK' files are also supplied. For examples, see the package
        homepage <https://pbreheny.github.io/plmmr/>.
License: GPL-3
URL: https://pbreheny.github.io/plmmr/,
        https://github.com/pbreheny/plmmr/
BugReports: https://github.com/pbreheny/plmmr/issues/
Depends: bigalgebra, bigmemory, R (>= 4.4.0)
Imports: biglasso (>= 1.6.0), data.table, Matrix, ncvreg, parallel,
        utils
Suggests: bigsnpr, bigstatsr, graphics, grDevices, knitr, MASS,
        rmarkdown, R.utils, tinytest, withr
LinkingTo: BH, bigmemory, Rcpp, RcppArmadillo (>= 0.8.600)
LazyData: true
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.3
Repository: https://pbreheny.r-universe.dev
Date/Publication: 2026-07-01 15:15:12 UTC
RemoteUrl: https://github.com/pbreheny/plmmr
RemoteRef: HEAD
RemoteSha: d40916f74ebe3a5e1984aa00dbb184deed430660
NeedsCompilation: yes
Packaged: 2026-07-01 15:31:40 UTC; root
Author: Tabitha K. Peter [aut] (ORCID: <https://orcid.org/0009-0005-2524-4751>),
  Anna C. Reisetter [aut] (ORCID:
    <https://orcid.org/0000-0001-8332-4585>),
  Yujing Lu [aut],
  Oscar A. Rysavy [aut] (ORCID: <https://orcid.org/0000-0002-1019-5724>),
  Patrick J. Breheny [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-0650-1119>)
Maintainer: Patrick J. Breheny <patrick-breheny@uiowa.edu>