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  "Date": "2025-11-21",
  "Title": "Generalized Linear Mixed Model Association Tests",
  "Authors@R": "c(person(\"Han\", \"Chen\", role = c(\"aut\", \"cre\"), email = \"hanchenphd@gmail.com\"),\nperson(\"Matthew\", \"Conomos\", role = \"aut\"),\nperson(\"Duy\", \"Pham\", role = \"aut\"),\nperson(\"Arthor\", \"Gilly\", role = \"ctb\"),\nperson(\"Robert\", \"Gentleman\", role = c(\"ctb\", \"cph\"), comment = \"Author and copyright holder of the C function Brent_fmin\"),\nperson(\"Ross\", \"Ihaka\", role = c(\"ctb\", \"cph\"), comment = \"Author and copyright holder of the C function Brent_fmin\"),\nperson(\"The R Core Team\", role = c(\"ctb\", \"cph\"), comment = \"Author and copyright holder of the C function Brent_fmin\"),\nperson(\"The R Foundation\", role = \"cph\", comment = \"Copyright holder of the C function Brent_fmin\"),\nperson(\"Eric\", \"Biggers\", role = c(\"ctb\", \"cph\"), comment = \"Author and copyright holder of included libdeflate library\"),\nperson(\"Tino\", \"Reichardt\", role = c(\"ctb\", \"cph\"), comment = \"Author and copyright holder of threading code used in the included Zstandard (zstd) library\"),\nperson(\"Meta Platforms, Inc. and affiliates\", role = \"cph\", comment = \"Copyright holder of included Zstandard (zstd) library\"))",
  "Description": "Perform association tests using generalized linear mixed\nmodels (GLMMs) in genome-wide association studies (GWAS) and\nsequencing association studies. First, GMMAT fits a GLMM with\ncovariate adjustment and random effects to account for\npopulation structure and familial or cryptic relatedness. For\nGWAS, GMMAT performs score tests for each genetic variant as\nproposed in Chen et al. (2016)\n<DOI:10.1016/j.ajhg.2016.02.012>. For candidate gene studies,\nGMMAT can also perform Wald tests to get the effect size\nestimate for each genetic variant. For rare variant analysis\nfrom sequencing association studies, GMMAT performs the variant\nSet Mixed Model Association Tests (SMMAT) as proposed in Chen\net al. (2019) <DOI:10.1016/j.ajhg.2018.12.012>, including the\nburden test, the sequence kernel association test (SKAT),\nSKAT-O and an efficient hybrid test of the burden test and\nSKAT, based on user-defined variant sets.",
  "License": "GPL (>= 3)",
  "Copyright": "See COPYRIGHTS for details.",
  "Encoding": "UTF-8",
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  "Author": "Han Chen [aut, cre], Matthew Conomos [aut], Duy Pham [aut],\nArthor Gilly [ctb], Robert Gentleman [ctb, cph] (Author and\ncopyright holder of the C function Brent_fmin), Ross Ihaka\n[ctb, cph] (Author and copyright holder of the C function\nBrent_fmin), The R Core Team [ctb, cph] (Author and copyright\nholder of the C function Brent_fmin), The R Foundation [cph]\n(Copyright holder of the C function Brent_fmin), Eric Biggers\n[ctb, cph] (Author and copyright holder of included libdeflate\nlibrary), Tino Reichardt [ctb, cph] (Author and copyright\nholder of threading code used in the included Zstandard (zstd)\nlibrary), Meta Platforms, Inc. and affiliates [cph] (Copyright\nholder of included Zstandard (zstd) library)",
  "Maintainer": "Han Chen <hanchenphd@gmail.com>",
  "Repository": "https://hanchenphd.r-universe.dev",
  "Date/Publication": "2025-11-21 21:55:15 UTC",
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    "message": " On branch master\n Your branch is up to date with 'origin/master'.\n\n Changes to be committed:\n\tmodified:   DESCRIPTION\n\tmodified:   NAMESPACE\n\tmodified:   R/glmm.wald.R\n\tmodified:   R/glmmkin.R\n\tmodified:   README.md\n\tmodified:   build/vignette.rds\n\tmodified:   configure\n\tmodified:   configure.ac\n\tmodified:   data/example.rda\n\tmodified:   inst/doc/GMMAT.Rnw\n\tmodified:   inst/doc/GMMAT.pdf\n\tmodified:   man/GMMAT-package.Rd\n\tmodified:   man/glmmkin.Rd\n\tmodified:   src/fitglmm.cpp\n\tmodified:   tests/testthat/test_glmmkin.R\n\tmodified:   vignettes/GMMAT.Rnw\n",
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