{
  "_id": "6a1ac7591d7bb097a09dbdf9",
  "Package": "lfa",
  "Title": "Logistic Factor Analysis for Categorical Data",
  "Version": "2.13.0",
  "Authors@R": "c(\nperson(given = \"Wei\",\nfamily = \"Hao\",\nrole = \"aut\",\nemail = \"whao@princeton.edu\"),\nperson(given = \"Minsun\",\nfamily = \"Song\",\nrole = \"aut\"),\nperson(given = \"Alejandro\",\nfamily = \"Ochoa\",\nrole = c(\"aut\", \"cre\"),\nemail = \"alejandro.ochoa@duke.edu\",\ncomment = c(ORCID = \"0000-0003-4928-3403\")),\nperson(given = \"John D.\",\nfamily = \"Storey\",\nrole = \"aut\",\nemail = \"jstorey@princeton.edu\",\ncomment = c(ORCID = \"0000-0001-5992-402X\"))\n)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Description": "Logistic Factor Analysis is a method for a PCA analogue on\nBinomial data via estimation of latent structure in the natural\nparameter.  The main method estimates genetic population\nstructure from genotype data.  There are also methods for\nestimating individual-specific allele frequencies using the\npopulation structure.  Lastly, a structured Hardy-Weinberg\nequilibrium (HWE) test is developed, which quantifies the\ngoodness of fit of the genotype data to the estimated\npopulation structure, via the estimated individual-specific\nallele frequencies (all of which generalizes traditional HWE\ntests).",
  "VignetteBuilder": "knitr",
  "License": "GPL (>= 3)",
  "biocViews": "SNP, DimensionReduction, PrincipalComponent, Regression",
  "BugReports": "https://github.com/StoreyLab/lfa/issues",
  "URL": "https://github.com/StoreyLab/lfa",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "libx11-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:00:58 UTC",
  "RemoteUrl": "https://github.com/bioc/lfa",
  "RemoteRef": "HEAD",
  "RemoteSha": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-30 07:47:44 UTC",
    "User": "root"
  },
  "Author": "Wei Hao [aut],\nMinsun Song [aut],\nAlejandro Ochoa [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4928-3403>),\nJohn D. Storey [aut] (ORCID: <https://orcid.org/0000-0001-5992-402X>)",
  "Maintainer": "Alejandro Ochoa <alejandro.ochoa@duke.edu>",
  "MD5sum": "c8381f69ba555a778b5b8b3f043080ec",
  "_user": "bioc",
  "_type": "src",
  "_file": "lfa_2.13.0.tar.gz",
  "_fileid": "41974ad9e3c82f83ef52cf46c50d8c206893066be1e6ff8e84620db304611bf7",
  "_filesize": 392995,
  "_sha256": "41974ad9e3c82f83ef52cf46c50d8c206893066be1e6ff8e84620db304611bf7",
  "_created": "2026-05-30T07:47:44.000Z",
  "_published": "2026-05-30T11:17:45.524Z",
  "_jobs": [
    {
      "job": 78634520367,
      "time": 146,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306604673"
    },
    {
      "job": 78634520381,
      "time": 143,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306604396"
    },
    {
      "job": 78634520383,
      "time": 192,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306609362"
    },
    {
      "job": 78634520389,
      "time": 139,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306604077"
    },
    {
      "job": 78634520373,
      "time": 409,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306630418"
    },
    {
      "job": 78634520384,
      "time": 97,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7307783958"
    },
    {
      "job": 78634520392,
      "time": 253,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306615769"
    },
    {
      "job": 78634520388,
      "time": 118,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7307785790"
    },
    {
      "job": 78634520377,
      "time": 327,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306622714"
    },
    {
      "job": 78634385174,
      "time": 172,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306590414"
    },
    {
      "job": 78634520363,
      "time": 98,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306600211"
    },
    {
      "job": 78634520374,
      "time": 135,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306603654"
    },
    {
      "job": 78634520372,
      "time": 102,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306600507"
    },
    {
      "job": 78634520366,
      "time": 92,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306599598"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 3,
    "note": 7
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/lfa",
  "_commit": {
    "id": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381258
  },
  "_maintainer": {
    "name": "Alejandro Ochoa",
    "email": "alejandro.ochoa@duke.edu",
    "login": "alexviiia",
    "orcid": "0000-0003-4928-3403",
    "description": "Statistical geneticist, computational biologist.  Well-rounded nerd, also love languages and music.",
    "uuid": 12603341
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "corpcor",
      "role": "Imports"
    },
    {
      "package": "RSpectra",
      "role": "Imports"
    },
    {
      "package": "BEDMatrix",
      "role": "Imports"
    },
    {
      "package": "genio",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-05",
      "n": 4
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.13.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.12.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "snp",
    "dimensionreduction",
    "principalcomponent",
    "regression",
    "openblas"
  ],
  "_stars": 16,
  "_contributors": [
    {
      "user": "whao89",
      "count": 30,
      "uuid": 5931197
    },
    {
      "user": "alexviiia",
      "count": 22,
      "uuid": 12603341
    },
    {
      "user": "jwokaty",
      "count": 10,
      "uuid": 1744257
    },
    {
      "user": "ncchung",
      "count": 6,
      "uuid": 8022966
    },
    {
      "user": "jdstorey",
      "count": 2,
      "uuid": 6211610
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 697,
    "source": "https://www.bioconductor.org/packages/stats/bioc/lfa"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/storeylab/lfa",
  "_searchresults": 59,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/lfa.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/storeylab/lfa",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "af",
    "af_snp",
    "centerscale",
    "lfa",
    "pca_af",
    "sHWE",
    "trunc_svd"
  ],
  "_datasets": [
    {
      "name": "hgdp_subset",
      "title": "HGDP subset",
      "object": "hgdp_subset",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "EUROPE",
        "EUROPE",
        "EUROPE",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "AFRICA",
        "AFRICA",
        "AFRICA",
        "AFRICA",
        "AFRICA",
        "AFRICA",
        "EUROPE",
        "EUROPE",
        "EUROPE",
        "MIDDLE_EAST",
        "MIDDLE_EAST",
        "MIDDLE_EAST",
        "AFRICA",
        "AFRICA",
        "AFRICA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "AMERICA",
        "AMERICA",
        "AMERICA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "MIDDLE_EAST",
        "MIDDLE_EAST",
        "MIDDLE_EAST",
        "EUROPE",
        "EUROPE",
        "EUROPE",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EUROPE",
        "EUROPE",
        "EUROPE",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "AMERICA",
        "AMERICA",
        "AMERICA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "AFRICA",
        "AFRICA",
        "AFRICA",
        "AMERICA",
        "AMERICA",
        "AMERICA",
        "AFRICA",
        "AFRICA",
        "AFRICA",
        "OCEANIA",
        "OCEANIA",
        "OCEANIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "MIDDLE_EAST",
        "MIDDLE_EAST",
        "MIDDLE_EAST",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EUROPE",
        "EUROPE",
        "EUROPE",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "MIDDLE_EAST",
        "MIDDLE_EAST",
        "MIDDLE_EAST",
        "OCEANIA",
        "OCEANIA",
        "OCEANIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "AMERICA",
        "AMERICA",
        "AMERICA",
        "EUROPE",
        "EUROPE",
        "EUROPE",
        "AFRICA",
        "AFRICA",
        "AFRICA",
        "EUROPE",
        "EUROPE",
        "EUROPE",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "AMERICA",
        "AMERICA",
        "AMERICA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EUROPE",
        "EUROPE",
        "EUROPE",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "CENTRAL_SOUTH_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "EAST_ASIA",
        "AFRICA",
        "AFRICA",
        "AFRICA"
      ],
      "rows": 5000,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "af",
      "title": "Allele frequencies",
      "topics": [
        "af"
      ]
    },
    {
      "page": "af_snp",
      "title": "Allele frequencies for SNP",
      "topics": [
        "af_snp"
      ]
    },
    {
      "page": "centerscale",
      "title": "Matrix centering and scaling",
      "topics": [
        "centerscale"
      ]
    },
    {
      "page": "hgdp_subset",
      "title": "HGDP subset",
      "topics": [
        "hgdp_subset"
      ]
    },
    {
      "page": "lfa",
      "title": "Logistic factor analysis",
      "topics": [
        "lfa"
      ]
    },
    {
      "page": "lfa-defunct",
      "title": "Defunct functions in package 'lfa'.",
      "topics": [
        "lfa-defunct"
      ]
    },
    {
      "page": "pca_af",
      "title": "PCA Allele frequencies",
      "topics": [
        "pca_af"
      ]
    },
    {
      "page": "sHWE",
      "title": "Hardy-Weinberg Equilibrium in structure populations",
      "topics": [
        "sHWE"
      ]
    },
    {
      "page": "trunc_svd",
      "title": "Truncated singular value decomposition",
      "topics": [
        "trunc_svd"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/lfa/raw/HEAD/README.md",
  "_rundeps": [
    "BEDMatrix",
    "bit",
    "bit64",
    "cli",
    "clipr",
    "corpcor",
    "cpp11",
    "crayon",
    "crochet",
    "dplyr",
    "generics",
    "genio",
    "glue",
    "hms",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "R6",
    "Rcpp",
    "RcppEigen",
    "readr",
    "rlang",
    "RSpectra",
    "tibble",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    }
  ],
  "_vignettes": [
    {
      "source": "lfa.Rmd",
      "filename": "lfa.html",
      "title": "Logistic Factor Analysis Vignette",
      "author": "Wei Hao, Minsun Song, Alejandro Ochoa, John D. Storey",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Sample usage",
        "lfa",
        "af",
        "Data Input",
        "References"
      ],
      "created": "2026-01-28 18:06:11",
      "modified": "2026-01-28 18:06:11",
      "commits": 1
    }
  ],
  "_score": 7.230244499401376,
  "_indexed": true,
  "_nocasepkg": "lfa",
  "_universes": [
    "bioc",
    "alexviiia",
    "storeylab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.13.0",
      "date": "2026-05-30T07:50:09.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "19bdba0cc6eb2a39fcaf4c97cdc217bbf677c2d157c1c3d0ca908e107d750bfd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.13.0",
      "date": "2026-05-30T07:50:54.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "31b9be1a576df5ba0d6409084be04f9e6cdfcceb0cc39fcb23583dff9d304874",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.13.0",
      "date": "2026-05-30T07:50:05.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "a07667f90cb19b20f871ee5c92496ce2e676b8426385d607750a8c1fd2a55838",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.13.0",
      "date": "2026-05-30T07:50:07.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "d0ca294d57e09b61fa58cb274ad516fc60978b3b5d8cc650c0a9f3256e9a17b2",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.13.0",
      "date": "2026-05-30T11:16:00.000Z",
      "arch": "aarch64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "c2ecdcdc6b26032e9b8da318d76d7f689450d93aabdc72e816747256571b8be1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.13.0",
      "date": "2026-05-30T07:51:14.000Z",
      "arch": "x86_64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "372eda36470d8156cf57461d95c887f309a654f3d4e2f588ed4e7ec88afd22b1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.13.0",
      "date": "2026-05-30T11:16:16.000Z",
      "arch": "aarch64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "35c5572b5ec0e44f0219a93e8f0dbaa54ccd1846a70d4a2d020c5b8f72ea20de",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.13.0",
      "date": "2026-05-30T07:52:05.000Z",
      "arch": "x86_64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "9dfb497a06ff1185c867a9515845732af22e46f04a3cb6aeb2e1f6ce5d9af133",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.13.0",
      "date": "2026-05-30T07:49:40.000Z",
      "arch": "emscripten",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "4461f40166f94f1b154daed3ce837a77d44034472aa8a96f7fcdb736d06101e5",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.13.0",
      "date": "2026-05-30T07:49:38.000Z",
      "arch": "x86_64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "b00c20d5d6efd2e4440a0678c91977a680ee6229bcc9c9088391181fadb4dd69",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.13.0",
      "date": "2026-05-30T07:49:08.000Z",
      "arch": "x86_64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "baf2dfd007d54446d5e3f6b9eaa6abd2bcef2604d099e97b2d54d2d4cb9cb40a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.13.0",
      "date": "2026-05-30T07:48:55.000Z",
      "arch": "x86_64",
      "commit": "c956db953cf9ec42c65e1b8b4f954a6470a8de10",
      "fileid": "7848700a4753de811a0ed97a92cb18823d899cb90ca1892b50d223d45f3b6661",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678398823"
    }
  ]
}