{
  "_id": "6a572074ff0138dec5d6e125",
  "Package": "imputeLCMD",
  "Type": "Package",
  "Title": "A Collection of Methods for Left-Censored Missing Data\nImputation",
  "Version": "2.1",
  "Date": "2022-06-09",
  "Authors@R": "c(\nperson(\"Cosmin\", \"Lazar\", email = \"vcosminlazar@gmail.com\", role = c(\"aut\")),\nperson(\"Thomas\", \"Burger\", email = \"thomas.burger@cea.fr\", role = c(\"aut\")),\nperson(\"Samuel\", \"Wieczorek\", email = \"samuel.wieczorek@cea.fr\", role = c(\"cre\", \"ctb\"))\n)",
  "Maintainer": "Samuel Wieczorek <samuel.wieczorek@cea.fr>",
  "Description": "A collection of functions for left-censored missing data\nimputation. Left-censoring is a special case of missing not at\nrandom (MNAR) mechanism that generates non-responses in\nproteomics experiments. The package also contains functions to\nartificially generate peptide/protein expression data\n(log-transformed) as random draws from a multivariate Gaussian\ndistribution as well as a function to generate missing data\n(both randomly and non-randomly). For comparison reasons, the\npackage also contains several wrapper functions for the\nimputation of non-responses that are missing at random. * New\nfunctionality has been added: a hybrid method that allows the\nimputation of missing values in a more complex scenario where\nthe missing data are both MAR and MNAR.",
  "License": "GPL (>= 2)",
  "Packaged": {
    "Date": "2026-07-15 05:50:10 UTC",
    "User": "root"
  },
  "NeedsCompilation": "no",
  "RoxygenNote": "7.2.0",
  "Encoding": "UTF-8",
  "Author": "Cosmin Lazar [aut], Thomas Burger [aut], Samuel Wieczorek [cre,\nctb]",
  "Repository": "https://samwieczorek.r-universe.dev",
  "Date/Publication": "2022-06-10 10:50:02 UTC",
  "RemoteUrl": "https://github.com/cran/imputeLCMD",
  "RemoteRef": "HEAD",
  "RemoteSha": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
  "_user": "samwieczorek",
  "_type": "src",
  "_file": "imputeLCMD_2.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/2455929f65ec09147024dc98c63f813c15a76d9634b0226faa5b26721f59fccb",
  "_filesize": 709651,
  "_sha256": "2455929f65ec09147024dc98c63f813c15a76d9634b0226faa5b26721f59fccb",
  "_expires": "2026-10-23T05:53:55.000Z",
  "_created": "2026-07-15T05:50:10.000Z",
  "_published": "2026-07-15T05:53:56.779Z",
  "_jobs": [
    {
      "job": 87278863662,
      "time": 187,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8333849493"
    },
    {
      "job": 87278863637,
      "time": 154,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8333839691"
    },
    {
      "job": 87278863633,
      "time": 162,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8333831012"
    },
    {
      "job": 87278863658,
      "time": 181,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8333835830"
    },
    {
      "job": 87278395123,
      "time": 201,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8333791870"
    },
    {
      "job": 87278863647,
      "time": 113,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8333827313"
    },
    {
      "job": 87278863663,
      "time": 138,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8333834231"
    },
    {
      "job": 87278863656,
      "time": 137,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8333834044"
    },
    {
      "job": 87278863646,
      "time": 89,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8333819786"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779",
  "_status": "success",
  "_upstream": "https://github.com/cran/imputeLCMD",
  "_commit": {
    "id": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
    "author": "Samuel Wieczorek <samuel.wieczorek@cea.fr>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.1\n",
    "time": 1654858202
  },
  "_maintainer": {
    "name": "Samuel Wieczorek",
    "email": "samuel.wieczorek@cea.fr",
    "login": "samwieczorek",
    "description": "",
    "uuid": 2912670
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "tmvtnorm",
      "role": "Depends"
    },
    {
      "package": "norm",
      "role": "Depends"
    },
    {
      "package": "pcaMethods",
      "role": "Depends"
    },
    {
      "package": "impute",
      "role": "Depends"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 6,
  "_updates": [],
  "_tags": [],
  "_stars": 3,
  "_contributors": [
    {
      "user": "samwieczorek",
      "count": 1,
      "uuid": 2912670
    }
  ],
  "_userbio": {
    "uuid": 2912670,
    "type": "user",
    "name": "Samuel Wieczorek",
    "followers": 0
  },
  "_downloads": {
    "count": 2388,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/imputeLCMD"
  },
  "_mentions": 8,
  "_searchresults": 184,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/imputeLCMD.html",
    "manual.pdf"
  ],
  "_realowner": "samwieczorek",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2014-07-12"
    },
    {
      "version": "2.0",
      "date": "2015-01-19"
    },
    {
      "version": "2.1",
      "date": "2022-06-10"
    }
  ],
  "_exports": [
    "generate.ExpressionData",
    "generate.RollUpMap",
    "impute.MAR",
    "impute.MAR.MNAR",
    "impute.MinDet",
    "impute.MinProb",
    "impute.QRILC",
    "impute.wrapper.KNN",
    "impute.wrapper.MLE",
    "impute.wrapper.SVD",
    "impute.ZERO",
    "insertMVs",
    "model.Selector",
    "pep2prot"
  ],
  "_datasets": [
    {
      "name": "intensity_PXD000022",
      "title": "Dataset PXD000022 from ProteomeXchange.",
      "object": "intensity_PXD000022",
      "file": "intensity_PXD000022.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Protein.IDs",
        "Intensity.MB.1",
        "Intensity.MB.2",
        "Intensity.MB.3",
        "Intensity.MT.1",
        "Intensity.MT.2",
        "Intensity.MT.3"
      ],
      "rows": 660,
      "table": true,
      "tojson": true
    },
    {
      "name": "intensity_PXD000052",
      "title": "Dataset PXD000052 from ProteomeXchange.",
      "object": "intensity_PXD000052",
      "file": "intensity_PXD000052.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Protein.IDs",
        "iBAQ.stSLP_activ1",
        "iBAQ.stSLP_activ2",
        "iBAQ.stSLP_activ3",
        "iBAQ.stSLP_activ4",
        "iBAQ.stSLP_rest1",
        "iBAQ.stSLP_rest2",
        "iBAQ.stSLP_rest3",
        "iBAQ.stSLP_rest4",
        "iBAQ.WT_activ1",
        "iBAQ.WT_activ2",
        "iBAQ.WT_activ3",
        "iBAQ.WT_activ4",
        "iBAQ.WT_rest1",
        "iBAQ.WT_rest2",
        "iBAQ.WT_rest3",
        "iBAQ.WT_rest4"
      ],
      "rows": 1991,
      "table": true,
      "tojson": true
    },
    {
      "name": "intensity_PXD000438",
      "title": "Dataset PXD000438 from ProteomeXchange.",
      "object": "intensity_PXD000438",
      "file": "intensity_PXD000438.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Protein.IDs",
        "Intensity.092.1",
        "Intensity.092.2",
        "Intensity.092.3",
        "Intensity.441.1",
        "Intensity.441.2",
        "Intensity.441.3",
        "Intensity.561.1",
        "Intensity.561.2",
        "Intensity.561.3",
        "Intensity.691.1",
        "Intensity.691.2",
        "Intensity.691.3"
      ],
      "rows": 3709,
      "table": true,
      "tojson": true
    },
    {
      "name": "intensity_PXD000501",
      "title": "Dataset PXD000501 from ProteomeXchange.",
      "object": "intensity_PXD000501",
      "file": "intensity_PXD000501.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Protein.IDs",
        "iBAQ.secretome_set1_tech1",
        "iBAQ.secretome_set1_tech2",
        "iBAQ.secretome_set1_tech3",
        "iBAQ.secretome_set2_tech1",
        "iBAQ.secretome_set2_tech2",
        "iBAQ.secretome_set2_tech3",
        "iBAQ.secretome_set3_tech1",
        "iBAQ.secretome_set3_tech2",
        "iBAQ.secretome_set3_tech3",
        "iBAQ.whole_set1_tech1",
        "iBAQ.whole_set1_tech2",
        "iBAQ.whole_set1_tech3",
        "iBAQ.whole_set2_tech1",
        "iBAQ.whole_set2_tech2",
        "iBAQ.whole_set2_tech3",
        "iBAQ.whole_set3_tech1",
        "iBAQ.whole_set3_tech2",
        "iBAQ.whole_set3_tech3"
      ],
      "rows": 7363,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "generate.ExpressionData",
      "title": "Generate expression data",
      "topics": [
        "generate.ExpressionData"
      ]
    },
    {
      "page": "generate.RollUpMap",
      "title": "Generate roll up map",
      "topics": [
        "generate.RollUpMap"
      ]
    },
    {
      "page": "impute.MAR",
      "title": "imputation under MAR/MCAR hypothesis",
      "topics": [
        "impute.MAR"
      ]
    },
    {
      "page": "impute.MAR.MNAR",
      "title": "Imputation under MCAR and MNAR hypothesis",
      "topics": [
        "impute.MAR.MNAR"
      ]
    },
    {
      "page": "impute.MinDet",
      "title": "Imputation with min value",
      "topics": [
        "impute.MinDet"
      ]
    },
    {
      "page": "impute.MinProb",
      "title": "Imputation by random draws",
      "topics": [
        "impute.MinProb"
      ]
    },
    {
      "page": "impute.QRILC",
      "title": "imputation based on quantile regression",
      "topics": [
        "impute.QRILC"
      ]
    },
    {
      "page": "impute.wrapper.KNN",
      "title": "Imputation with KNN",
      "topics": [
        "impute.wrapper.KNN"
      ]
    },
    {
      "page": "impute.wrapper.MLE",
      "title": "imputation using the EM algorithm",
      "topics": [
        "impute.wrapper.MLE"
      ]
    },
    {
      "page": "impute.wrapper.SVD",
      "title": "imputation based on SVD algorithm",
      "topics": [
        "impute.wrapper.SVD"
      ]
    },
    {
      "page": "impute.ZERO",
      "title": "Imputation by 0.",
      "topics": [
        "impute.ZERO"
      ]
    },
    {
      "page": "insertMVs",
      "title": "Generates missing values in data.",
      "topics": [
        "insertMVs"
      ]
    },
    {
      "page": "intensity_PXD000022",
      "title": "Dataset PXD000022 from ProteomeXchange.",
      "topics": [
        "intensity_PXD000022"
      ]
    },
    {
      "page": "intensity_PXD000052",
      "title": "Dataset PXD000052 from ProteomeXchange.",
      "topics": [
        "intensity_PXD000052"
      ]
    },
    {
      "page": "intensity_PXD000438",
      "title": "Dataset PXD000438 from ProteomeXchange.",
      "topics": [
        "intensity_PXD000438"
      ]
    },
    {
      "page": "intensity_PXD000501",
      "title": "Dataset PXD000501 from ProteomeXchange.",
      "topics": [
        "intensity_PXD000501"
      ]
    },
    {
      "page": "model.Selector",
      "title": "Identifies row in the data matrix affected by a MNAR missingness mechanism",
      "topics": [
        "model.Selector"
      ]
    },
    {
      "page": "pep2prot",
      "title": "peptide to protein roll-up",
      "topics": [
        "pep2prot"
      ]
    }
  ],
  "_rundeps": [
    "Biobase",
    "BiocGenerics",
    "generics",
    "gmm",
    "impute",
    "lattice",
    "MASS",
    "Matrix",
    "mvtnorm",
    "norm",
    "pcaMethods",
    "Rcpp",
    "sandwich",
    "tmvtnorm",
    "zoo"
  ],
  "_score": 5.278335892281779,
  "_indexed": true,
  "_nocasepkg": "imputelcmd",
  "_universes": [
    "samwieczorek"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.1",
      "date": "2026-07-15T05:53:01.000Z",
      "distro": "resolute",
      "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
      "fileid": "https://r2.ropensci.org/d4f23eb2eabe23896cee72ed5eaf40bc4058d88c2d4f4dd08e77ba9f0e0b13b4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "2.1",
      "date": "2026-07-15T05:52:29.000Z",
      "distro": "resolute",
      "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
      "fileid": "https://r2.ropensci.org/50ed5599d55d231548c5f8da68d14b2a30a8fa2070e74d7b3cec59e0c9bb82be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.1",
      "date": "2026-07-15T05:52:14.000Z",
      "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
      "fileid": "https://r2.ropensci.org/cde234dd5c82794c9ed8164b4839988268328daef51f702357b1d7308647a40c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "2.1",
      "date": "2026-07-15T05:52:26.000Z",
      "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
      "fileid": "https://r2.ropensci.org/bf7128a2083ea4914cdc8eef287d5eebc3747a9e8aa8479a05d4757a7f844097",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.1",
      "date": "2026-07-15T05:52:23.000Z",
      "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
      "fileid": "https://r2.ropensci.org/1c62d7b10f16be85d8d55883d1bcb1f6f72f658d336394d31bb7bcea37977076",
      "status": "success",
      "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.1",
      "date": "2026-07-15T05:52:05.000Z",
      "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
      "fileid": "https://r2.ropensci.org/7710b33642a1dd1c7f4a6d1adcf6d68abec8d110fca422d73c88f71842072f75",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.1",
      "date": "2026-07-15T05:52:08.000Z",
      "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
      "fileid": "https://r2.ropensci.org/f45e47eff54e586308ecb9aeb7f64c8c92bb5162d8869a96489d9c8bf2e4ad36",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "2.1",
      "date": "2026-07-15T05:51:20.000Z",
      "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2",
      "fileid": "https://r2.ropensci.org/0a06eaa07974328872555b89f0c232b1c75d1ede386a4db8bd3fd3aa83d00360",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/29392336779"
    }
  ]
}