{ "_id": "6a1f1da9b401979e7341fc29", "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 ", "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": "2026-05-16 08:36:10 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", "MD5sum": "bda8bb9c4369e86d300d3b15bf61e071", "_user": "samwieczorek", "_type": "src", "_file": "imputeLCMD_2.1.tar.gz", "_fileid": "00097335f1a136f6b70bd4870c9df89bd7c7285e5155e0b32a4ffcfb10d9e0b8", "_filesize": 709632, "_sha256": "00097335f1a136f6b70bd4870c9df89bd7c7285e5155e0b32a4ffcfb10d9e0b8", "_created": "2026-05-16T08:36:10.000Z", "_published": "2026-06-02T18:15:05.230Z", "_distro": "noble", "_jobs": [ { "job": 79140820073, "time": 128, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7032009466" }, { "job": 79140820468, "time": 128, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7032009425" }, { "job": 79140820081, "time": 154, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7032009948" }, { "job": 79140819655, "time": 167, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7032008108" }, { "job": 79140819378, "time": 169, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7031995516" }, { "job": 79140819011, "time": 94, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7366154454" }, { "job": 79140819918, "time": 103, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7032006834" }, { "job": 79140820121, "time": 87, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7032005288" }, { "job": 79140819770, "time": 87, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7032005224" } ], "_buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/imputeLCMD", "_commit": { "id": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "author": "Samuel Wieczorek ", "committer": "cran-robot ", "message": "version 2.1\n", "time": 1654858202 }, "_maintainer": { "name": "Samuel Wieczorek", "email": "samuel.wieczorek@cea.fr", "login": "samwieczorek", "uuid": 2912670 }, "_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" }, "_downloads": { "count": 2771, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/imputeLCMD" }, "_mentions": 8, "_searchresults": 178, "_rbuild": "4.6.0", "_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": 5.328540274906038, "_indexed": true, "_nocasepkg": "imputelcmd", "_universes": [ "samwieczorek" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1", "date": "2026-05-16T08:38:03.000Z", "distro": "noble", "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "fileid": "cc978785d4d6e7690569c6297161bb68acf3cdb3f822c9a9ba2abe30143f5d4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280" }, { "r": "4.6.0", "os": "linux", "version": "2.1", "date": "2026-05-16T08:38:06.000Z", "distro": "noble", "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "fileid": "306dd62a39c32117a7209b82af851b9097166228f69d4d44ff8bf91c40c4a52a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280" }, { "r": "4.5.3", "os": "mac", "version": "2.1", "date": "2026-05-16T08:38:20.000Z", "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "fileid": "d4f84bdccbbe58702887f6a3842526eef51ec023ffcbe01fb2f3688def10c6ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280" }, { "r": "4.6.0", "os": "mac", "version": "2.1", "date": "2026-05-16T08:38:03.000Z", "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "fileid": "f483fa107edf216c2e5734d321a6e4942c22fd81fbd2d2d382dea298b52a4cf6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280" }, { "r": "4.7.0", "os": "win", "version": "2.1", "date": "2026-05-16T08:37:34.000Z", "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "fileid": "a157164bd5890ca8e6d717afd0ebca9004d8174b014f8a9ca06a24e882432ce3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280" }, { "r": "4.5.3", "os": "win", "version": "2.1", "date": "2026-05-16T08:37:20.000Z", "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "fileid": "5f5678e95f67d32f4b6ee17903e80232acaaf356ee43e46573bb8be5da08ec61", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280" }, { "r": "4.6.0", "os": "win", "version": "2.1", "date": "2026-05-16T08:37:21.000Z", "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "fileid": "6a6dc2858e09d8a253a38c3b0f8014c047964bb0a59f8fe90367670f45c55d47", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280" }, { "r": "4.6.0", "os": "wasm", "version": "2.1", "date": "2026-06-02T18:14:39.000Z", "commit": "23debc0c095e85072f9d352ec7c531e17a5c70b2", "fileid": "d95ce099ea695dab35a76d7a79a118c872bb93d09807d4c3c707875cfb20e472", "status": "success", "buildurl": "https://github.com/r-universe/samwieczorek/actions/runs/25957422280" } ] }