{ "_id": "6aaf8c283d719c1f8407ec17", "Package": "RPMM", "Type": "Package", "Title": "Recursively Partitioned Mixture Model", "Version": "1.25", "Date": "2017-02-28", "Author": "E. Andres Houseman, Sc.D. and Devin C. Koestler, Ph.D.", "Maintainer": "E. Andres Houseman ", "Description": "Recursively Partitioned Mixture Model for Beta and\nGaussian Mixtures. This is a model-based clustering algorithm\nthat returns a hierarchy of classes, similar to hierarchical\nclustering, but also similar to finite mixture models.", "License": "GPL (>= 2)", "Packaged": { "Date": "2026-09-20 07:29:22 UTC", "User": "root" }, "NeedsCompilation": "no", "Repository": "https://eahouseman.r-universe.dev", "Date/Publication": "2017-02-28 22:05:39 UTC", "RemoteUrl": "https://github.com/cran/RPMM", "RemoteRef": "HEAD", "RemoteSha": "7cae8050edf089b1a4dd5c476ed40820736027c9", "_user": "eahouseman", "_type": "src", "_file": "RPMM_1.25.tar.gz", "_fileid": "https://r2.ropensci.org/2a2a866f048fa7ec054293473091a6bcbe33cc03d1574c7452406954d5d21807", "_filesize": 305324, "_sha256": "2a2a866f048fa7ec054293473091a6bcbe33cc03d1574c7452406954d5d21807", "_expires": "2026-12-29T07:32:55.000Z", "_created": "2026-09-20T07:29:22.000Z", "_published": "2026-09-20T07:32:56.725Z", "_jobs": [ { "job": 106041742454, "time": 106, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "10601660958" }, { "job": 106041742416, "time": 103, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "10601720716" }, { "job": 106041742439, "time": 171, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "10601241564" }, { "job": 106041742492, "time": 122, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "10601341353" }, { "job": 106041249605, "time": 240, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10600636630" }, { "job": 106041742410, "time": 100, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10601581069" }, { "job": 106041742479, "time": 55, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "10601286445" }, { "job": 106041742428, "time": 67, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "10601735616" }, { "job": 106041742485, "time": 67, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "10601311436" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668", "_status": "success", "_upstream": "https://github.com/cran/RPMM", "_commit": { "id": "7cae8050edf089b1a4dd5c476ed40820736027c9", "author": "E. Andres Houseman ", "committer": "cran-robot ", "message": "version 1.25\n", "time": 1488319539 }, "_maintainer": { "name": "E. Andres Houseman", "email": "eahouseman@gmail.com", "login": "eahouseman", "description": "I hold a doctorate in Biostatistics and have held faculty positions in Public Health. I am currently working on some community projects to learn ML/AI.", "uuid": 46732893 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.3.12", "role": "Depends" }, { "package": "cluster", "role": "Depends" } ], "_owner": "cran", "_selfowned": true, "_usedby": 10, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "eahouseman", "count": 1, "uuid": 46732893 } ], "_userbio": { "uuid": 46732893, "type": "user", "name": "Eugene Andres Houseman", "followers": 4, "description": "I hold a doctorate in Biostatistics and have held faculty positions in Public Health. I am currently working on some community projects to learn ML/AI." }, "_downloads": { "count": 1296, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/RPMM" }, "_mentions": 20, "_searchresults": 88, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/RPMM.html" ], "_realowner": "eahouseman", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2009-09-09" }, { "version": "1.05", "date": "2009-11-16" }, { "version": "1.06", "date": "2010-08-10" }, { "version": "1.10", "date": "2012-03-16" }, { "version": "1.20", "date": "2014-09-14" }, { "version": "1.25", "date": "2017-02-28" } ], "_exports": [ "betaEst", "betaEstMultiple", "betaObjf", "blc", "blcInitializeSplitDichotomizeUsingMean", "blcInitializeSplitEigen", "blcInitializeSplitFanny", "blcInitializeSplitHClust", "blcSplit", "blcSplitCriterionBIC", "blcSplitCriterionBICICL", "blcSplitCriterionJustRecordEverything", "blcSplitCriterionLevelWtdBIC", "blcSplitCriterionLRT", "blcSubTree", "blcTree", "blcTreeApply", "blcTreeLeafClasses", "blcTreeLeafMatrix", "blcTreeOverallBIC", "ebayes", "gaussEstMultiple", "glc", "glcInitializeSplitEigen", "glcInitializeSplitFanny", "glcInitializeSplitHClust", "glcSplit", "glcSplitCriterionBIC", "glcSplitCriterionBICICL", "glcSplitCriterionJustRecordEverything", "glcSplitCriterionLevelWtdBIC", "glcSplitCriterionLRT", "glcSubTree", "glcTree", "glcTreeApply", "glcTreeLeafClasses", "glcTreeLeafMatrix", "glcTreeOverallBIC", "glmLC", "llikeRPMMObject", "plot.blcTree", "plot.glcTree", "plotImage.blcTree", "plotImage.glcTree", "plotTree.blcTree", "plotTree.glcTree", "predict.blcTree", "predict.glcTree", "print.blcTree", "print.glcTree" ], "_datasets": [ { "name": "IllumBeta", "title": "DNA Methylation Data for Normal Tissue Types", "object": "IlluminaMethylation", "file": "IlluminaMethylation.RData", "class": [ "matrix", "array" ], "fields": [ "OSM_P188_F", "EVI2A_P94_R", "RHOH_P121_F", "AFF3_P122_F", "TNFSF8_E258_R", "NTRK1_E74_F", "CD2_P68_F", "OSM_P34_F", "CD86_P3_F", "LAT_E46_F", "VAV1_E9_F", "TNFSF8_P184_F", "HIC-1_seq_48_S103_R", "LTB4R_E64_R", "IL10_P85_F", "PTPN6_P282_R", "LMO2_P794_R", "TNFSF10_P2_R", "IL18BP_P51_R", "EMR3_P39_R", "LMO2_E148_F", "VAV1_P317_F", "LTB4R_P163_F", "MEST_P4_F", "PADI4_E24_F", "TIE1_E66_R", "STAT5A_P704_R", "EMR3_E61_F", "JAK3_P156_R", "NPY_P295_F", "SPI1_P48_F", "RARA_P1076_R", "CAPG_E228_F", "MT1A_P600_F", "ALOX12_E85_R", "RIPK3_P124_F", "PTPN6_E171_R", "HPN_P823_F", "TRIP6_P1090_F", "PLAT_E158_F", "PECAM1_P135_F", "GP1BB_P278_R", "PTHLH_P15_R", "PECAM1_E32_R", "MMP9_P189_F", "PTPRH_E173_F", "PSCA_E359_F", "IL8_P83_F", "WNT10B_P823_R", "RIPK3_P24_F", "HPN_P374_R", "CARD15_P665_F", "CD34_P339_R", "RASSF1_P244_F", "CEACAM1_P44_R", "ALOX12_P223_R", "GML_E144_F", "THBS2_P605_R", "GSTM1_P266_F", "SNCG_E119_F", "NFKB1_P496_F", "HOXA11_P698_F", "HOXA5_E187_F", "MPL_P62_F", "NOTCH4_E4_F", "CDH13_P88_F", "SMARCB1_P220_R", "NEFL_E23_R", "HOXB13_E21_F", "MEST_P62_R", "S100A4_E315_F", "CD34_P780_R", "MFAP4_P197_F", "GJB2_P931_R", "GUCY2D_E419_R", "DNMT1_P100_R", "TSC2_E140_F", "COL1A2_E299_F", "TAL1_P594_F", "PTPRO_E56_F", "MC2R_P1025_F", "VAMP8_P114_F", "ERCC6_P698_R", "PI3_E107_F", "IGF1_P933_F", "SNCG_P53_F", "RASSF1_E116_F", "PDGFRB_E195_R", "SPP1_E140_R", "APC_P14_F", "HCK_P858_F", "IPF1_P750_F", "DLC1_E276_F", "DDR1_P332_R", "GFI1_P208_R", "NBL1_P24_F", "RAD50_P191_F", "HOXA9_P1141_R", "CARD15_P302_R", "HOXA9_E252_R" ], "rows": 217, "table": true, "tojson": true }, { "name": "tissue", "title": "DNA Methylation Data for Normal Tissue Types", "object": "IlluminaMethylation", "file": "IlluminaMethylation.RData", "class": [ "factor" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "betaEst", "title": "Beta Distribution Maximum Likelihood Estimator", "topics": [ "betaEst" ] }, { "page": "betaEstMultiple", "title": "Beta Maximum Likelihood on a Matrix", "topics": [ "betaEstMultiple" ] }, { "page": "betaObjf", "title": "Beta Maximum Likelihood Objective Function", "topics": [ "betaObjf" ] }, { "page": "blc", "title": "Beta Latent Class Model", "topics": [ "blc" ] }, { "page": "blcInitializeSplitDichotomizeUsingMean", "title": "Initialize Gaussian Latent Class via Mean Dichotomization", "topics": [ "blcInitializeSplitDichotomizeUsingMean" ] }, { "page": "blcInitializeSplitEigen", "title": "Initialize Gaussian Latent Class via Eigendecomposition", "topics": [ "blcInitializeSplitEigen" ] }, { "page": "blcInitializeSplitFanny", "title": "Initialize Beta Latent Class via Fanny", "topics": [ "blcInitializeSplitFanny" ] }, { "page": "blcInitializeSplitHClust", "title": "Initialize Beta Latent Class via Hierarchical Clustering", "topics": [ "blcInitializeSplitHClust" ] }, { "page": "blcSplit", "title": "Beta Latent Class Splitter", "topics": [ "blcSplit" ] }, { "page": "blcSplitCriterionBIC", "title": "Beta RPMM Split Criterion: Use BIC", "topics": [ "blcSplitCriterionBIC" ] }, { "page": "blcSplitCriterionBICICL", "title": "Beta RPMM Split Criterion: Use ICL-BIC", "topics": [ "blcSplitCriterionBICICL" ] }, { "page": "blcSplitCriterionJustRecordEverything", "title": "Beta RPMM Split Criterion: Always Split and Record Everything", "topics": [ "blcSplitCriterionJustRecordEverything" ] }, { "page": "blcSplitCriterionLevelWtdBIC", "title": "Beta RPMM Split Criterion: Level-Weighted BIC", "topics": [ "blcSplitCriterionLevelWtdBIC" ] }, { "page": "blcSplitCriterionLRT", "title": "Beta RPMM Split Criterion: use likelihood ratio test p value", "topics": [ "blcSplitCriterionLRT" ] }, { "page": "blcSubTree", "title": "Beta Subtree", "topics": [ "blcSubTree" ] }, { "page": "blcTree", "title": "Beta RPMM Tree", "topics": [ "blcTree" ] }, { "page": "blcTreeApply", "title": "Recursive Apply Function for Beta RPMM Objects", "topics": [ "blcTreeApply" ] }, { "page": "blcTreeLeafClasses", "title": "Posterior Class Assignments for Beta RPMM", "topics": [ "blcTreeLeafClasses" ] }, { "page": "blcTreeLeafMatrix", "title": "Posterior Weight Matrix for Beta RPMM", "topics": [ "blcTreeLeafMatrix" ] }, { "page": "blcTreeOverallBIC", "title": "Overall BIC for Entire RPMM Tree (Beta version)", "topics": [ "blcTreeOverallBIC" ] }, { "page": "ebayes", "title": "Empirical Bayes predictions for a specific RPMM model", "topics": [ "ebayes" ] }, { "page": "gaussEstMultiple", "title": "Gaussian Maximum Likelihood on a Matrix", "topics": [ "gaussEstMultiple" ] }, { "page": "glc", "title": "Gaussian Finite Mixture Model", "topics": [ "glc" ] }, { "page": "glcInitializeSplitEigen", "title": "Initialize Gaussian Latent Class via Eigendecomposition", "topics": [ "glcInitializeSplitEigen" ] }, { "page": "glcInitializeSplitFanny", "title": "Initialize Gaussian Latent Class via Fanny", "topics": [ "glcInitializeSplitFanny" ] }, { "page": "glcInitializeSplitHClust", "title": "Initialize Gaussian Latent Class via Hierarchical Clustering", "topics": [ "glcInitializeSplitHClust" ] }, { "page": "glcSplit", "title": "Gaussian Latent Class Splitter", "topics": [ "glcSplit" ] }, { "page": "glcSplitCriterionBIC", "title": "Gaussian RPMM Split Criterion: Use BIC", "topics": [ "glcSplitCriterionBIC" ] }, { "page": "glcSplitCriterionBICICL", "title": "Gaussian RPMM Split Criterion: Use ICL-BIC", "topics": [ "glcSplitCriterionBICICL" ] }, { "page": "glcSplitCriterionJustRecordEverything", "title": "Gaussian RPMM Split Criterion: Always Split and Record Everything", "topics": [ "glcSplitCriterionJustRecordEverything" ] }, { "page": "glcSplitCriterionLevelWtdBIC", "title": "Gaussian RPMM Split Criterion: Level-Weighted BIC", "topics": [ "glcSplitCriterionLevelWtdBIC" ] }, { "page": "glcSplitCriterionLRT", "title": "Gaussian RPMM Split Criterion: Use likelihood ratio test p value", "topics": [ "glcSplitCriterionLRT" ] }, { "page": "glcSubTree", "title": "Gaussian Subtree", "topics": [ "glcSubTree" ] }, { "page": "glcTree", "title": "Gaussian RPMM Tree", "topics": [ "glcTree" ] }, { "page": "glcTreeApply", "title": "Recursive Apply Function for Gaussian RPMM Objects", "topics": [ "glcTreeApply" ] }, { "page": "glcTreeLeafClasses", "title": "Posterior Class Assignments for Gaussian RPMM", "topics": [ "glcTreeLeafClasses" ] }, { "page": "glcTreeLeafMatrix", "title": "Posterior Weight Matrix for Gaussian RPMM", "topics": [ "glcTreeLeafMatrix" ] }, { "page": "glcTreeOverallBIC", "title": "Overall BIC for Entire RPMM Tree (Gaussian version)", "topics": [ "glcTreeOverallBIC" ] }, { "page": "glmLC", "title": "Weighted GLM for latent class covariates", "topics": [ "glmLC" ] }, { "page": "IlluminaMethylation", "title": "DNA Methylation Data for Normal Tissue Types", "topics": [ "IllumBeta", "IlluminaMethylation", "tissue" ] }, { "page": "llikeRPMMObject", "title": "Data log-likelihood implied by a specific RPMM model", "topics": [ "llikeRPMMObject" ] }, { "page": "plot.blcTree", "title": "Plot a Beta RPMM Tree Profile", "topics": [ "plot.blcTree" ] }, { "page": "plot.glcTree", "title": "Plot a Gaussian RPMM Tree Profile", "topics": [ "plot.glcTree" ] }, { "page": "plotImage.blcTree", "title": "Plot a Beta RPMM Tree Profile", "topics": [ "plotImage.blcTree" ] }, { "page": "plotImage.glcTree", "title": "Plot a Gaussian RPMM Tree Profile", "topics": [ "plotImage.glcTree" ] }, { "page": "plotTree.blcTree", "title": "Plot a Beta RPMM Tree Dendrogram", "topics": [ "plotTree.blcTree" ] }, { "page": "plotTree.glcTree", "title": "Plot a Gaussian RPMM Tree Dendrogram", "topics": [ "plotTree.glcTree" ] }, { "page": "predict.blcTree", "title": "Predict using a Beta RPMM object", "topics": [ "predict.blcTree" ] }, { "page": "predict.glcTree", "title": "Predict using a Gaussian RPMM object", "topics": [ "predict.glcTree" ] }, { "page": "print.blcTree", "title": "Print a Beta RPMM object", "topics": [ "print.blcTree" ] }, { "page": "print.glcTree", "title": "Print a Gaussian RPMM object", "topics": [ "print.glcTree" ] } ], "_rundeps": [ "cluster" ], "_score": 4.534208928404405, "_indexed": true, "_nocasepkg": "rpmm", "_universes": [ "eahouseman" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25", "date": "2026-09-20T07:31:12.000Z", "distro": "resolute", "commit": "7cae8050edf089b1a4dd5c476ed40820736027c9", "fileid": "https://r2.ropensci.org/4bc9888308b99ac5d6eaeec156abc7b726240fc34cdd66c1fc97fa17cf59b797", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668" }, { "r": "4.6.1", "os": "linux", "version": "1.25", "date": "2026-09-20T07:31:10.000Z", "distro": "resolute", "commit": "7cae8050edf089b1a4dd5c476ed40820736027c9", "fileid": "https://r2.ropensci.org/e68a9e6302a6611f39a31276c64b7d6546a06d454a9af55d830361f95529f318", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668" }, { "r": "4.5.3", "os": "mac", "version": "1.25", "date": "2026-09-20T07:31:50.000Z", "commit": "7cae8050edf089b1a4dd5c476ed40820736027c9", "fileid": "https://r2.ropensci.org/8e7e57a990b7891f3077836fd52d71cc2901d9e080a8f9857ea2b132df16f023", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668" }, { "r": "4.6.1", "os": "mac", "version": "1.25", "date": "2026-09-20T07:31:12.000Z", "commit": "7cae8050edf089b1a4dd5c476ed40820736027c9", "fileid": "https://r2.ropensci.org/c20413cb13f1d06dc12782e364665d765be4a576e485914de7582b85754c7ffc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668" }, { "r": "4.6.0", "os": "wasm", "version": "1.25", "date": "2026-09-20T07:31:16.000Z", "commit": "7cae8050edf089b1a4dd5c476ed40820736027c9", "fileid": "https://r2.ropensci.org/4529be11d0b7ac75111c06a85fb5fc6bc203c710400c62fb9d67ee63506de255", "status": "success", "buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668" }, { "r": "4.7.0", "os": "win", "version": "1.25", "date": "2026-09-20T07:30:15.000Z", "commit": "7cae8050edf089b1a4dd5c476ed40820736027c9", "fileid": "https://r2.ropensci.org/6d447fa7cea6edc4d8909736804c41cf2a6d8ef524fac164680d4ae54959fd7f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668" }, { "r": "4.5.3", "os": "win", "version": "1.25", "date": "2026-09-20T07:30:29.000Z", "commit": "7cae8050edf089b1a4dd5c476ed40820736027c9", "fileid": "https://r2.ropensci.org/98842d6e19c017843839fd6bc581a8e403fccb5029f05e405d51d48e3b93cfd3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668" }, { "r": "4.6.1", "os": "win", "version": "1.25", "date": "2026-09-20T07:30:27.000Z", "commit": "7cae8050edf089b1a4dd5c476ed40820736027c9", "fileid": "https://r2.ropensci.org/bf37dd281be8bab544eb09ea95382179264b2455c61ccd9b37a6795bc971d814", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/eahouseman/actions/runs/35496816668" } ] }