{ "_id": "6a141990acfb0bcc41d3d052", "Package": "HDclust", "Type": "Package", "Title": "Clustering High Dimensional Data with Hidden Markov Model on\nVariable Blocks", "Version": "1.0.4", "Date": "2024-09-14", "Authors@R": "c(\nperson(\"Yevhen\", \"Tupikov\", email = \"yzt116@psu.edu\", role = c(\"aut\")),\nperson(\"Lin\", \"Lin\", email = \"lynn.lin@duke.edu\", role = \"aut\"),\nperson(\"Lixiang\", \"Zhang\", email = \"phoelief@gmail.com\", role = \"aut\"),\nperson(\"Jia\", \"Li\", email = \"jiali@psu.edu\", role = c(\"aut\", \"cre\")))", "Description": "Clustering of high dimensional data with Hidden Markov\nModel on Variable Blocks (HMM-VB) fitted via Baum-Welch\nalgorithm. Clustering is performed by the Modal Baum-Welch\nalgorithm (MBW), which finds modes of the density function. Lin\nLin and Jia Li (2017)\n.", "License": "GPL (>= 2)", "Collate": "'AllClass.R' 'AllGeneric.R' 'AllMethod.R' 'clustControl.R'\n'trainControl.R' 'hmmvbClust.R' 'hmmvbTrain.R'\n'vbSearchControl.R' 'package-HDclust.R' 'RcppExports.R'\n'sim3.R' 'sim2.R' 'hmmvbBIC.R' 'hmmvbFindModes.R'\n'clustModes.R'", "LazyData": "true", "RoxygenNote": "7.1.2", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "Encoding": "UTF-8", "Packaged": { "Date": "2026-05-25 09:39:28 UTC", "User": "root" }, "Author": "Yevhen Tupikov [aut], Lin Lin [aut], Lixiang Zhang [aut], Jia\nLi [aut, cre]", "Maintainer": "Jia Li ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2024-09-21 02:53:44 UTC", "RemoteUrl": "https://github.com/cran/HDclust", "RemoteRef": "HEAD", "RemoteSha": "224847c4309fd2cb22d9012cd965ec63c1c1b403", "MD5sum": "e3cf6bbcfa1385cc658ce2607bb7c8cb", "_user": "cran", "_type": "src", "_file": "HDclust_1.0.4.tar.gz", "_fileid": "0550403efda506e40b9ea0ecf04cb2ff6fcca48af0863771a390cc9a3042b1a0", "_filesize": 1550332, "_sha256": "0550403efda506e40b9ea0ecf04cb2ff6fcca48af0863771a390cc9a3042b1a0", "_created": "2026-05-25T09:39:28.000Z", "_published": "2026-05-25T09:42:40.543Z", "_distro": "noble", "_jobs": [ { "job": 77690095112, "time": 139, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7195707625" }, { "job": 77690095103, "time": 141, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7195707912" }, { "job": 77690095109, "time": 140, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7195707723" }, { "job": 77690095102, "time": 137, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7195707018" }, { "job": 77689546812, "time": 257, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7195669379" }, { "job": 77690095083, "time": 123, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7195703155" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26393780351", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/HDclust", "_commit": { "id": "224847c4309fd2cb22d9012cd965ec63c1c1b403", "author": "Jia Li ", "committer": "cran-robot ", "message": "version 1.0.4\n", "time": 1726887224 }, "_maintainer": { "name": "Jia Li", "email": "jiali@psu.edu" }, "_registered": true, "_dependencies": [ { "package": "methods", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppProgress", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.16", "role": "Imports" }, { "package": "RcppProgress", "version": ">= 0.1", "role": "Imports" }, { "package": "Rtsne", "version": ">= 0.11.0", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "yevhenvt", "count": 1, "uuid": 39964254 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 211, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/HDclust" }, "_searchresults": 18, "_topics": [ "cpp", "openmp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HDclust.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2018-07-29" }, { "version": "1.0.3", "date": "2019-04-11" }, { "version": "1.0.4", "date": "2024-09-20" } ], "_exports": [ "clustControl", "clustModes", "getBdim", "getBIC", "getClsid", "getClustParam", "getDiagCov", "getDim", "getHmmChain", "getHmmParam", "getLoglikehd", "getNb", "getNumst", "getOptHMMVB", "getPrenumst", "getSize", "getVarorder", "getVb", "hmmvbBIC", "hmmvbClust", "hmmvbFindModes", "hmmvbTrain", "plot", "show", "trainControl", "vb", "vbSearchControl" ], "_datasets": [ { "name": "sim2", "title": "Synthetic dataset used in section 5.1.2 of the reference paper.", "object": "sim2", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "clsid" ], "rows": 5000, "table": true, "tojson": true }, { "name": "sim3", "title": "Synthetic dataset used in section 5.1.3 of the reference paper", "object": "sim3", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11", "V12", "V13", "V14", "V15", "V16", "V17", "V18", "V19", "V20", "V21", "V22", "V23", "V24", "V25", "V26", "V27", "V28", "V29", "V30", "V31", "V32", "V33", "V34", "V35", "V36", "V37", "V38", "V39", "V40", "clsid" ], "rows": 1000, "table": true, "tojson": true } ], "_help": [ { "page": "HDclust-package", "title": "Clustering high dimensional data with Hidden Markov Model on Variable Blocks", "topics": [ "HDclust-package", "HDclust" ] }, { "page": "clustControl", "title": "Parameters for MBM clustering algorithm.", "topics": [ "clustControl" ] }, { "page": "clustModes", "title": "Hierarchical clustering of density modes", "topics": [ "clustModes" ] }, { "page": "getBdim", "title": "Accessor for 'bdim' slot", "topics": [ "getBdim", "getBdim,HMMVB-method", "getBdim,VB-method" ] }, { "page": "getBIC", "title": "Accessor for 'BIC' slot.", "topics": [ "getBIC", "getBIC,HMMVB-method", "getBIC,HMMVBBIC-method" ] }, { "page": "getClsid", "title": "Accessor for 'clsid' slot.", "topics": [ "getClsid" ] }, { "page": "getClustParam", "title": "Accessor for 'clustParam' slot.", "topics": [ "getClustParam" ] }, { "page": "getDiagCov", "title": "Accessor for 'diagCov' slot.", "topics": [ "getDiagCov" ] }, { "page": "getDim", "title": "Accessor for 'dim' slot", "topics": [ "getDim", "getDim,HMM-method", "getDim,HMMVB-method", "getDim,VB-method" ] }, { "page": "getHmmChain", "title": "Accessor for 'HmmChain' slot.", "topics": [ "getHmmChain" ] }, { "page": "getHmmParam", "title": "Accessor for parameters of HMM", "topics": [ "getHmmParam" ] }, { "page": "getLoglikehd", "title": "Accessor for 'Loglikehd' slot.", "topics": [ "getLoglikehd", "getLoglikehd,HMMVB-method", "getLoglikehd,HMMVBBIC-method", "getLoglikehd,HMMVBclust-method" ] }, { "page": "getNb", "title": "Accessor for 'nb' slot", "topics": [ "getNb", "getNb,HMMVB-method", "getNb,VB-method" ] }, { "page": "getNumst", "title": "Accessor for 'numst' slot", "topics": [ "getNumst", "getNumst,HMM-method", "getNumst,HMMVB-method", "getNumst,VB-method" ] }, { "page": "getOptHMMVB", "title": "Accessor for 'optHMMVB' slot.", "topics": [ "getOptHMMVB" ] }, { "page": "getPrenumst", "title": "Accessor for 'prenumst' slot", "topics": [ "getPrenumst" ] }, { "page": "getSize", "title": "Accessor for 'size' slot.", "topics": [ "getSize" ] }, { "page": "getVarorder", "title": "Accessor for 'varorder' slot", "topics": [ "getVarorder", "getVarorder,HMMVB-method", "getVarorder,VB-method" ] }, { "page": "getVb", "title": "Accessor for 'VbStructure' slot.", "topics": [ "getVb" ] }, { "page": "HMM-class", "title": "Class \"HMM\" to represent parameters associated with a variable block in the HMM-VB", "topics": [ "getHmmParam,HMM-method", "getPrenumst,HMM-method", "HMM", "HMM-class", "show,HMM-method" ] }, { "page": "HMMVB-class", "title": "Class \"HMMVB\" to represent a Hidden Markov Model on Variable Blocks (HMM-VB).", "topics": [ "getDiagCov,HMMVB-method", "getHmmChain,HMMVB-method", "getVb,HMMVB-method", "HMMVB", "HMMVB-class", "show,HMMVB-method" ] }, { "page": "hmmvbBIC", "title": "BIC for HMM-VB", "topics": [ "hmmvbBIC" ] }, { "page": "HMMVBBIC-class", "title": "Class \"HMMVBBIC\" to represent results of HMM-VB model selection.", "topics": [ "getOptHMMVB,HMMVBBIC-method", "HMMVBBIC", "HMMVBBIC-class", "plot,HMMVBBIC,missing-method", "show,HMMVBBIC-method" ] }, { "page": "hmmvbClust", "title": "Cluster data with HMM-VB", "topics": [ "hmmvbClust" ] }, { "page": "HMMVBclust-class", "title": "Class \"HMMVBclust\" to represent clustering results with Hidden Markov Model on variable block structure.", "topics": [ "getClsid,HMMVBclust-method", "getClustParam,HMMVBclust-method", "getSize,HMMVBclust-method", "HMMVBclust", "HMMVBclust-class", "plot,HMMVBclust,missing-method", "show,HMMVBclust-method" ] }, { "page": "hmmvbFindModes", "title": "Find density modes with HMM-VB", "topics": [ "hmmvbFindModes" ] }, { "page": "hmmvbTrain", "title": "Train HMM-VB", "topics": [ "hmmvbTrain" ] }, { "page": "sim2", "title": "Synthetic dataset used in section 5.1.2 of the reference paper.", "topics": [ "sim2" ] }, { "page": "sim3", "title": "Synthetic dataset used in section 5.1.3 of the reference paper", "topics": [ "sim3" ] }, { "page": "trainControl", "title": "Parameters for HMM-VB training.", "topics": [ "trainControl" ] }, { "page": "vb", "title": "Make an instance of class \"VB\"", "topics": [ "vb" ] }, { "page": "VB-class", "title": "Class \"VB\" to represent a variable block structure.", "topics": [ "show,VB-method", "VB", "VB-class" ] }, { "page": "vbSearchControl", "title": "Parameters for variable block structure search.", "topics": [ "vbSearchControl" ] } ], "_rundeps": [ "Rcpp", "RcppProgress", "Rtsne" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "HDclust.Rmd", "filename": "HDclust.html", "title": "A quick tour of HDclust", "author": "Yevhen Tupikov, Lixiang Zhang", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Define a variable block structure", "Model selection", "Train an HMM-VB model", "Train an HMM-VB model with unknown variable block structure", "Clustering with HMM-VB", "Cluster alignment", "Solution for slow data clustering with many changes in mode merging parameters", "References" ], "created": "2018-07-29 21:00:07", "modified": "2024-09-21 02:53:44", "commits": 3 } ], "_score": 2.255272505103306, "_indexed": true, "_nocasepkg": "hdclust", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.4", "date": "2026-05-25T09:41:48.000Z", "distro": "noble", "arch": "aarch64", "commit": "224847c4309fd2cb22d9012cd965ec63c1c1b403", "fileid": "d7bd2c502ec7539a37e6b097ad53c16012a93c32edd835d45c7928a346a076d2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/26393780351" }, { "r": "4.7.0", "os": "linux", "version": "1.0.4", "date": "2026-05-25T09:41:47.000Z", "distro": "noble", "arch": "x86_64", "commit": "224847c4309fd2cb22d9012cd965ec63c1c1b403", "fileid": "ffee86b76c5ebc1ebc32028a3859223c81b6322dcb0aa7719155181fd1387954", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/26393780351" }, { "r": "4.6.0", "os": "linux", "version": "1.0.4", "date": "2026-05-25T09:41:49.000Z", "distro": "noble", "arch": "aarch64", "commit": "224847c4309fd2cb22d9012cd965ec63c1c1b403", "fileid": "51829e51cc9b7e4b0daf8771eee064b4ac22d98b43225e403d62075b63bf8ca7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/26393780351" }, { "r": "4.6.0", "os": "linux", "version": "1.0.4", "date": "2026-05-25T09:41:44.000Z", "distro": "noble", "arch": "x86_64", "commit": "224847c4309fd2cb22d9012cd965ec63c1c1b403", "fileid": "af23c29000962374af6e0d115f5e3df0b9c07968064a891cae30492915bad727", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/cran/actions/runs/26393780351" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.4", "date": "2026-05-25T09:41:48.000Z", "arch": "emscripten", "commit": "224847c4309fd2cb22d9012cd965ec63c1c1b403", "fileid": "1d79a09596bfa1830210509e4990c6a6ed78974a50ce35ea7fcd9bcfdeb382da", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26393780351" } ] }