{ "_id": "6a1d66c31d7bb097a0a4cf31", "Package": "PReMiuM", "Type": "Package", "Title": "Dirichlet Process Bayesian Clustering, Profile Regression", "Version": "3.2.13", "Author": "David I. Hastie, Silvia Liverani and\nSylvia Richardson with contributions from Aurore J. Lavigne,\nLucy Leigh, Lamiae Azizi, Xi Liu, Ruizhu Huang, Austin Gratton,\nWei Jing", "Maintainer": "Silvia Liverani ", "Description": "Bayesian clustering using a Dirichlet process mixture\nmodel. This model is an alternative to regression models,\nnon-parametrically linking a response vector to covariate data\nthrough cluster membership. The package allows Bernoulli,\nBinomial, Poisson, Normal, survival and categorical response,\nas well as Normal and discrete covariates. It also allows for\nfixed effects in the response model, where a spatial CAR\n(conditional autoregressive) term can be also included.\nAdditionally, predictions may be made for the response, and\nmissing values for the covariates are handled. Several samplers\nand label switching moves are implemented along with diagnostic\ntools to assess convergence. A number of R functions for\npost-processing of the output are also provided. In addition to\nfitting mixtures, it may additionally be of interest to\ndetermine which covariates actively drive the mixture\ncomponents. This is implemented in the package as variable\nselection. The main reference for the package is Liverani,\nHastie, Azizi, Papathomas and Richardson (2015)\n.", "URL": "https://www.silvialiverani.com/software/", "License": "GPL-2", "LazyLoad": "yes", "SystemRequirements": "GNU make", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-01 10:44:18 UTC", "User": "root" }, "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libssl-dev libproj-dev libsqlite3-dev libudunits2-dev", "Repository": "https://silvialiverani.r-universe.dev", "Date/Publication": "2024-01-10 02:39:43 UTC", "RemoteUrl": "https://github.com/cran/PReMiuM", "RemoteRef": "HEAD", "RemoteSha": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "MD5sum": "ce077e48f3a184afcf7ad6c6a522ecf5", "_user": "silvialiverani", "_type": "src", "_file": "PReMiuM_3.2.13.tar.gz", "_fileid": "f96672b014df256d0368362716e3eac646192572dc0304d8081163242cc6194e", "_filesize": 363893, "_sha256": "f96672b014df256d0368362716e3eac646192572dc0304d8081163242cc6194e", "_created": "2026-06-01T10:44:18.000Z", "_published": "2026-06-01T11:02:27.628Z", "_distro": "noble", "_jobs": [ { "job": 78835713076, "time": 216, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7329508003" }, { "job": 78835713062, "time": 209, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7329505248" }, { "job": 78835713089, "time": 177, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7329744094" }, { "job": 78835712929, "time": 452, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7329666136" }, { "job": 78835712954, "time": 226, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7329660490" }, { "job": 78835712967, "time": 622, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "" }, { "job": 78835171606, "time": 208, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7329437591" }, { "job": 78835713000, "time": 148, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7329485792" }, { "job": 78835713052, "time": 178, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7329495735" }, { "job": 78835712964, "time": 301, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7329534913" }, { "job": 78835712948, "time": 160, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7329489672" } ], "_buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/PReMiuM", "_commit": { "id": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "author": "Silvia Liverani ", "committer": "cran-robot ", "message": "version 3.2.13\n", "time": 1704854383 }, "_maintainer": { "name": "Silvia Liverani", "email": "liveranis@gmail.com", "login": "silvialiverani", "description": "Reader in Statistics at Queen Mary University of London, UK", "uuid": 1337047 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.1", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "version": ">= 0.3.3.3.0", "role": "LinkingTo" }, { "package": "BH", "version": ">= 1.65.0-1", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.13", "role": "Imports" }, { "package": "ggplot2", "version": ">= 2.2", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "plotrix", "version": ">= 3.6-6", "role": "Imports" }, { "package": "gamlss.dist", "version": ">= 4.3-1", "role": "Imports" }, { "package": "data.table", "version": ">= 1.10.4-3", "role": "Imports" }, { "package": "spdep", "version": ">= 0.7-7", "role": "Imports" }, { "package": "sf", "version": ">= 1.0-8", "role": "Imports" }, { "package": "testthat", "version": ">= 1.0.2", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "silvialiverani", "count": 36, "uuid": 1337047 } ], "_userbio": { "uuid": 1337047, "type": "user", "name": "Silvia Liverani", "description": "Reader in Statistics at Queen Mary University of London, UK" }, "_downloads": { "count": 375, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PReMiuM" }, "_mentions": 10, "_searchresults": 134, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PReMiuM.html", "manual.pdf" ], "_realowner": "silvialiverani", "_cranurl": false, "_releases": [ { "version": "3.0.11", "date": "2013-01-29" }, { "version": "3.0.13", "date": "2013-01-30" }, { "version": "3.0.15", "date": "2013-02-07" }, { "version": "3.0.16", "date": "2013-03-15" }, { "version": "3.0.17", "date": "2013-04-22" }, { "version": "3.0.18", "date": "2013-04-24" }, { "version": "3.0.20", "date": "2013-05-04" }, { "version": "3.0.21", "date": "2013-10-01" }, { "version": "3.0.23", "date": "2014-04-03" }, { "version": "3.0.24", "date": "2014-04-07" }, { "version": "3.0.26", "date": "2014-05-06" }, { "version": "3.0.28", "date": "2014-06-30" }, { "version": "3.0.29", "date": "2014-09-09" }, { "version": "3.0.30", "date": "2014-09-12" }, { "version": "3.0.32", "date": "2014-12-29" }, { "version": "3.1.0", "date": "2015-03-13" }, { "version": "3.1.1", "date": "2015-06-12" }, { "version": "3.1.2", "date": "2015-08-26" }, { "version": "3.1.3", "date": "2016-02-23" }, { "version": "3.1.4", "date": "2016-12-28" }, { "version": "3.1.5", "date": "2017-10-27" }, { "version": "3.1.6", "date": "2017-11-02" }, { "version": "3.1.7", "date": "2018-04-01" }, { "version": "3.1.8", "date": "2018-06-14" }, { "version": "3.2.0", "date": "2018-06-15" }, { "version": "3.2.1", "date": "2018-09-26" }, { "version": "3.2.2", "date": "2019-06-20" }, { "version": "3.2.3", "date": "2019-11-02" }, { "version": "3.2.5", "date": "2021-04-08" }, { "version": "3.2.6", "date": "2021-04-26" }, { "version": "3.2.7", "date": "2021-10-08" }, { "version": "3.2.8", "date": "2022-10-13" }, { "version": "3.2.9", "date": "2023-06-06" }, { "version": "3.2.10", "date": "2023-08-26" }, { "version": "3.2.11", "date": "2023-11-13" }, { "version": "3.2.13", "date": "2024-01-09" } ], "_exports": [ "calcAvgRiskAndProfile", "calcDissimilarityMatrix", "calcOptimalClustering", "calcPredictions", "clusSummaryBernoulliDiscrete", "clusSummaryBernoulliDiscreteSmall", "clusSummaryBernoulliMixed", "clusSummaryBernoulliNormal", "clusSummaryBinomialNormal", "clusSummaryCategoricalDiscrete", "clusSummaryGammaNormal", "clusSummaryNormalDiscrete", "clusSummaryNormalNormal", "clusSummaryNormalNormalSpatial", "clusSummaryPoissonDiscrete", "clusSummaryPoissonNormal", "clusSummaryPoissonNormalSpatial", "clusSummaryQuantileNormal", "clusSummaryVarSelectBernoulliDiscrete", "clusSummaryWeibullDiscrete", "computeRatioOfVariance", "generateSampleDataFile", "globalParsTrace", "heatDissMat", "is.wholenumber", "mapforGeneratedData", "margModelPosterior", "plotPredictions", "plotRiskProfile", "profRegr", "qALD", "rALD", "setHyperparams", "simBenchmark", "summariseVarSelectRho", "vec2mat" ], "_help": [ { "page": "PReMiuM-package", "title": "Dirichlet Process Bayesian Clustering", "topics": [ "PReMiuM-package", "PReMiuM", "PReMiuMpackage" ] }, { "page": "calcAvgRiskAndProfile", "title": "Calculation of the average risks and profiles", "topics": [ "calcAvgRiskAndProfile" ] }, { "page": "calcDissimilarityMatrix", "title": "Calculates the dissimilarity matrix", "topics": [ "calcDissimilarityMatrix" ] }, { "page": "calcOptimalClustering", "title": "Calculation of the optimal clustering", "topics": [ "calcOptimalClustering" ] }, { "page": "calcPredictions", "title": "Calculates the predictions", "topics": [ "calcPredictions" ] }, { "page": "clusSummaryBernoulliDiscrete", "title": "Sample datasets for profile regression", "topics": [ "clusSummaryBernoulliDiscrete", "clusSummaryBernoulliDiscreteSmall", "clusSummaryBernoulliMixed", "clusSummaryBernoulliNormal", "clusSummaryBinomialNormal", "clusSummaryCategoricalDiscrete", "clusSummaryGammaNormal", "clusSummaryNormalDiscrete", "clusSummaryNormalNormal", "clusSummaryNormalNormalSpatial", "clusSummaryPoissonDiscrete", "clusSummaryPoissonNormal", "clusSummaryPoissonNormalSpatial", "clusSummaryQuantileNormal", "clusSummaryVarSelectBernoulliDiscrete", "clusSummaryWeibullDiscrete" ] }, { "page": "computeRatioOfVariance", "title": "computeRatioOfVariance", "topics": [ "computeRatioOfVariance" ] }, { "page": "generateSampleDataFile", "title": "Generate sample data files for profile regression", "topics": [ "generateSampleDataFile" ] }, { "page": "globalParsTrace", "title": "Plot of the trace of some of the global parameters", "topics": [ "globalParsTrace" ] }, { "page": "heatDissMat", "title": "Plot the heatmap of the dissimilarity matrix", "topics": [ "heatDissMat" ] }, { "page": "is.wholenumber", "title": "Function to check if a number is a whole number", "topics": [ "is.wholenumber" ] }, { "page": "mapforGeneratedData", "title": "Map generated data", "topics": [ "mapforGeneratedData" ] }, { "page": "margModelPosterior", "title": "Marginal Model Posterior", "topics": [ "margModelPosterior" ] }, { "page": "plotPredictions", "title": "Plot the conditional density using the predicted scenarios", "topics": [ "plotPredictions" ] }, { "page": "plotRiskProfile", "title": "Plot the Risk Profiles", "topics": [ "plotRiskProfile" ] }, { "page": "profRegr", "title": "Profile Regression", "topics": [ "profRegr" ] }, { "page": "rALD", "title": "Asymmetric Laplace Distribution", "topics": [ "qALD", "rALD" ] }, { "page": "setHyperparams", "title": "Definition of characteristics of sample datasets for profile regression", "topics": [ "setHyperparams" ] }, { "page": "simBenchmark", "title": "Benchmark for simulated examples", "topics": [ "simBenchmark" ] }, { "page": "summariseVarSelectRho", "title": "summariseVarSelectRho", "topics": [ "summariseVarSelectRho" ] }, { "page": "vec2mat", "title": "Vector to upper triangular matrix", "topics": [ "vec2mat" ] } ], "_rundeps": [ "BH", "boot", "class", "classInt", "cli", "cluster", "cpp11", "data.table", "DBI", "deldir", "e1071", "farver", "gamlss.dist", "ggplot2", "glue", "gtable", "isoband", "KernSmooth", "labeling", "lattice", "lifecycle", "MASS", "plotrix", "proxy", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "rlang", "s2", "S7", "scales", "sf", "sp", "spData", "spdep", "units", "vctrs", "viridisLite", "withr", "wk" ], "_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" } ], "_score": 3.1271047983648077, "_indexed": true, "_nocasepkg": "premium", "_universes": [ "silvialiverani" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.2.13", "date": "2026-05-02T07:26:42.000Z", "distro": "noble", "arch": "aarch64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "4c311cfb9fdb379d38b47818f4cd759e647aab9504e48ef1f1eb7e5a6104cf6e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/25246706211" }, { "r": "4.6.0", "os": "linux", "version": "3.2.13", "date": "2026-05-02T07:26:41.000Z", "distro": "noble", "arch": "aarch64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "840ba2d5fa36bd1f199882ec66a9b592358a174dffdea9317e962e9d374a35a7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/25246706211" }, { "r": "4.6.0", "os": "mac", "version": "3.2.13", "date": "2026-05-02T07:26:31.000Z", "arch": "x86_64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "13569425053fe7b6584bb335808e38e96f7df660739ce93b0c6f25e72a64bf35", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/25246706211" }, { "r": "4.7.0", "os": "linux", "version": "3.2.13", "date": "2026-06-01T10:47:30.000Z", "distro": "noble", "arch": "x86_64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "14849ce9f62f027f3d71747bae91de8f43047d2f738760bb60bf8fa2d3504a48", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" }, { "r": "4.6.0", "os": "linux", "version": "3.2.13", "date": "2026-06-01T10:47:30.000Z", "distro": "noble", "arch": "x86_64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "1203cb221ca7701bd40fea601a0fa165d1dc565d7f9b840b86646b794fb7957c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" }, { "r": "4.5.3", "os": "mac", "version": "3.2.13", "date": "2026-06-01T10:59:49.000Z", "arch": "aarch64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "469209856c1cec34787e1bc3eb5fbcfd3a6a143b75c2e000ea577b8e005575f9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" }, { "r": "4.5.3", "os": "mac", "version": "3.2.13", "date": "2026-06-01T10:54:35.000Z", "arch": "x86_64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "92752b062ea1ed46390da958a366b81228bdc9ea3d63fc0d3ccf46c0baf49b67", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" }, { "r": "4.6.0", "os": "mac", "version": "3.2.13", "date": "2026-06-01T10:55:42.000Z", "arch": "aarch64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "e38ad12859e6110c6fe8d78cb739f9c1dae4dc5635de1cfaa811792dfdb9d0a2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" }, { "r": "4.6.0", "os": "wasm", "version": "3.2.13", "date": "2026-06-01T10:47:17.000Z", "arch": "emscripten", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "19b57342e49a0a2b124a41e68ede9a71dfbeab8ea60d21465868f0d948879b42", "status": "success", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" }, { "r": "4.7.0", "os": "win", "version": "3.2.13", "date": "2026-06-01T10:46:23.000Z", "arch": "x86_64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "55e467fb6e02ec5903f33c992bced6e6f6d83dc1dcfd0b73faf5fbce17b27a7f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" }, { "r": "4.5.3", "os": "win", "version": "3.2.13", "date": "2026-06-01T10:47:28.000Z", "arch": "x86_64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "fb891df3160ab9a321faa87f699320640288d5de171a9ba50229f186ce4d33d4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" }, { "r": "4.6.0", "os": "win", "version": "3.2.13", "date": "2026-06-01T10:46:07.000Z", "arch": "x86_64", "commit": "c0dbdc2f1e5bad7fd1eb38a7269a09b377515644", "fileid": "c5af0727575bb2807ef2afca86cf7c62cb62f1e317390fb0b7bb165950863293", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/silvialiverani/actions/runs/26749963775" } ] }