{ "_id": "6a5c947a9baadeef8ab51c97", "Package": "bayesCureRateModel", "Type": "Package", "Title": "Bayesian Cure Rate Modeling for Time-to-Event Data", "Version": "1.6", "Date": "2026-01-19", "Authors@R": "c(person(given = \"Panagiotis\",\nfamily = \"Papastamoulis\",\nemail = \"papapast@yahoo.gr\",\nrole = c( \"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9468-7613\")),\nperson(given = \"Fotios\",\nfamily = \"Milienos\",\nemail = \"milienos@panteion.gr\",\nrole = c( \"aut\"),\ncomment = c(ORCID = \"0000-0003-1423-7132\"))\n)", "Maintainer": "Panagiotis Papastamoulis ", "Description": "A fully Bayesian approach in order to estimate a general\nfamily of cure rate models under the presence of covariates,\nsee Papastamoulis and Milienos (2024)\n and Papastamoulis and Milienos\n(2024b) . The promotion time can\nbe modelled (a) parametrically using typical distributional\nassumptions for time to event data (including the Weibull,\nExponential, Gompertz, log-Logistic distributions), or (b)\nsemiparametrically using finite mixtures of distributions. In\nboth cases, user-defined families of distributions are allowed\nunder some specific requirements. Posterior inference is\ncarried out by constructing a Metropolis-coupled Markov chain\nMonte Carlo (MCMC) sampler, which combines Gibbs sampling for\nthe latent cure indicators and Metropolis-Hastings steps with\nLangevin diffusion dynamics for parameter updates. The main\nMCMC algorithm is embedded within a parallel tempering scheme\nby considering heated versions of the target posterior\ndistribution.", "License": "GPL-2", "URL": "https://github.com/mqbssppe/Bayesian_cure_rate_model", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-19 09:03:52 UTC", "User": "root" }, "Author": "Panagiotis Papastamoulis [aut, cre] (ORCID:\n), Fotios Milienos [aut]\n(ORCID: )", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://mqbssppe.r-universe.dev", "Date/Publication": "2026-01-19 06:40:03 UTC", "RemoteUrl": "https://github.com/cran/bayesCureRateModel", "RemoteRef": "HEAD", "RemoteSha": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "_user": "mqbssppe", "_type": "src", "_file": "bayesCureRateModel_1.6.tar.gz", "_fileid": "https://r2.ropensci.org/dbf9acd2ec70b08424fcfda7489fe1a3b28b4d8750e46cc1cdeefba9a325efa6", "_filesize": 401167, "_sha256": "dbf9acd2ec70b08424fcfda7489fe1a3b28b4d8750e46cc1cdeefba9a325efa6", "_expires": "2026-10-27T09:10:16.000Z", "_created": "2026-07-19T09:03:52.000Z", "_published": "2026-07-19T09:10:17.909Z", "_jobs": [ { "job": 88176841110, "time": 177, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8440563159" }, { "job": 88176841117, "time": 173, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8440562052" }, { "job": 88176841127, "time": 179, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8440563406" }, { "job": 88176841112, "time": 185, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8440563782" }, { "job": 88176841144, "time": 109, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8440551869" }, { "job": 88176841121, "time": 221, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8440569313" }, { "job": 88176841115, "time": 121, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8440553450" }, { "job": 88176841106, "time": 335, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8440586884" }, { "job": 88176565537, "time": 197, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8440534127" }, { "job": 88176841105, "time": 128, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8440554795" }, { "job": 88176841100, "time": 163, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8440560394" }, { "job": 88176841111, "time": 150, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8440558369" }, { "job": 88176841101, "time": 169, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8440561537" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698", "_status": "success", "_upstream": "https://github.com/cran/bayesCureRateModel", "_commit": { "id": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "author": "Panagiotis Papastamoulis ", "committer": "cran-robot ", "message": "version 1.6\n", "time": 1768804803 }, "_maintainer": { "name": "Panagiotis Papastamoulis", "email": "papapast@yahoo.gr", "login": "mqbssppe", "description": "", "uuid": 3490226, "orcid": "0000-0001-9468-7613" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.12", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": "coda", "role": "Imports" }, { "package": "HDInterval", "role": "Imports" }, { "package": "VGAM", "role": "Imports" }, { "package": "calculus", "role": "Imports" }, { "package": "flexsurv", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 1 }, { "week": "2026-04", "n": 1 } ], "_tags": [ { "name": "1.5", "date": "2025-10-31" }, { "name": "1.6", "date": "2026-01-19" } ], "_stars": 0, "_contributors": [ { "user": "mqbssppe", "count": 7, "uuid": 3490226 } ], "_userbio": { "uuid": 3490226, "type": "user", "name": "Panagiotis Papastamoulis", "followers": 4 }, "_downloads": { "count": 434, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bayesCureRateModel" }, "_devurl": "https://github.com/mqbssppe/bayesian_cure_rate_model", "_searchresults": 1, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/bayesCureRateModel.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "manual.pdf" ], "_realowner": "mqbssppe", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2024-06-27" }, { "version": "1.1", "date": "2024-07-24" }, { "version": "1.2", "date": "2024-09-14" }, { "version": "1.3", "date": "2024-10-03" }, { "version": "1.4", "date": "2025-06-18" }, { "version": "1.5", "date": "2025-10-31" }, { "version": "1.6", "date": "2026-01-19" } ], "_exports": [ "complete_log_likelihood_general", "compute_fdr_tpr", "cure_rate_MC3", "cure_rate_mcmc", "log_dagum", "log_gamma", "log_gamma_mixture", "log_gompertz", "log_logLogistic", "log_lomax", "log_user_mixture", "log_weibull", "logLik.bayesCureModel", "plot.bayesCureModel", "plot.predict_bayesCureModel", "predict.bayesCureModel", "print.bayesCureModel", "print.predict_bayesCureModel", "print.summary_bayesCureModel", "residuals.bayesCureModel", "summary.bayesCureModel", "summary.predict_bayesCureModel", "Surv" ], "_datasets": [ { "name": "marriage_dataset", "title": "Marriage data", "object": "marriage_dataset", "file": "marriage_dataset.RData", "class": [ "data.frame" ], "fields": [ "id", "censoring", "time", "age", "kids", "race" ], "rows": 1500, "table": true, "tojson": true }, { "name": "sim_mix_data", "title": "Simulated dataset", "object": "sim_mix_data", "file": "sim_mix_data.RData", "class": [ "data.frame" ], "fields": [ "time", "censoring", "x1", "x2", "true_status" ], "rows": 500, "table": true, "tojson": true } ], "_help": [ { "page": "bayesCureRateModel-package", "title": "Bayesian Cure Rate Modeling for Time-to-Event Data", "topics": [ "bayesCureRateModel-package", "bayesCureRateModel" ] }, { "page": "complete_log_likelihood_general", "title": "Logarithm of the complete log-likelihood for the general cure rate model.", "topics": [ "complete_log_likelihood_general" ] }, { "page": "compute_fdr_tpr", "title": "Compute the achieved FDR and TPR", "topics": [ "compute_fdr_tpr" ] }, { "page": "cure_rate_MC3", "title": "Main function of the package", "topics": [ "cure_rate_MC3" ] }, { "page": "cure_rate_mcmc", "title": "The basic MCMC scheme.", "topics": [ "cure_rate_mcmc" ] }, { "page": "log_dagum", "title": "PDF and CDF of the Dagum distribution", "topics": [ "log_dagum" ] }, { "page": "log_gamma", "title": "PDF and CDF of the Gamma distribution", "topics": [ "log_gamma" ] }, { "page": "log_gamma_mixture", "title": "PDF and CDF of a Gamma mixture distribution", "topics": [ "log_gamma_mixture" ] }, { "page": "log_gompertz", "title": "PDF and CDF of the Gompertz distribution", "topics": [ "log_gompertz" ] }, { "page": "log_logLogistic", "title": "PDF and CDF of the log-Logistic distribution.", "topics": [ "log_logLogistic" ] }, { "page": "log_lomax", "title": "PDF and CDF of the Lomax distribution", "topics": [ "log_lomax" ] }, { "page": "log_user_mixture", "title": "Define a finite mixture of a given family of distributions.", "topics": [ "log_user_mixture" ] }, { "page": "log_weibull", "title": "PDF and CDF of the Weibull distribution", "topics": [ "log_weibull" ] }, { "page": "logLik.bayesCureModel", "title": "Extract the log-likelihood.", "topics": [ "logLik.bayesCureModel" ] }, { "page": "marriage_dataset", "title": "Marriage data", "topics": [ "marriage_dataset" ] }, { "page": "plot.bayesCureModel", "title": "Plot method", "topics": [ "plot.bayesCureModel" ] }, { "page": "plot.predict_bayesCureModel", "title": "Plot method", "topics": [ "plot.predict_bayesCureModel" ] }, { "page": "predict.bayesCureModel", "title": "Predict method.", "topics": [ "predict.bayesCureModel" ] }, { "page": "print.bayesCureModel", "title": "Print method", "topics": [ "print.bayesCureModel" ] }, { "page": "print.predict_bayesCureModel", "title": "Print method for the 'predict' object", "topics": [ "print.predict_bayesCureModel" ] }, { "page": "print.summary_bayesCureModel", "title": "Print method for the summary", "topics": [ "print.summary_bayesCureModel" ] }, { "page": "residuals.bayesCureModel", "title": "Computation of residuals.", "topics": [ "residuals.bayesCureModel" ] }, { "page": "sim_mix_data", "title": "Simulated dataset", "topics": [ "sim_mix_data" ] }, { "page": "summary.bayesCureModel", "title": "Summary method.", "topics": [ "summary.bayesCureModel" ] }, { "page": "summary.predict_bayesCureModel", "title": "Summary method for predictions.", "topics": [ "summary.predict_bayesCureModel" ] }, { "page": "Surv", "title": "Create a Survival Object", "topics": [ "Surv" ] } ], "_rundeps": [ "assertthat", "bbmle", "bdsmatrix", "calculus", "cli", "coda", "codetools", "cpp11", "data.table", "deSolve", "doParallel", "dplyr", "farver", "fastGHQuad", "flexsurv", "foreach", "generics", "ggplot2", "glue", "gtable", "HDInterval", "isoband", "iterators", "labeling", "lattice", "lifecycle", "lsoda", "magrittr", "MASS", "Matrix", "mclust", "mgcv", "mstate", "muhaz", "mvtnorm", "nlme", "numDeriv", "pillar", "pkgconfig", "purrr", "quadprog", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "rstpm2", "S7", "scales", "statmod", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "VGAM", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.32+ds-5", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 1.3010299956639813, "_indexed": true, "_nocasepkg": "bayescureratemodel", "_universes": [ "mqbssppe" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.6", "date": "2026-07-19T09:06:32.000Z", "distro": "resolute", "arch": "aarch64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/f3d0c4e9492b74c30a0598802537db98c0e4089f38dd818e2af824bb6db39739", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.7.0", "os": "linux", "version": "1.6", "date": "2026-07-19T09:06:12.000Z", "distro": "resolute", "arch": "x86_64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/df4fd1e4a4e5a1b5dc06f55ef8a4a7d3b8c4b94b8a9337ea6218ab6bbe67fd0d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.6.1", "os": "linux", "version": "1.6", "date": "2026-07-19T09:06:31.000Z", "distro": "resolute", "arch": "aarch64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/d2551d0cac85948a5e7ce144c5180e382617339cc5c7d8468ff0fe6fd8c1563b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.6.1", "os": "linux", "version": "1.6", "date": "2026-07-19T09:06:19.000Z", "distro": "resolute", "arch": "x86_64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/05b9564a81ff116c4fae484a8ca993ed91ef16cb95d5df00afd9ffabcb45bd04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.5.3", "os": "mac", "version": "1.6", "date": "2026-07-19T09:05:28.000Z", "arch": "aarch64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/b610ecdab35c34d4301bcdefac1e97969693b97f9949a6bbe11e3b87c0860e6a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.5.3", "os": "mac", "version": "1.6", "date": "2026-07-19T09:06:36.000Z", "arch": "x86_64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/6e88def5b6a1da5e1c793137f0a92609372d75d41a297844e1cbe67b4e52c011", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.6.1", "os": "mac", "version": "1.6", "date": "2026-07-19T09:05:33.000Z", "arch": "aarch64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/597b5190d1792af9f5f1f246b92e9df30a47e87e767f2523e0e4fa30dbfe740b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.6.1", "os": "mac", "version": "1.6", "date": "2026-07-19T09:07:44.000Z", "arch": "x86_64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/43608d22ab1adde4e5059ef142dabcb76b5499705336eb4a4f13f53b9015a33b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.6.0", "os": "wasm", "version": "1.6", "date": "2026-07-19T09:06:14.000Z", "arch": "emscripten", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/9c65c5053c11893e7e8765f30a9f984b9c514ffdcefbf863178765deafc8551b", "status": "success", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.7.0", "os": "win", "version": "1.6", "date": "2026-07-19T09:05:24.000Z", "arch": "x86_64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/5a4936e11576dbe28179a16b3574f693188325a65f61bbeb9594eb0eebbe8df3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.5.3", "os": "win", "version": "1.6", "date": "2026-07-19T09:05:22.000Z", "arch": "x86_64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/dcc35d1bbfe9f1cf108288fd61fe7f6df2dceb275eb00a3b7c7de8e65149acc3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" }, { "r": "4.6.1", "os": "win", "version": "1.6", "date": "2026-07-19T09:05:31.000Z", "arch": "x86_64", "commit": "f06e7de9e1d64a742bb938a81886fbdb121dac9e", "fileid": "https://r2.ropensci.org/77d517f51f99119327ea2f0ea20d0ae603204054c13fe763ba45f25f6536bc89", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/mqbssppe/actions/runs/29680812698" } ] }