{ "_id": "6a105410acfb0bcc41ca1f84", "Package": "PERSUADE", "Title": "Parametric Survival Model Selection for Decision-Analytic Models", "Version": "0.1.2", "Authors@R": "c(\nperson(\"Bram\", \"Ramaekers\", , \"bram.ramaekers@mumc.nl\", role = c(\"aut\", \"cre\", \"ths\"),\ncomment = c(ORCID = \"0000-0001-5785-9228\")),\nperson(\"Xavier\", \"Pouwels\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0003-3563-0013\")),\nperson(\"Sabine\", \"Grimm\", role = \"ths\",\ncomment = c(ORCID = \"0000-0002-2175-7999\")),\nperson(\"Manuela\", \"Joore\", role = \"ths\",\ncomment = c(ORCID = \"0000-0002-5649-6768\"))\n)", "Description": "Provides a standardized framework to support the selection\nand evaluation of parametric survival models for time-to-event\ndata. Includes tools for visualizing survival data, checking\nproportional hazards assumptions (Grambsch and Therneau, 1994,\n), comparing parametric (Ishak and\ncolleagues, 2013, ), spline\n(Royston and Parmar, 2002, ) and cure\nmodels, examining hazard functions, and evaluating model\nextrapolation. Methods are consistent with recommendations in\nthe NICE Decision Support Unit Technical Support Documents (14\nand 21\n).\nResults are structured to facilitate integration into\ndecision-analytic models, and reports can be generated with\n'rmarkdown'. The package builds on existing tools including\n'flexsurv' (Jackson, 2016, )) and\n'flexsurvcure' for estimating cure models.", "License": "GPL (>= 3)", "URL": "https://github.com/Bram-R/PERSUADE", "BugReports": "https://github.com/Bram-R/PERSUADE/issues", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev", "Repository": "https://bram-r.r-universe.dev", "Date/Publication": "2025-10-10 14:13:48 UTC", "RemoteUrl": "https://github.com/bram-r/persuade", "RemoteRef": "HEAD", "RemoteSha": "8b2a8c510d058152c11485657cc05540d64ecb09", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-09 08:44:58 UTC", "User": "root" }, "Author": "Bram Ramaekers [aut, cre, ths] (ORCID:\n),\nXavier Pouwels [ctb] (ORCID: ),\nSabine Grimm [ths] (ORCID: ),\nManuela Joore [ths] (ORCID: )", "Maintainer": "Bram Ramaekers ", "MD5sum": "51c85f1d4543de1c372f05edfe5ba4ae", "_user": "bram-r", "_type": "src", "_file": "PERSUADE_0.1.2.tar.gz", "_fileid": "35fb16e98142f5d98f30db9676f925bcff173d37543c4f7d57c0baf37302356d", "_filesize": 578890, "_sha256": "35fb16e98142f5d98f30db9676f925bcff173d37543c4f7d57c0baf37302356d", "_created": "2026-05-09T08:44:58.000Z", "_published": "2026-05-22T13:03:12.801Z", "_distro": "noble", "_jobs": [ { "job": 77384760940, "time": 191, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6894428151" }, { "job": 77384761299, "time": 202, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6894429315" }, { "job": 77384761386, "time": 175, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6894424429" }, { "job": 77384761017, "time": 130, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6894420190" }, { "job": 77384760181, "time": 236, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6894409444" }, { "job": 77384760320, "time": 158, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7161140919" }, { "job": 77384761311, "time": 135, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6894422766" }, { "job": 77384761793, "time": 90, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6894418684" }, { "job": 77384761042, "time": 188, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6894427953" } ], "_buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bram-r/persuade", "_commit": { "id": "8b2a8c510d058152c11485657cc05540d64ecb09", "author": "Bram Ramaekers <67429090+Bram-R@users.noreply.github.com>", "committer": "GitHub ", "message": "Delete tests/testthat/grid_test directory", "time": 1760105628 }, "_maintainer": { "name": "Bram Ramaekers", "email": "bram.ramaekers@mumc.nl", "login": "bram-r", "uuid": 67429090, "orcid": "0000-0001-5785-9228" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "flexsurv", "role": "Imports" }, { "package": "flexsurvcure", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "muhaz", "role": "Imports" }, { "package": "rmarkdown", "role": "Imports" }, { "package": "rms", "role": "Imports" }, { "package": "sft", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "survminer", "role": "Imports" }, { "package": "kableExtra", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.1.2", "role": "Suggests" }, { "package": "utils", "role": "Suggests" } ], "_owner": "bram-r", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-31", "n": 3 }, { "week": "2025-32", "n": 3 }, { "week": "2025-33", "n": 8 }, { "week": "2025-34", "n": 15 }, { "week": "2025-37", "n": 5 }, { "week": "2025-39", "n": 11 }, { "week": "2025-40", "n": 7 }, { "week": "2025-41", "n": 8 } ], "_tags": [ { "name": "CRAN", "date": "2025-10-06" }, { "name": "PERSUADEv0.1.2", "date": "2025-10-10" } ], "_stars": 4, "_contributors": [ { "user": "bram-r", "count": 175, "uuid": 67429090 }, { "user": "xa4p", "count": 17, "uuid": 77057518 } ], "_userbio": { "uuid": 67429090, "type": "user", "name": "Bram Ramaekers" }, "_downloads": { "count": 169, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PERSUADE" }, "_devurl": "https://github.com/bram-r/persuade", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/PERSUADE.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/bram-r/persuade", "_realowner": "bram-r", "_cranurl": true, "_releases": [ { "version": "0.1.2", "date": "2025-10-09" } ], "_exports": [ "f_cum_hazard", "f_generate_report", "f_get_excel_template", "f_hazard", "f_PERSUADE", "f_plot_cure_surv_extrap", "f_plot_cure_surv_model", "f_plot_diag_cure_surv_model", "f_plot_diag_param_surv_model", "f_plot_diag_spline_surv_model", "f_plot_hazard_cure_extrap", "f_plot_hazard_parametric_extrap", "f_plot_hazard_spline_extrap", "f_plot_hazard_with_models", "f_plot_km_survival", "f_plot_km_survival_base", "f_plot_log_cumhaz", "f_plot_param_surv_extrap", "f_plot_param_surv_model", "f_plot_schoenfeld_residuals", "f_plot_smoothed_hazard", "f_plot_spline_surv_extrap", "f_plot_spline_surv_model", "f_plot_tp_cure_surv_extrap", "f_plot_tp_cure_surv_model", "f_plot_tp_param_surv_extrap", "f_plot_tp_param_surv_model", "f_plot_tp_spline_surv_extrap", "f_plot_tp_spline_surv_model", "f_summary", "f_surv_model", "f_surv_model_excel", "f_surv_model_pred", "f_surv_model_pred_gr", "f_surv_model_pred_tp_gr", "f_tp" ], "_help": [ { "page": "f_cum_hazard", "title": "Calculate Cumulative Hazard Estimates", "topics": [ "f_cum_hazard" ] }, { "page": "f_generate_report", "title": "Generate PDF Report for a PERSUADE Analysis", "topics": [ "f_generate_report" ] }, { "page": "f_get_excel_template", "title": "Copy Excel Template for Model Parameters", "topics": [ "f_get_excel_template" ] }, { "page": "f_hazard", "title": "Calculate Smoothed Hazard Estimates", "topics": [ "f_hazard" ] }, { "page": "f_PERSUADE", "title": "Main PERSUADE Function", "topics": [ "f_PERSUADE" ] }, { "page": "f_plot_cure_surv_extrap", "title": "Plot Extrapolated Cure Survival Models per Group", "topics": [ "f_plot_cure_surv_extrap" ] }, { "page": "f_plot_cure_surv_model", "title": "Cure Survival Model Overlay", "topics": [ "f_plot_cure_surv_model" ] }, { "page": "f_plot_diag_cure_surv_model", "title": "Diagnostic Plot for Cure Survival Models", "topics": [ "f_plot_diag_cure_surv_model" ] }, { "page": "f_plot_diag_param_surv_model", "title": "Diagnostic Plot for Parametric Survival Models", "topics": [ "f_plot_diag_param_surv_model" ] }, { "page": "f_plot_diag_spline_surv_model", "title": "Diagnostic Plot for Spline Survival Models", "topics": [ "f_plot_diag_spline_surv_model" ] }, { "page": "f_plot_hazard_cure_extrap", "title": "Plot Extrapolated Hazard Functions (Cure Models)", "topics": [ "f_plot_hazard_cure_extrap" ] }, { "page": "f_plot_hazard_parametric_extrap", "title": "Plot Extrapolated Hazard Functions (Parametric Models)", "topics": [ "f_plot_hazard_parametric_extrap" ] }, { "page": "f_plot_hazard_spline_extrap", "title": "Plot Extrapolated Hazard Functions (Spline Models)", "topics": [ "f_plot_hazard_spline_extrap" ] }, { "page": "f_plot_hazard_with_models", "title": "Hazard Plot with Model Overlays", "topics": [ "f_plot_hazard_with_models" ] }, { "page": "f_plot_km_survival", "title": "Plot Kaplan-Meier Survival Curves (ggsurvplot)", "topics": [ "f_plot_km_survival" ] }, { "page": "f_plot_km_survival_base", "title": "Plot Kaplan-Meier Survival Curves (Base R)", "topics": [ "f_plot_km_survival_base" ] }, { "page": "f_plot_log_cumhaz", "title": "Log-Log Survival Diagnostic Plot", "topics": [ "f_plot_log_cumhaz" ] }, { "page": "f_plot_param_surv_extrap", "title": "Plot Extrapolated Parametric Survival Models per Group", "topics": [ "f_plot_param_surv_extrap" ] }, { "page": "f_plot_param_surv_model", "title": "Parametric Survival Model Overlay", "topics": [ "f_plot_param_surv_model" ] }, { "page": "f_plot_schoenfeld_residuals", "title": "Schoenfeld Residuals Plot", "topics": [ "f_plot_schoenfeld_residuals" ] }, { "page": "f_plot_smoothed_hazard", "title": "Smoothed Hazard Function Plot", "topics": [ "f_plot_smoothed_hazard" ] }, { "page": "f_plot_spline_surv_extrap", "title": "Plot Extrapolated Spline Survival Models per Group", "topics": [ "f_plot_spline_surv_extrap" ] }, { "page": "f_plot_spline_surv_model", "title": "Spline Survival Model Overlay", "topics": [ "f_plot_spline_surv_model" ] }, { "page": "f_plot_tp_cure_surv_extrap", "title": "Plot Extrapolated Annual Transition Probabilities (Cure Models)", "topics": [ "f_plot_tp_cure_surv_extrap" ] }, { "page": "f_plot_tp_cure_surv_model", "title": "Plot Annual Transition Probabilities for Cure Survival Models", "topics": [ "f_plot_tp_cure_surv_model" ] }, { "page": "f_plot_tp_param_surv_extrap", "title": "Plot Extrapolated Annual Transition Probabilities (Parametric Models)", "topics": [ "f_plot_tp_param_surv_extrap" ] }, { "page": "f_plot_tp_param_surv_model", "title": "Plot Annual Transition Probabilities for Parametric Survival Models", "topics": [ "f_plot_tp_param_surv_model" ] }, { "page": "f_plot_tp_spline_surv_extrap", "title": "Plot Extrapolated Annual Transition Probabilities (Spline Models)", "topics": [ "f_plot_tp_spline_surv_extrap" ] }, { "page": "f_plot_tp_spline_surv_model", "title": "Plot Annual Transition Probabilities for Spline Survival Models", "topics": [ "f_plot_tp_spline_surv_model" ] }, { "page": "f_summary", "title": "Compute Summary Statistics for Numeric Variables", "topics": [ "f_summary" ] }, { "page": "f_surv_model", "title": "Fit Parametric Survival Models", "topics": [ "f_surv_model" ] }, { "page": "f_surv_model_excel", "title": "Prepare Excel-Ready Survival Model Output", "topics": [ "f_surv_model_excel" ] }, { "page": "f_surv_model_pred", "title": "Predict from Survival Models", "topics": [ "f_surv_model_pred" ] }, { "page": "f_surv_model_pred_gr", "title": "Group Predictions by Survival Model", "topics": [ "f_surv_model_pred_gr" ] }, { "page": "f_surv_model_pred_tp_gr", "title": "Compute Transition Probabilities for Survival Model Predictions", "topics": [ "f_surv_model_pred_tp_gr" ] }, { "page": "f_tp", "title": "Calculate Transition Probabilities", "topics": [ "f_tp" ] }, { "page": "plot.PERSUADE", "title": "Plot Method for PERSUADE Objects", "topics": [ "plot.PERSUADE" ] }, { "page": "print.PERSUADE", "title": "Print Method for PERSUADE Objects", "topics": [ "print.PERSUADE" ] }, { "page": "summary.PERSUADE", "title": "Summary Method for PERSUADE Objects", "topics": [ "summary.PERSUADE" ] } ], "_readme": "https://github.com/bram-r/persuade/raw/HEAD/README.md", "_rundeps": [ "abind", "ash", "assertthat", "backports", "base64enc", "bbmle", "bdsmatrix", "bitops", "boot", "broom", "bslib", "cachem", "car", "carData", "checkmate", "cli", "cluster", "codetools", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "curl", "data.table", "Deriv", "deSolve", "digest", "doBy", "dplyr", "evaluate", "exactRankTests", "farver", "fastGHQuad", "fastmap", "fda", "fds", "flexsurv", "flexsurvcure", "FNN", "fontawesome", "forecast", "foreign", "Formula", "fracdiff", "fs", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggtext", "glue", "gridExtra", "gridtext", "gtable", "hdrcde", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "isoband", "jpeg", "jquerylib", "jsonlite", "kernlab", "KernSmooth", "knitr", "ks", "labeling", "lattice", "lifecycle", "litedown", "lme4", "lmtest", "locfit", "lsoda", "magrittr", "markdown", "MASS", "Matrix", "MatrixModels", "maxstat", "mclust", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "mstate", "muhaz", "multcomp", "multicool", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "pcaPP", "pillar", "pkgconfig", "png", "polspline", "polynom", "pracma", "purrr", "quadprog", "quantreg", "R6", "rainbow", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RCurl", "Rdpack", "reformulas", "rlang", "rmarkdown", "rms", "rpart", "rstatix", "rstpm2", "rstudioapi", "S7", "sandwich", "sass", "scales", "sft", "SparseM", "statmod", "stringi", "stringr", "SuppDists", "survival", "survminer", "TH.data", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "vctrs", "viridisLite", "withr", "xfun", "xml2", "yaml", "zoo" ], "_vignettes": [ { "source": "PERSUADE_introduction.Rmd", "filename": "PERSUADE_introduction.html", "title": "Introduction to PERSUADE", "author": "Bram Ramaekers", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Install and load the PERSUADE package", "Example workflow", "Define analysis settings", "Running PERSUADE", "Inspecting results", "Generate diagnostic and model plots:", "Reporting", "Exporting model parameters", "Obtain Excel template", "Next steps" ], "created": "2025-09-09 07:13:26", "modified": "2025-09-26 12:55:09", "commits": 4 } ], "_score": 5.204119982655925, "_indexed": true, "_nocasepkg": "persuade", "_universes": [ "bram-r" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-05-09T08:48:02.000Z", "distro": "noble", "commit": "8b2a8c510d058152c11485657cc05540d64ecb09", "fileid": "8df73ba9ab27fff3390d7d9bd6768e1d99d357ec6b8746e64e969b1584d602c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287" }, { "r": "4.6.0", "os": "linux", "version": "0.1.2", "date": "2026-05-09T08:48:16.000Z", "distro": "noble", "commit": "8b2a8c510d058152c11485657cc05540d64ecb09", "fileid": "60b360092b638ead18c4b657e8971e2105230bc07c79872897653403aa7a8221", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-05-09T08:47:30.000Z", "commit": "8b2a8c510d058152c11485657cc05540d64ecb09", "fileid": "fe94e9f5c958669f51e5f3d0264d9885dc25df063f3fbfc8b8374b8cdbb4a572", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287" }, { "r": "4.6.0", "os": "mac", "version": "0.1.2", "date": "2026-05-09T08:46:44.000Z", "commit": "8b2a8c510d058152c11485657cc05540d64ecb09", "fileid": "4204b18f67170f1d2af76636af338f21187f511ea7b69fd471ab3e4b8117a684", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287" }, { "r": "4.7.0", "os": "win", "version": "0.1.2", "date": "2026-05-09T08:46:56.000Z", "commit": "8b2a8c510d058152c11485657cc05540d64ecb09", "fileid": "cbdb292504de22b0867d06e152f4c1349343f624523026831ae888fc49c28267", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287" }, { "r": "4.5.3", "os": "win", "version": "0.1.2", "date": "2026-05-09T08:46:16.000Z", "commit": "8b2a8c510d058152c11485657cc05540d64ecb09", "fileid": "0b2c19869af08efba87ecf7b0e22f250638874fd9ada9a560f9d1dcbcd79df4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287" }, { "r": "4.6.0", "os": "win", "version": "0.1.2", "date": "2026-05-09T08:47:59.000Z", "commit": "8b2a8c510d058152c11485657cc05540d64ecb09", "fileid": "0009beecf704cd0d4c72338d423415c001bfe6116fc0cd12e1a959eb28703a62", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.2", "date": "2026-05-22T13:02:54.000Z", "commit": "8b2a8c510d058152c11485657cc05540d64ecb09", "fileid": "82234497b1458b543532a2088130373ed2760b235f4f039c03dac6dcb405185c", "status": "success", "buildurl": "https://github.com/r-universe/bram-r/actions/runs/25596768287" } ] }