{ "_id": "6acdffbaa14063b82c3ae3b0", "Package": "hdcuremodels", "Title": "High-Dimensional Cure Models", "Version": "0.0.8", "Date": "2026-05-17", "Authors@R": "c(person(\"Han\", \"Fu\", role = \"aut\"), person(c(\"Kellie J.\"), \"Archer\", email=\n\"archer.43@osu.edu\", role = c(\"aut\",\"cre\"), comment = c(ORCID=\"0000-0003-1555-5781\")),\nperson(\"Tung Lam\", \"Nguyen\", email = \"nguyenlamtung10@gmail.com\", role = \"rev\", comment = \"Reviewed the package for ROpenSci\"),\nperson(\"Panagiotis\", \"Papastamoulis\", email = \"papapast@yahoo.gr\", role = \"rev\", comment = \"Reviewed the package for ROpenSci\"))", "Description": "Provides functions for fitting various penalized\nparametric and semi-parametric mixture cure models with\ndifferent penalty functions, testing for a significant cure\nfraction, and testing for sufficient follow-up as described in\nFu et al (2022) and Archer et al\n(2024). False discovery rate\ncontrolled variable selection is provided using model-X\nknock-offs.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Config/Roxygen": "list(markdown = TRUE, roclets = c(\"namespace\", \"rd\",\n\"srr::srr_stats_roclet\"))", "Config/Remotes": "ropensci-review-tools/srr", "VignetteBuilder": "knitr", "LazyData": "true", "URL": "https://github.com/ropensci/hdcuremodels", "BugReports": "https://github.com/ropensci/hdcuremodels/issues", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-13 09:45:56 UTC", "User": "root" }, "Author": "Han Fu [aut], Kellie J. Archer [aut, cre] (ORCID:\n), Tung Lam Nguyen [rev]\n(Reviewed the package for ROpenSci), Panagiotis Papastamoulis\n[rev] (Reviewed the package for ROpenSci)", "Maintainer": "Kellie J. Archer ", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://kelliejarcher.r-universe.dev", "Date/Publication": "2026-05-18 08:55:23 UTC", "RemoteUrl": "https://github.com/cran/hdcuremodels", "RemoteRef": "HEAD", "RemoteSha": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "_user": "kelliejarcher", "_type": "src", "_file": "hdcuremodels_0.0.8.tar.gz", "_fileid": "https://r2.ropensci.org/61be4329c2abf312d6f62eb925cfcfe7624349edf7ad959ae68f50047beab3e6", "_filesize": 2495373, "_sha256": "61be4329c2abf312d6f62eb925cfcfe7624349edf7ad959ae68f50047beab3e6", "_expires": "2027-01-21T09:54:00.000Z", "_created": "2026-10-13T09:45:56.000Z", "_published": "2026-10-13T09:54:02.399Z", "_buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 115233464582, "time": 375, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11802362427" }, { "job": 115233464543, "time": 362, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11803360228" }, { "job": 115233464844, "time": 236, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11802177879" }, { "job": 115233464512, "time": 318, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11802437266" }, { "job": 115231800226, "time": 250, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11802475998" }, { "job": 115233464676, "time": 133, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11802281970" }, { "job": 115233464885, "time": 434, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11802577536" }, { "job": 115233464881, "time": 371, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11803355213" }, { "job": 115233464638, "time": 367, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11802781253" } ], "_upstream": "https://github.com/cran/hdcuremodels", "_commit": { "id": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "author": "Kellie J. Archer ", "committer": "cran-robot ", "message": "version 0.0.8\n", "time": 1779094523 }, "_maintainer": { "name": "Kellie J. Archer", "email": "archer.43@osu.edu", "login": "kelliejarcher", "description": "", "uuid": 85199330, "orcid": "0000-0003-1555-5781" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "doParallel", "role": "Imports" }, { "package": "flexsurv", "role": "Imports" }, { "package": "flexsurvcure", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "knockoff", "role": "Imports" }, { "package": "mvnfast", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "plyr", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "Rdsdp", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-49", "n": 1 }, { "week": "2026-20", "n": 1 }, { "week": "2026-21", "n": 1 } ], "_tags": [ { "name": "0.0.6", "date": "2025-12-03" }, { "name": "0.0.7", "date": "2026-05-15" }, { "name": "0.0.8", "date": "2026-05-18" } ], "_stars": 0, "_contributors": [ { "user": "kelliejarcher", "count": 5, "uuid": 85199330 } ], "_userbio": { "uuid": 85199330, "type": "user", "name": "kelliejarcher", "followers": 4 }, "_downloads": { "count": 382, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/hdcuremodels" }, "_devurl": "https://github.com/ropensci/hdcuremodels", "_pkgdown": "https://docs.ropensci.org/hdcuremodels", "_searchresults": 7, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/hdcuremodels.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_realowner": "ropensci", "_cranurl": false, "_releases": [ { "version": "0.0.1", "date": "2024-06-14" }, { "version": "0.0.5", "date": "2025-08-01" }, { "version": "0.0.6", "date": "2025-12-11" }, { "version": "0.0.7", "date": "2026-05-15" }, { "version": "0.0.8", "date": "2026-05-18" } ], "_exports": [ "auc_mcm", "concordance_mcm", "cure_estimate", "cureem", "curegmifs", "cv_cureem", "cv_curegmifs", "generate_cure_data", "nonzerocure_test", "sufficient_fu_test" ], "_datasets": [ { "name": "amltest", "title": "AML test data", "object": "amltest", "class": [ "data.frame" ], "fields": [], "rows": 40, "table": true, "tojson": true }, { "name": "amltrain", "title": "AML training data", "object": "amltrain", "class": [ "data.frame" ], "fields": [], "rows": 306, "table": true, "tojson": true }, { "name": "pediatric_flt3", "title": "Pediatric acute myeloid leukemia patients with FLT3-ITD rearrangement data", "object": "pediatric_flt3", "class": [ "data.frame" ], "fields": [], "rows": 246, "table": true, "tojson": true } ], "_help": [ { "page": "amltest", "title": "AML test data", "topics": [ "amltest" ] }, { "page": "amltrain", "title": "AML training data", "topics": [ "amltrain" ] }, { "page": "auc_mcm", "title": "AUC for cure prediction using mean score imputation", "topics": [ "auc_mcm" ] }, { "page": "coef.mixturecure", "title": "Extract model coefficients from a fitted mixturecure object", "topics": [ "coef.mixturecure", "coefficients" ] }, { "page": "concordance_mcm", "title": "C-statistic for mixture cure models", "topics": [ "concordance_mcm" ] }, { "page": "cure_estimate", "title": "Estimate cured fraction", "topics": [ "cure_estimate" ] }, { "page": "cureem", "title": "Fit penalized mixture cure model using the E-M algorithm", "topics": [ "cureem" ] }, { "page": "curegmifs", "title": "Fit penalized parametric mixture cure model using the GMIFS algorithm", "topics": [ "curegmifs" ] }, { "page": "cv_cureem", "title": "Fit penalized mixture cure model using the E-M algorithm with cross-validation for parameter tuning", "topics": [ "cv_cureem" ] }, { "page": "cv_curegmifs", "title": "Fit a penalized parametric mixture cure model using the generalized monotone incremental forward stagewise (GMIFS) algorithm (Hastie et al 2007) with cross-validation for model selection", "topics": [ "cv_curegmifs" ] }, { "page": "dim.mixturecure", "title": "Dimension method for mixturecure objects", "topics": [ "dim.mixturecure" ] }, { "page": "family.mixturecure", "title": "Return model family and fitting algorithm for mixturecure model fits", "topics": [ "family.mixturecure" ] }, { "page": "formula.mixturecure", "title": "Extract model formula for mixturecure object", "topics": [ "formula.mixturecure" ] }, { "page": "generate_cure_data", "title": "Simulate data under a mixture cure model", "topics": [ "generate_cure_data" ] }, { "page": "logLik.mixturecure", "title": "Log-likelihood for fitted mixture cure model", "topics": [ "logLik.mixturecure" ] }, { "page": "nobs.mixturecure", "title": "Number of observations in mixturecure object", "topics": [ "nobs.mixturecure" ] }, { "page": "nonzerocure_test", "title": "Non-parametric test for a non-zero cured fraction", "topics": [ "nonzerocure_test" ] }, { "page": "npar_mixturecure", "title": "Number of parameters in fitted mixture cure model", "topics": [ "npar_mixturecure" ] }, { "page": "pediatric_flt3", "title": "Pediatric acute myeloid leukemia patients with FLT3-ITD rearrangement data", "topics": [ "pediatric_flt3" ] }, { "page": "plot.mixturecure", "title": "Plot fitted mixture cure model", "topics": [ "plot.mixturecure" ] }, { "page": "predict.mixturecure", "title": "Predicted probabilities for susceptibles, linear predictor for latency, and risk class for latency for mixture cure fit", "topics": [ "predict.mixturecure" ] }, { "page": "print.mixturecure", "title": "Print the contents of a mixture cure fitted object", "topics": [ "print.mixturecure" ] }, { "page": "sufficient_fu_test", "title": "Test for sufficient follow-up", "topics": [ "sufficient_fu_test" ] }, { "page": "summary.mixturecure", "title": "Summarize a fitted mixture cure object", "topics": [ "summary.mixturecure" ] } ], "_readme": "https://github.com/cran/hdcuremodels/raw/HEAD/README.md", "_rundeps": [ "abind", "assertthat", "backports", "bbmle", "bdsmatrix", "BH", "boot", "broom", "car", "carData", "cli", "codetools", "colorspace", "corpcor", "corrplot", "cowplot", "cpp11", "data.table", "Deriv", "deSolve", "doBy", "doParallel", "dplyr", "farver", "fastGHQuad", "flexsurv", "flexsurvcure", "foreach", "forecast", "Formula", "fracdiff", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glmnet", "glue", "gridExtra", "gtable", "gtools", "isoband", "iterators", "knockoff", "labeling", "lattice", "lifecycle", "lme4", "lmtest", "lsoda", "magrittr", "MASS", "Matrix", "MatrixModels", "mgcv", "minqa", "modelr", "mstate", "muhaz", "mvnfast", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "pbkrtest", "pillar", "pkgconfig", "plyr", "polynom", "purrr", "quadprog", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "Rdsdp", "reformulas", "rlang", "RSpectra", "rstatix", "rstpm2", "S7", "scales", "shape", "SparseM", "statmod", "stringi", "stringr", "survival", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "zoo" ], "_vignettes": [ { "source": "hdcuremodels.Rmd", "filename": "hdcuremodels.html", "title": "Estimating Cure Models in High Dimensions: A Guide with hdcuremodels", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Package description", "Data examples", "Assessing model assumptions for fitting a mixture cure model", "Penalized mixture cure models", "Fitting penalized mixture cure models using GMIFS", "Fitting penalized mixture cure models using E-M algorithm", "Cross-validation", "Other Package Functions", "Comparison to other mixture cure modeling packages", "Conclusions", "References" ], "created": "2025-07-31 21:02:06", "modified": "2025-12-03 17:50:02", "commits": 2 } ], "_score": 3.1760912590556813, "_indexed": false, "_nocasepkg": "hdcuremodels", "_universes": [ "kelliejarcher" ], "_indexurl": "https://ropensci.r-universe.dev/hdcuremodels", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.0.8", "date": "2026-10-13T09:48:47.000Z", "distro": "resolute", "commit": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "fileid": "https://r2.ropensci.org/85f58a9ca7f865d69dba4656495c5c0547e3e48e842ee10c8e32bd35adb16127", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664" }, { "r": "4.6.1", "os": "linux", "version": "0.0.8", "date": "2026-10-13T09:48:48.000Z", "distro": "resolute", "commit": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "fileid": "https://r2.ropensci.org/624c0ec7e9ecd9784cc9b75a607471fb248ccf8680906867342c2101ec9e81f9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664" }, { "r": "4.5.3", "os": "mac", "version": "0.0.8", "date": "2026-10-13T09:49:01.000Z", "commit": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "fileid": "https://r2.ropensci.org/dfaa15470ad60ee4e0f3c6c5f7cbcd26274325640c9a797dc1e144ba26876a37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664" }, { "r": "4.6.1", "os": "mac", "version": "0.0.8", "date": "2026-10-13T09:48:53.000Z", "commit": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "fileid": "https://r2.ropensci.org/73697cf81a677e8501ac744e259a3c37aada9c06ea6dfa1b7083445421dc2f2f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664" }, { "r": "4.6.0", "os": "wasm", "version": "0.0.8", "date": "2026-10-13T09:48:35.000Z", "commit": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "fileid": "https://r2.ropensci.org/914450780d30857ac710a6d42f41e3a02e2c97a54b2d33d1a9e3341328f81ac4", "status": "success", "buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664" }, { "r": "4.7.0", "os": "win", "version": "0.0.8", "date": "2026-10-13T09:49:09.000Z", "commit": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "fileid": "https://r2.ropensci.org/95121b8d2f3c50da7b5c256228180cefacfda73d3e08f13be130de4a866c0d6e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664" }, { "r": "4.5.3", "os": "win", "version": "0.0.8", "date": "2026-10-13T09:47:40.000Z", "commit": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "fileid": "https://r2.ropensci.org/2321dd9d7124a347a58f69b2bddad00ae5c53c225ca54265750687f1a44ded6b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664" }, { "r": "4.6.1", "os": "win", "version": "0.0.8", "date": "2026-10-13T09:47:41.000Z", "commit": "44337bfec4ebaaf7a83aac5262b0a9e1cb8bf17c", "fileid": "https://r2.ropensci.org/91bf734951ee44611ca49b56e3a0d1f085f429b80e565638fcc79e67b3085834", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/kelliejarcher/actions/runs/38378164664" } ] }