{ "_id": "6a49fd089a7b00bcc12f5ff4", "Package": "JMH", "Type": "Package", "Title": "Joint Model of Heterogeneous Repeated Measures and Survival Data", "Version": "1.0.4", "Date": "2026-03-29", "Authors@R": "c(\nperson(\"Shanpeng\", \"Li\", email = \"lishanpeng0913@ucla.edu\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Gang\", \"Li\", email = \"vli@ucla.edu\",\nrole = \"ctb\")\n)", "Maintainer": "Shanpeng Li ", "Description": "Maximum likelihood estimation for the semi-parametric\njoint modeling of competing risks and longitudinal data in the\npresence of heterogeneous within-subject variability, proposed\nby Li and colleagues (2023) .\nThe proposed method models the within-subject variability of\nthe biomarker and associates it with the risk of the competing\nrisks event. The time-to-event data is modeled using a\n(cause-specific) Cox proportional hazards regression model with\ntime-fixed covariates. The longitudinal outcome is modeled\nusing a mixed-effects location and scale model. The association\nis captured by shared random effects. The model is estimated\nusing an Expectation Maximization algorithm. This is the final\nrelease of the 'JMH' package. Active development has been moved\nto the 'FastJM' package, which provides improved functionality\nand ongoing support. Users are strongly encouraged to\ntransition to 'FastJM'.", "License": "GPL (>= 3)", "NeedsCompilation": "yes", "RoxygenNote": "7.3.2", "Language": "en-US", "LazyData": "true", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev", "Repository": "https://shanpengli.r-universe.dev", "Date/Publication": "2026-04-02 05:22:23 UTC", "RemoteUrl": "https://github.com/shanpengli/jmh", "RemoteRef": "HEAD", "RemoteSha": "7a69edb461f6b085194e03e69469c1a9486e935b", "Packaged": { "Date": "2026-07-05 06:30:02 UTC", "User": "root" }, "Author": "Shanpeng Li [aut, cre],\nGang Li [ctb]", "_user": "shanpengli", "_type": "src", "_file": "JMH_1.0.4.tar.gz", "_fileid": "https://r2.ropensci.org/d419704ae979bfb1bf1d35c3d4f007a818d6ac2e29b64dbead80893019effc2d", "_filesize": 268783, "_sha256": "d419704ae979bfb1bf1d35c3d4f007a818d6ac2e29b64dbead80893019effc2d", "_expires": "2026-10-13T06:43:18.000Z", "_created": "2026-07-05T06:30:02.000Z", "_published": "2026-07-05T06:43:20.615Z", "_jobs": [ { "job": 85199563931, "time": 331, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "8089121944" }, { "job": 85199563907, "time": 372, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8089126064" }, { "job": 85199563916, "time": 324, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8089120953" }, { "job": 85199563915, "time": 386, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8089127684" }, { "job": 85199563920, "time": 290, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8089112137" }, { "job": 85199563934, "time": 596, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "8089149629" }, { "job": 85199563921, "time": 275, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8089111262" }, { "job": 85199563923, "time": 519, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8089141419" }, { "job": 85199194015, "time": 367, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8089080808" }, { "job": 85199563885, "time": 307, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8089118664" }, { "job": 85199563908, "time": 423, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8089131972" }, { "job": 85199563899, "time": 426, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8089132340" }, { "job": 85199563912, "time": 416, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8089131423" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673", "_status": "success", "_upstream": "https://github.com/shanpengli/jmh", "_commit": { "id": "7a69edb461f6b085194e03e69469c1a9486e935b", "author": "Shanpeng Li ", "committer": "Shanpeng Li ", "message": "small fix\n", "time": 1775107343 }, "_maintainer": { "name": "Shanpeng Li", "email": "lishanpeng0913@ucla.edu", "login": "shanpengli", "description": "Ph.D. in Biostatistics", "uuid": 18046660 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "survival", "role": "Depends" }, { "package": "nlme", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "MASS", "role": "Depends" }, { "package": "statmod", "role": "Depends" }, { "package": "magrittr", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.7", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "pec", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" } ], "_owner": "shanpengli", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-14", "n": 7 } ], "_tags": [], "_stars": 3, "_contributors": [ { "user": "shanpengli", "count": 3, "uuid": 18046660 }, { "user": "andrjohns", "count": 1, "uuid": 27717896 } ], "_userbio": { "uuid": 18046660, "type": "user", "name": "Shanpeng Li", "followers": 1, "description": "Ph.D. in Biostatistics" }, "_downloads": { "count": 341, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/JMH" }, "_devurl": "https://github.com/shanpengli/jmh", "_searchresults": 2, "_topics": [ "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/JMH.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/shanpengli/jmh", "_realowner": "shanpengli", "_cranurl": true, "_releases": [ { "version": "1.0.2", "date": "2023-06-15" }, { "version": "1.0.3", "date": "2024-02-20" }, { "version": "1.0.4", "date": "2026-04-02" } ], "_exports": [ "AUCJMMLSM", "ConcordanceJMMLSM", "JMMLSM", "MAEQJMMLSM", "PEJMMLSM", "survfitJMMLSM" ], "_datasets": [ { "name": "cdata", "title": "Simulated competing risks data", "object": "cdata", "class": [ "data.frame" ], "fields": [ "ID", "survtime", "cmprsk", "var1", "var2", "var3" ], "rows": 200, "table": true, "tojson": true }, { "name": "ydata", "title": "Simulated longitudinal data", "object": "ydata", "class": [ "data.frame" ], "fields": [ "ID", "Y", "time", "Z1", "Z2", "Z3" ], "rows": 1353, "table": true, "tojson": true } ], "_help": [ { "page": "AUCJMMLSM", "title": "Time-dependent AUC for joint models", "topics": [ "AUCJMMLSM" ] }, { "page": "cdata", "title": "Simulated competing risks data", "topics": [ "cdata" ] }, { "page": "ConcordanceJMMLSM", "title": "Concordance for joint models", "topics": [ "ConcordanceJMMLSM" ] }, { "page": "JMMLSM", "title": "Joint Modeling for Continuous outcomes", "topics": [ "JMMLSM" ] }, { "page": "MAEQJMMLSM", "title": "A metric of prediction accuracy of joint model by comparing the predicted risk with the empirical risks stratified on different predicted risk group.", "topics": [ "MAEQJMMLSM" ] }, { "page": "PEJMMLSM", "title": "A metric of prediction accuracy of joint model by comparing the predicted risk with the counting process.", "topics": [ "PEJMMLSM" ] }, { "page": "plot.survfitJMMLSM", "title": "Plot conditional probabilities for new subjects", "topics": [ "plot.survfitJMMLSM" ] }, { "page": "print.JMMLSM", "title": "Print JMMLSM", "topics": [ "print.JMMLSM" ] }, { "page": "print.survfitJMMLSM", "title": "Print survfitJMMLSM", "topics": [ "print.survfitJMMLSM" ] }, { "page": "summary", "title": "Summaries of evaluation metrics for joint models", "topics": [ "summary", "summary.AUCJMMLSM", "summary.ConcordanceJMMLSM", "summary.JMMLSM", "summary.MAEQJMMLSM", "summary.PEJMMLSM" ] }, { "page": "survfitJMMLSM", "title": "Prediction in Joint Models", "topics": [ "survfitJMMLSM" ] }, { "page": "vcov", "title": "Variance-covariance matrix of the estimated parameters for joint models", "topics": [ "vcov", "vcov.JMMLSM" ] }, { "page": "ydata", "title": "Simulated longitudinal data", "topics": [ "ydata" ] } ], "_readme": "https://github.com/shanpengli/jmh/raw/HEAD/README.md", "_rundeps": [ "backports", "base64enc", "bslib", "cachem", "caret", "checkmate", "class", "cli", "clock", "cluster", "cmprsk", "codetools", "colorspace", "cpp11", "data.table", "diagram", "digest", "doParallel", "dplyr", "e1071", "evaluate", "farver", "fastmap", "fontawesome", "foreach", "foreign", "Formula", "fs", "future", "future.apply", "generics", "ggplot2", "glmnet", "globals", "glue", "gower", "gridExtra", "gtable", "hardhat", "highr", "Hmisc", "htmlTable", "htmltools", "htmlwidgets", "ipred", "isoband", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lattice", "lava", "lifecycle", "listenv", "lubridate", "magrittr", "MASS", "Matrix", "MatrixModels", "memoise", "mets", "mime", "ModelMetrics", "multcomp", "mvtnorm", "nlme", "nnet", "numDeriv", "parallelly", "pec", "pillar", "pkgconfig", "plotrix", "plyr", "polspline", "pROC", "prodlim", "progressr", "proxy", "Publish", "purrr", "quantreg", "R6", "ranger", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "recipes", "reshape2", "riskRegression", "rlang", "rmarkdown", "rms", "rpart", "rstudioapi", "S7", "sandwich", "sass", "scales", "shape", "SparseM", "sparsevctrs", "SQUAREM", "statmod", "stringi", "stringr", "survival", "TH.data", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "timereg", "tinytex", "tzdb", "utf8", "vctrs", "viridisLite", "withr", "xfun", "yaml", "zoo" ], "_sysdeps": [ { "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": 3.1760912590556813, "_indexed": true, "_nocasepkg": "jmh", "_universes": [ "shanpengli" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.4", "date": "2026-07-05T06:35:27.000Z", "distro": "resolute", "arch": "aarch64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/d4eed18b806e75c1548921382d182332bf33adee5754c18802c687be1cb44667", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.7.0", "os": "linux", "version": "1.0.4", "date": "2026-07-05T06:35:22.000Z", "distro": "resolute", "arch": "x86_64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/0c3a05904d2d6904a0086a42294d38a2e24d0af1588aff9845d22bebc1ff8fd2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.6.1", "os": "linux", "version": "1.0.4", "date": "2026-07-05T06:35:25.000Z", "distro": "resolute", "arch": "aarch64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/0119c9bd1d3e95e798762133084c3504f3395c03de883644a8c06a5fa6784bea", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.6.1", "os": "linux", "version": "1.0.4", "date": "2026-07-05T06:35:29.000Z", "distro": "resolute", "arch": "x86_64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/78bbc8c4c3fe1d3195a561098714e5406b4aa61d97c3d9c1cf2c406665f80d7f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.5.3", "os": "mac", "version": "1.0.4", "date": "2026-07-05T06:35:05.000Z", "arch": "aarch64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/de0891f72bee332cf7a8b33a39d880ceb426ee09f9ef9cf7fc868dbaf6c7c6f1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.5.3", "os": "mac", "version": "1.0.4", "date": "2026-07-05T06:36:55.000Z", "arch": "x86_64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/0c383a57dcea47c9ae7eff31e3edc1af99af44a9b5be2360be0a169396960150", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.6.1", "os": "mac", "version": "1.0.4", "date": "2026-07-05T06:34:38.000Z", "arch": "aarch64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/15d67bcf42b8af2cf1e3303ea5b8aaf930fa165132127f692f23f95b4d28c719", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.6.1", "os": "mac", "version": "1.0.4", "date": "2026-07-05T06:36:02.000Z", "arch": "x86_64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/eb67ee0b71db67fbfee4f889878dda684c1c522d8a083d7d74bd93488b4c6297", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.4", "date": "2026-07-05T06:36:02.000Z", "arch": "emscripten", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/abb5c7f7021a052c7c49353d3f2efaccd3611d67a525272a4c03a7175f06971f", "status": "success", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.7.0", "os": "win", "version": "1.0.4", "date": "2026-07-05T06:34:24.000Z", "arch": "x86_64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/61f1dfea31314d873282e903e55c5a4726269a07ad2598830242223f5f7ceaed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.5.3", "os": "win", "version": "1.0.4", "date": "2026-07-05T06:34:10.000Z", "arch": "x86_64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/16e26b351560a2b17b9626e9664b49c40ee52181b556d4bad598a30cfb38b706", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" }, { "r": "4.6.1", "os": "win", "version": "1.0.4", "date": "2026-07-05T06:34:17.000Z", "arch": "x86_64", "commit": "7a69edb461f6b085194e03e69469c1a9486e935b", "fileid": "https://r2.ropensci.org/42bc6f5dfc33daaebe1ec51204f2841a1a06e6af29045277fca637cd7a504f4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/shanpengli/actions/runs/28731958673" } ] }