{ "_id": "6ad07551e2d863f662954ad3", "Package": "LSJM", "Title": "Estimate Location-Scale Joint Models", "Version": "0.1.1", "Authors@R": "c(person(\"Léonie\", \"Courcoul\", email =\"courcoul.leonie498@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Antoine\", \"Barbieri\", ,email = \"antoine.barbieri@u-bordeaux.fr\", role = c(\"aut\")),\nperson(\"Hélène\", \"Jacqmin-Gadda\", email = \"helene.jacqmin-gadda@u-bordeaux.fr\", role = c(\"aut\"))\n)", "Description": "Estimation of mixed models including a subject-specific\nvariance that can be time- and covariate-dependent or defined\nfor within- and between-visit variability. In the joint\nmodeling framework, the package handles left truncation,\ninterval censoring, and multistate models, and allows a\nflexible dependence structure between competing events and the\nlongitudinal marker. Estimation is performed in a frequentist\nframework using the Marquardt-Levenberg algorithm. Methods are\ndescribed in Courcoul et al. (2025) and\nin Courcoul et al. (2026) .", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-15 06:20:33 UTC", "User": "root" }, "Author": "Léonie Courcoul [aut, cre], Antoine Barbieri [aut], Hélène\nJacqmin-Gadda [aut]", "Maintainer": "Léonie Courcoul ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-09-14 21:30:07 UTC", "RemoteUrl": "https://github.com/cran/LSJM", "RemoteRef": "HEAD", "RemoteSha": "c28a350bb569c743595259f7ed51e7db9074ccf5", "_user": "cran", "_type": "src", "_file": "LSJM_0.1.1.tar.gz", "_fileid": "https://r2.ropensci.org/3af4c1d220e76407b3e869cf5131618c76a8ec43c37c01a88a3ffe332736bfff", "_filesize": 695026, "_sha256": "3af4c1d220e76407b3e869cf5131618c76a8ec43c37c01a88a3ffe332736bfff", "_expires": "2027-01-23T06:40:15.000Z", "_created": "2026-10-15T06:20:33.000Z", "_published": "2026-10-15T06:40:17.273Z", "_buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116281204249, "time": 544, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11953071424" }, { "job": 116281204262, "time": 588, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11953021601" }, { "job": 116281204239, "time": 539, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11952971763" }, { "job": 116281204382, "time": 617, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11952848941" }, { "job": 116278364535, "time": 540, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11952492292" }, { "job": 116281204195, "time": 285, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11952937764" }, { "job": 116281204315, "time": 744, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "11952349872" }, { "job": 116281204461, "time": 800, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11952824593" }, { "job": 116281204329, "time": 724, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11953076643" }, { "job": 116281204254, "time": 505, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11952868650" } ], "_upstream": "https://github.com/cran/LSJM", "_commit": { "id": "c28a350bb569c743595259f7ed51e7db9074ccf5", "author": "Léonie Courcoul ", "committer": "cran-robot ", "message": "version 0.1.1\n", "time": 1789421407 }, "_maintainer": { "name": "Léonie Courcoul", "email": "courcoul.leonie498@gmail.com", "login": "leoniecourcoul", "description": "", "uuid": 55279118 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "marqLevAlg", "role": "Imports" }, { "package": "survival", "role": "Imports" }, { "package": "flexsurv", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "spacefillr", "role": "Imports" }, { "package": "survminer", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "SmoothHazard", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "dplyr", "role": "Imports" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2026-32", "n": 1 }, { "week": "2026-38", "n": 1 } ], "_tags": [ { "name": "0.1.0", "date": "2026-08-04" }, { "name": "0.1.1", "date": "2026-09-14" } ], "_stars": 0, "_contributors": [ { "user": "leoniecourcoul", "count": 2, "uuid": 55279118 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 630, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 334, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/LSJM" }, "_searchresults": 0, "_topics": [ "openblas", "cpp" ], "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/LSJM.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/leoniecourcoul/lsjm", "_realowner": "leoniecourcoul", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2026-08-04" }, { "version": "0.1.1", "date": "2026-09-15" } ], "_exports": [ "dynpred", "lsjm", "lsmm", "ranef", "survmarg" ], "_datasets": [ { "name": "threeC", "title": "ThreeC dataset", "object": "threeC", "file": "threeC.RData", "class": [ "data.frame" ], "fields": [ "ID", "age.visit", "num.visit", "SBP", "age.final", "age0", "age.last", "age.first", "dem", "death", "sex", "Edu", "Apoe4", "age.visit65", "age.final65", "age0_65", "age.last65", "age.first65" ], "rows": 5248, "table": true, "tojson": true } ], "_help": [ { "page": "data.manag.long", "title": "Management of longitudinal data", "topics": [ "data.manag.long" ] }, { "page": "data.manag.sigma", "title": "Management of data for residual part", "topics": [ "data.manag.sigma" ] }, { "page": "data.manag.surv", "title": "Management of survival data", "topics": [ "data.manag.surv" ] }, { "page": "dynpred", "title": "dynpred: compute the dynamic predictions of an event.", "topics": [ "dynpred", "dynpred.lsjm_classicCR", "dynpred.lsjm_classicIDM", "dynpred.lsjm_classicSingle", "dynpred.lsjm_covDepCR", "dynpred.lsjm_covDepIDM", "dynpred.lsjm_covDepSingle", "dynpred.lsjm_interintraCR", "dynpred.lsjm_interintraIDM", "dynpred.lsjm_interintraSingle" ] }, { "page": "initial.long", "title": "Initialisation of Longitudinal Submodel", "topics": [ "initial.long" ] }, { "page": "lsjm", "title": "lsjm : Estimation of a location-scale joint model for longitudinal data with flexible subject-specific variability and complex survival structures", "topics": [ "lsjm" ] }, { "page": "lsmm", "title": "lsmm : Estimation of a linear mixed model for longitudinal data with flexible subject-specific variability.", "topics": [ "lsmm" ] }, { "page": "plot.lsjm", "title": "plot: Plot methods for 'lsjm' or 'lsmm' objects", "topics": [ "plot.lsjm", "plot.lsjm_classicCR", "plot.lsjm_classicIDM", "plot.lsjm_classicSingle", "plot.lsjm_covDepCR", "plot.lsjm_covDepIDM", "plot.lsjm_covDepSingle", "plot.lsjm_interintraCR", "plot.lsjm_interintraIDM", "plot.lsjm_interintraSingle", "plot.lsmm_classic", "plot.lsmm_covDep", "plot.lsmm_interintra" ] }, { "page": "predict.lsjm", "title": "predict: Prediction of some quantities for each subjects", "topics": [ "predict.lsjm", "predict.lsjm_classicCR", "predict.lsjm_classicIDM", "predict.lsjm_classicSingle", "predict.lsjm_covDepCR", "predict.lsjm_covDepIDM", "predict.lsjm_covDepSingle", "predict.lsjm_interintraCR", "predict.lsjm_interintraIDM", "predict.lsjm_interintraSingle", "predict.lsmm_classic", "predict.lsmm_covDep", "predict.lsmm_interintra" ] }, { "page": "ranef", "title": "ranef: the predicted random effects for all subjects", "topics": [ "ranef", "ranef.lsjm_classicCR", "ranef.lsjm_classicIDM", "ranef.lsjm_classicSingle", "ranef.lsjm_covDepCR", "ranef.lsjm_covDepIDM", "ranef.lsjm_covDepSingle", "ranef.lsjm_interintraCR", "ranef.lsjm_interintraIDM", "ranef.lsjm_interintraSingle", "ranef.lsmm_classic", "ranef.lsmm_covDep", "ranef.lsmm_interintra" ] }, { "page": "survmarg", "title": "The population-average probability of being free of any events at a given time $t$ and covariates", "topics": [ "survmarg", "survmarg.lsjm_classicCR", "survmarg.lsjm_classicIDM", "survmarg.lsjm_classicSingle", "survmarg.lsjm_covDepCR", "survmarg.lsjm_covDepIDM", "survmarg.lsjm_covDepSingle", "survmarg.lsjm_interintraCR", "survmarg.lsjm_interintraIDM", "survmarg.lsjm_interintraSingle" ] }, { "page": "threeC", "title": "ThreeC dataset", "topics": [ "threeC" ] } ], "_readme": "https://github.com/cran/LSJM/raw/HEAD/README.md", "_rundeps": [ "abind", "assertthat", "backports", "bbmle", "bdsmatrix", "boot", "broom", "car", "carData", "cli", "codetools", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "curl", "data.table", "Deriv", "deSolve", "diagram", "digest", "doBy", "doParallel", "dplyr", "exactRankTests", "farver", "fastGHQuad", "flexsurv", "foreach", "forecast", "Formula", "fracdiff", "future", "future.apply", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "ggtext", "globals", "glue", "gridExtra", "gridtext", "gtable", "isoband", "iterators", "jpeg", "KernSmooth", "labeling", "lattice", "lava", "lifecycle", "listenv", "litedown", "lme4", "lmtest", "lsoda", "magrittr", "markdown", "marqLevAlg", "MASS", "Matrix", "MatrixModels", "maxstat", "mgcv", "minqa", "modelr", "mstate", "muhaz", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "parallelly", "pbkrtest", "pillar", "pkgconfig", "png", "polynom", "prodlim", "progressr", "purrr", "quadprog", "quantreg", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "rlang", "rstatix", "rstpm2", "S7", "scales", "shape", "SmoothHazard", "spacefillr", "SparseM", "SQUAREM", "statmod", "stringi", "stringr", "survival", "survminer", "tibble", "tidyr", "tidyselect", "timeDate", "urca", "utf8", "vctrs", "viridisLite", "withr", "xfun", "xml2", "zoo" ], "_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": 2, "_indexed": false, "_nocasepkg": "lsjm", "_universes": [ "cran" ], "_indexurl": "https://leoniecourcoul.r-universe.dev/LSJM", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-10-15T06:28:44.000Z", "distro": "resolute", "arch": "aarch64", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/f8f9d450c441e964ec8f18ac0d8349ef3f12e6851fef9aba9fd6e4049799d7bc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" }, { "r": "4.7.0", "os": "linux", "version": "0.1.1", "date": "2026-10-15T06:28:31.000Z", "distro": "resolute", "arch": "x86_64", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/2d8d9bd533a90aa321975e76ab0af7a3d8ce2457701696860903e5a20be6528f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" }, { "r": "4.6.1", "os": "linux", "version": "0.1.1", "date": "2026-10-15T06:28:39.000Z", "distro": "resolute", "arch": "aarch64", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/a2187f6d14ce503e917bd15092b2d3587361922d064beff96d82c4b69970c1ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" }, { "r": "4.6.1", "os": "linux", "version": "0.1.1", "date": "2026-10-15T06:28:50.000Z", "distro": "resolute", "arch": "x86_64", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/089628236150b882715ab9853f32647074f361ce1cfee4ef83f44a945206af84", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.1", "date": "2026-10-15T06:29:04.000Z", "arch": "emscripten", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/dbd4045bca4ea8f5284d0ceb8f7cf3568c6510f69630490aaf8100623eaa6b4b", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-10-15T06:29:45.000Z", "arch": "aarch64", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/0a26a687684fe1c9c5440cf6bc9931092f0868d3f6fe239bcff15d519f0f40b1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" }, { "r": "4.7.0", "os": "win", "version": "0.1.1", "date": "2026-10-15T06:27:40.000Z", "arch": "x86_64", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/3483df5bb8f2d3c7eee73348bbe6a6e6edf3174fa9ed91c80d43d99ce044b1d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" }, { "r": "4.6.1", "os": "win", "version": "0.1.1", "date": "2026-10-15T06:29:56.000Z", "arch": "aarch64", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/28337f57f2b081f7f1dcb0307f30374aa475cd6382ff8fa3648c940040f0ed85", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" }, { "r": "4.6.1", "os": "win", "version": "0.1.1", "date": "2026-10-15T06:27:44.000Z", "arch": "x86_64", "commit": "c28a350bb569c743595259f7ed51e7db9074ccf5", "fileid": "https://r2.ropensci.org/b66b87246420b095d88ebfe11e5d6e8f9d6e8ee0719b334e878a37f6cdc236e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/38691505996" } ] }