{
  "_id": "6a27bab424555f66ed53a9b7",
  "Package": "mstate",
  "Version": "0.3.3",
  "Date": "2024-07-03",
  "Title": "Data Preparation, Estimation and Prediction in Multi-State\nModels",
  "Authors@R": "c(\nperson(\ngiven = \"Hein\",\nfamily = \"Putter\",\nrole = c(\"aut\", \"cre\"),\nemail = \"H.Putter@lumc.nl\"),\nperson(\ngiven = \"Liesbeth C.\",\nfamily = \"de Wreede\",\nrole = \"aut\"\n),\nperson(\ngiven = \"Marta\",\nfamily = \"Fiocco\",\nrole = \"aut\"\n),\nperson(\ngiven = \"Ronald B.\",\nfamily = \"Geskus\",\nrole = \"ctb\"\n),\nperson(\ngiven = \"Edouard F.\",\nfamily = \"Bonneville\",\nrole = \"aut\"\n),\nperson(\ngiven = \"Damjan\",\nfamily = \"Manevski\",\nrole = \"ctb\"\n)\n)",
  "Description": "Contains functions for data preparation, descriptives,\nhazard estimation and prediction with Aalen-Johansen or\nsimulation in competing risks and multi-state models, see\nPutter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.",
  "License": "GPL (>= 2)",
  "Encoding": "UTF-8",
  "URL": "https://github.com/hputter/mstate",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-09 06:49:04 UTC",
    "User": "root"
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  "RoxygenNote": "7.3.3",
  "BugReports": "https://github.com/hputter/mstate/issues",
  "VignetteBuilder": "knitr",
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  "Repository": "https://hputter.r-universe.dev",
  "Date/Publication": "2026-03-11 19:51:55 UTC",
  "RemoteUrl": "https://github.com/hputter/mstate",
  "RemoteRef": "HEAD",
  "RemoteSha": "406e5856790c1649a7bcf03fff9a0afa247e7265",
  "Author": "Hein Putter [aut, cre],\nLiesbeth C. de Wreede [aut],\nMarta Fiocco [aut],\nRonald B. Geskus [ctb],\nEdouard F. Bonneville [aut],\nDamjan Manevski [ctb]",
  "Maintainer": "Hein Putter <H.Putter@lumc.nl>",
  "MD5sum": "07fce9eb171db1b0a2b21d455bf61031",
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  "_created": "2026-06-09T06:49:04.000Z",
  "_published": "2026-06-09T11:31:16.031Z",
  "_distro": "noble",
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    "message": "Updating #41 ggplot syntax, need to create issue on crprep with strata, and need to cleanup results from devtools::check()\n",
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      "package": "rlang",
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      "package": "lattice",
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  "_realowner": "hputter",
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    {
      "version": "0.2.3",
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    "crprep",
    "Cuminc",
    "cutLMms",
    "ELOS",
    "etm2msdata",
    "events",
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    "haz_function",
    "is.circular",
    "LMAJ",
    "MarkovTest",
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    "msboot.relsurv",
    "msboot.relsurv.boot",
    "msdata2etm",
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    "msfit_subjects_to_msfit",
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    "probtrans_subjects",
    "redrank",
    "to.trans2",
    "tra2trans",
    "trans.comprisk",
    "trans.illdeath",
    "trans2Q",
    "trans2tra",
    "transMat",
    "varHaz.fixed",
    "vis.mirror.pt",
    "vis.multiple.pt",
    "xsect"
  ],
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      "name": "aidssi",
      "title": "Data from the Amsterdam Cohort Studies on HIV infection and AIDS",
      "object": "aidssi",
      "file": "aidssi.RData",
      "class": [
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      ],
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        "time",
        "status",
        "cause",
        "ccr5"
      ],
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      "table": true,
      "tojson": true
    },
    {
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      "object": "aidssi2",
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        "age.inf",
        "ccr5"
      ],
      "rows": 329,
      "table": true,
      "tojson": true
    },
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      "object": "bmt",
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      ],
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      "table": true,
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    },
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      "class": [
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      ],
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      ],
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        "age"
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      "tojson": true
    },
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        "age",
        "drmatch",
        "tcd"
      ],
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      "table": true,
      "tojson": true
    },
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      "name": "ebmt4",
      "title": "Data from the European Society for Blood and Marrow Transplantation (EBMT)",
      "object": "ebmt4",
      "file": "ebmt4.RData",
      "class": [
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        "rec",
        "rec.s",
        "ae",
        "ae.s",
        "recae",
        "recae.s",
        "rel",
        "rel.s",
        "srv",
        "srv.s",
        "year",
        "agecl",
        "proph",
        "match"
      ],
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      "table": true,
      "tojson": true
    },
    {
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      "title": "Abnormal prothrombin levels in liver cirrhosis",
      "object": "prothr",
      "file": "prothr.RData",
      "class": [
        "msdata",
        "data.frame"
      ],
      "fields": [
        "id",
        "from",
        "to",
        "trans",
        "Tstart",
        "Tstop",
        "status",
        "treat"
      ],
      "rows": 2152,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "mstate-package",
      "title": "Data preparation, estimation and prediction in multi-state models",
      "topics": [
        "mstate-package",
        "mstate"
      ]
    },
    {
      "page": "aidssi",
      "title": "Data from the Amsterdam Cohort Studies on HIV infection and AIDS",
      "topics": [
        "aidssi",
        "aidssi2"
      ]
    },
    {
      "page": "bmt",
      "title": "BMT data from Klein and Moeschberger",
      "topics": [
        "bmt"
      ]
    },
    {
      "page": "crprep.default",
      "title": "Function to create weighted data set for competing risks analyses",
      "topics": [
        "crprep",
        "crprep.default"
      ]
    },
    {
      "page": "Cuminc",
      "title": "Calculate nonparametric cumulative incidence functions and associated standard errors",
      "topics": [
        "Cuminc",
        "print.Cuminc"
      ]
    },
    {
      "page": "cutLMms",
      "title": "Cut a multi-state data set at a landmark time point",
      "topics": [
        "cutLMms"
      ]
    },
    {
      "page": "EBMT-cause-of-death-data",
      "title": "Data from the European Society for Blood and Marrow Transplantation (EBMT)",
      "topics": [
        "EBMT cause of death data",
        "ebmt2"
      ]
    },
    {
      "page": "EBMT-data",
      "title": "Data from the European Society for Blood and Marrow Transplantation (EBMT)",
      "topics": [
        "EBMT data",
        "ebmt4"
      ]
    },
    {
      "page": "EBMT-platelet-recovery-data",
      "title": "Data from the European Society for Blood and Marrow Transplantation (EBMT)",
      "topics": [
        "EBMT platelet recovery data",
        "ebmt3"
      ]
    },
    {
      "page": "EBMT-year-of-relapse-data",
      "title": "Data from the European Society for Blood and Marrow Transplantation (EBMT)",
      "topics": [
        "EBMT year of relapse data",
        "ebmt1"
      ]
    },
    {
      "page": "ELOS",
      "title": "Expected length of stay",
      "topics": [
        "ELOS"
      ]
    },
    {
      "page": "etm2msdata",
      "title": "Converts between etm and msdata format",
      "topics": [
        "etm2msdata",
        "tra2trans"
      ]
    },
    {
      "page": "events",
      "title": "Count number of observed transitions",
      "topics": [
        "events"
      ]
    },
    {
      "page": "expand.covs",
      "title": "Expand covariates in competing risks dataset in stacked format",
      "topics": [
        "expand.covs",
        "expand.covs.default"
      ]
    },
    {
      "page": "expand.covs.msdata",
      "title": "Expand covariates in multi-state dataset in long format",
      "topics": [
        "expand.covs.msdata"
      ]
    },
    {
      "page": "haz_function",
      "title": "Helper function that calculates excess and population hazards for a given transition",
      "topics": [
        "haz_function"
      ]
    },
    {
      "page": "Liver-cirrhosis-data",
      "title": "Abnormal prothrombin levels in liver cirrhosis",
      "topics": [
        "Liver cirrhosis data",
        "prothr"
      ]
    },
    {
      "page": "LMAJ",
      "title": "Landmark Aalen-Johansen method",
      "topics": [
        "LMAJ"
      ]
    },
    {
      "page": "MarkovTest",
      "title": "Log-rank based test for the validity of the Markov assumption",
      "topics": [
        "MarkovTest",
        "optimal_weights_matrix",
        "optimal_weights_multiple"
      ]
    },
    {
      "page": "modify_transMat",
      "title": "Upgrade the transMat object for the multi-state/relsurv setting.",
      "topics": [
        "modify_transMat"
      ]
    },
    {
      "page": "msboot",
      "title": "Bootstrap function in multi-state models",
      "topics": [
        "msboot"
      ]
    },
    {
      "page": "msboot.relsurv",
      "title": "Bootstrap function for upgraded multi-state models using relsurv",
      "topics": [
        "msboot.relsurv"
      ]
    },
    {
      "page": "msboot.relsurv.boot",
      "title": "Default theta function used for msboot.relsurv",
      "topics": [
        "msboot.relsurv.boot"
      ]
    },
    {
      "page": "msdata2etm",
      "title": "msdata to etm format",
      "topics": [
        "msdata2etm"
      ]
    },
    {
      "page": "msfit",
      "title": "Compute subject-specific transition hazards with (co-)variances",
      "topics": [
        "msfit"
      ]
    },
    {
      "page": "msfit_subjects",
      "title": "Compute subject-specific transition hazards for multiple subjects at once",
      "topics": [
        "msfit_subjects"
      ]
    },
    {
      "page": "msfit_subjects_to_msfit",
      "title": "Obtain an 'msfit' object for a single subject from an 'msfit.subjects' object.",
      "topics": [
        "msfit_subjects_to_msfit"
      ]
    },
    {
      "page": "msfit.relsurv",
      "title": "Extend a multi-state model using relative survival",
      "topics": [
        "msfit.relsurv"
      ]
    },
    {
      "page": "msprep",
      "title": "Function to prepare dataset for multi-state modeling in long format from dataset in wide format",
      "topics": [
        "msprep"
      ]
    },
    {
      "page": "mssample",
      "title": "Sample paths through a multi-state model",
      "topics": [
        "mssample"
      ]
    },
    {
      "page": "paths",
      "title": "Find all possible trajectories through a given multi-state model",
      "topics": [
        "paths"
      ]
    },
    {
      "page": "plot.Cuminc",
      "title": "Plot method for Cuminc objects",
      "topics": [
        "plot.Cuminc"
      ]
    },
    {
      "page": "plot.MarkovTest",
      "title": "Plot method for a MarkovTest object",
      "topics": [
        "plot.MarkovTest"
      ]
    },
    {
      "page": "plot.msfit",
      "title": "Plot method for an msfit object",
      "topics": [
        "plot.msfit"
      ]
    },
    {
      "page": "plot.msfit.subjects",
      "title": "Plot method for an msfit.subjects object",
      "topics": [
        "plot.msfit.subjects"
      ]
    },
    {
      "page": "plot.probtrans",
      "title": "Plot method for a probtrans object",
      "topics": [
        "plot.probtrans"
      ]
    },
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