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  "Title": "Empirical Bayes Multi-State Cox Model",
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  "Description": "Implements an empirical Bayes, multi-state Cox model for\nsurvival analysis. Run \"?'ebmstate-package'\" for details. See\nalso Schall (1991) <doi:10.1093/biomet/78.4.719>.",
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  "Author": "Rui Costa [aut, cre], Moritz Gerstung [aut], Terry M Therneau\n[ctb] (author of 'survival', a package from which code parts\nwere copied), Thomas Lumley [ctb] (contributor to 'survival', a\npackage from which code parts were copied), Hein Putter [ctb]\n(co-author of 'mstate', a package from which code parts were\ncopied), Liesbeth de Wreede [ctb] (co-author of 'mstate', a\npackage from which code parts were copied), Marta Fiocco [ctb]\n(co-author of 'mstate', a package from which code parts were\ncopied), Ronald Geskus [ctb] (contributor to 'mstate', a\npackage from which code parts were copied)",
  "Maintainer": "Rui Costa <ruibarrigana@hotmail.com>",
  "Repository": "https://ruibarrigana.r-universe.dev",
  "Date/Publication": "2024-10-19 14:20:01 UTC",
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  "_topics": [
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
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  "_realowner": "ruibarrigana",
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      "date": "2020-08-19"
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      "date": "2023-12-04"
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    "CoxRFX",
    "loo_ebmstate",
    "msfit_generic",
    "probtrans_ebmstate",
    "probtrans_fft",
    "probtrans_mstate"
  ],
  "_datasets": [
    {
      "name": "coxrfx_object_sample",
      "title": "Example of an empirical Bayes model fit",
      "object": "coxrfx_object_sample",
      "class": [
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        "coxph.penal",
        "coxph"
      ],
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      "table": false,
      "tojson": false
    },
    {
      "name": "msfit_object_sample",
      "title": "Estimated cumulative hazard rates under an empirical Bayes Cox model (example)",
      "object": "msfit_object_sample",
      "class": [
        "msfit",
        "coxrfx"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mstate_data",
      "title": "An example of long-format multistate data",
      "object": "mstate_data",
      "class": [
        "data.frame"
      ],
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        "id",
        "from",
        "to",
        "trans",
        "Tstart",
        "Tstop",
        "time",
        "status",
        "ASXL1",
        "DNMT3A",
        "RUNX1",
        "SF3B1",
        "SRSF2",
        "TET2",
        "TP53",
        "U2AF1",
        "del5q",
        "other",
        "complex",
        "age_log",
        "sex",
        "pb_cytopenia",
        "hb",
        "anc_log",
        "plt_log",
        "bm_blasts_logit",
        "ring_sideroblasts_logit",
        "ipss",
        "who_simple_factor.RA",
        "who_simple_factor.RARS",
        "who_simple_factor.RCMD",
        "who_simple_factor.RCMD.RS",
        "who_simple_factor.RAEB",
        "who_simple_factor.CMML",
        "center1",
        "center3",
        "center4",
        "date",
        "strata"
      ],
      "rows": 1210,
      "table": true,
      "tojson": true
    },
    {
      "name": "mstate_data_sample",
      "title": "A simulated event-history data set",
      "object": "mstate_data_sample",
      "class": [
        "data.frame",
        "msdata"
      ],
      "fields": [
        "id",
        "from",
        "to",
        "trans",
        "Tstart",
        "Tstop",
        "time",
        "status",
        "Cov1",
        "Cov2",
        "Cov3",
        "Cov4",
        "Cov5",
        "Cov6",
        "Cov7",
        "Cov8",
        "Cov9",
        "Cov10"
      ],
      "rows": 649,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "ebmstate-package",
      "title": "Empirical Bayes multi-state Cox model",
      "topics": [
        "ebmstate-package"
      ]
    },
    {
      "page": "boot_coxrfx",
      "title": "Bootstrap confidence intervals for regression coefficients",
      "topics": [
        "boot_coxrfx"
      ]
    },
    {
      "page": "boot_ebmstate",
      "title": "Bootstrap samples and bootstrap interval estimates",
      "topics": [
        "boot_ebmstate"
      ]
    },
    {
      "page": "boot_probtrans",
      "title": "Bootstrap confidence intervals for transition probabilities",
      "topics": [
        "boot_probtrans"
      ]
    },
    {
      "page": "CIs_for_target_state",
      "title": "Ancillary function of 'boot_ebmstate'.",
      "topics": [
        "CIs_for_target_state"
      ]
    },
    {
      "page": "convolute_clockforward",
      "title": "Convolution function for clock-forward models",
      "topics": [
        "convolute_clockforward"
      ]
    },
    {
      "page": "convolute_clockreset",
      "title": "Convolution function for clock-reset models",
      "topics": [
        "convolute_clockreset"
      ]
    },
    {
      "page": "CoxRFX",
      "title": "Empirical Bayes, multi-state Cox model",
      "topics": [
        "CoxRFX"
      ]
    },
    {
      "page": "coxrfx_object_sample",
      "title": "Example of an empirical Bayes model fit",
      "topics": [
        "coxrfx_object_sample"
      ]
    },
    {
      "page": "cumhaz_splines",
      "title": "Spline approximations of the cumulative hazard functions",
      "topics": [
        "cumhaz_splines"
      ]
    },
    {
      "page": "cumhazCIs_for_target_transition",
      "title": "Ancillary function of 'boot_ebmstate'.",
      "topics": [
        "cumhazCIs_for_target_transition"
      ]
    },
    {
      "page": "extract_function",
      "title": "Ancillary function to 'boot_ebmstate'.",
      "topics": [
        "extract_function"
      ]
    },
    {
      "page": "joint_cum_hazard_function",
      "title": "Compute the cumulative hazard of leaving a given state",
      "topics": [
        "joint_cum_hazard_function"
      ]
    },
    {
      "page": "loo_ebmstate",
      "title": "Leave-one-out estimation",
      "topics": [
        "loo_ebmstate"
      ]
    },
    {
      "page": "MakeInteger",
      "title": "Convert factor to integer.",
      "topics": [
        "MakeInteger"
      ]
    },
    {
      "page": "msfit_generic",
      "title": "Compute subject-specific transition hazards.",
      "topics": [
        "msfit_generic",
        "msfit_generic.coxrfx",
        "msfit_generic.default"
      ]
    },
    {
      "page": "msfit_object_sample",
      "title": "Estimated cumulative hazard rates under an empirical Bayes Cox model (example)",
      "topics": [
        "msfit_object_sample"
      ]
    },
    {
      "page": "mstate_data",
      "title": "An example of long-format multistate data",
      "topics": [
        "mstate_data"
      ]
    },
    {
      "page": "mstate_data_sample",
      "title": "A simulated event-history data set",
      "topics": [
        "mstate_data_sample"
      ]
    },
    {
      "page": "print.coxrfx",
      "title": "Print method for CoxRFX objects",
      "topics": [
        "print.coxrfx"
      ]
    },
    {
      "page": "print.msfit",
      "title": "Print method for 'msfit' objects generated by 'msfit_generic'",
      "topics": [
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    },
    {
      "page": "probtrans_by_convolution",
      "title": "Compute all transition probabilities from a given state using convolution",
      "topics": [
        "probtrans_by_convolution"
      ]
    },
    {
      "page": "probtrans_by_convolution_clockforward",
      "title": "Compute transition probabilities under a clock-forward model using a convolution algorithm.",
      "topics": [
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      ]
    },
    {
      "page": "probtrans_by_convolution_clockreset",
      "title": "Compute transition probabilities under a clock-reset model using a convolution algorithm.",
      "topics": [
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      ]
    },
    {
      "page": "probtrans_ebmstate",
      "title": "Compute subject-specific transition probabilities using convolution.",
      "topics": [
        "probtrans_ebmstate"
      ]
    },
    {
      "page": "probtrans_fft",
      "title": "Compute subject-specific transition probabilities using a convolution algorithm based on the Fast Fourier transform.",
      "topics": [
        "probtrans_fft"
      ]
    },
    {
      "page": "probtrans_mstate",
      "title": "Compute subject-specific or overall transition probabilities",
      "topics": [
        "probtrans_mstate",
        "probtrans_mstate.coxrfx",
        "probtrans_mstate.default"
      ]
    },
    {
      "page": "successful_transitions",
      "title": "Find the unique possible path until an absorbing state",
      "topics": [
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    },
    {
      "page": "summary.coxrfx",
      "title": "A summary method for CoxRFX models",
      "topics": [
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      ]
    },
    {
      "page": "unique_paths",
      "title": "Find all possible paths until absorption from a given starting state",
      "topics": [
        "unique_paths"
      ]
    }
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