{
  "_id": "6a1f399eb401979e73428f23",
  "Package": "survextrap",
  "Title": "Bayesian Flexible Parametric Survival Modelling and\nExtrapolation",
  "Version": "1.0.1",
  "Date": "2026-01-11",
  "Authors@R": "c(person(\"Christopher\", \"Jackson\", , \"chris.jackson@mrc-bsu.cam.ac.uk\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-6656-8913\")),\nperson(\"Iain\", \"Timmins\", , \"\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-8761-582X\")),\nperson(\"Michael\", \"Sweeting\", , \"\", role = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0003-0980-8965\")))",
  "Description": "Survival analysis using a flexible Bayesian model for\nindividual-level right-censored data, optionally combined with\naggregate data on counts of survivors in different periods of\ntime. An M-spline is used to describe the hazard function, with\na prior on the coefficients that controls over-fitting.\nProportional hazards or flexible non-proportional hazards\nmodels can be used to relate survival to predictors. Additive\nhazards (relative survival) models, waning treatment effects,\nand mixture cure models are also supported. Priors can be\ncustomised and calibrated to substantive beliefs. Posterior\ndistributions are estimated using 'Stan', and outputs are\narranged in a tidy format. See Jackson (2023)\n<doi:10.1186/s12874-023-02094-1>.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Biarch": "true",
  "SystemRequirements": "GNU make",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/chjackson/survextrap,\nhttps://chjackson.github.io/survextrap/",
  "BugReports": "https://github.com/chjackson/survextrap/issues",
  "LazyData": "true",
  "Config/pak/sysreqs": "make",
  "Repository": "https://chjackson.r-universe.dev",
  "Date/Publication": "2026-03-10 10:18:51 UTC",
  "RemoteUrl": "https://github.com/chjackson/survextrap",
  "RemoteRef": "HEAD",
  "RemoteSha": "17cbe470c15c347da585efa564c29d0fc35f0461",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-09 08:14:30 UTC",
    "User": "root"
  },
  "Author": "Christopher Jackson [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0002-6656-8913>),\nIain Timmins [ctb] (ORCID: <https://orcid.org/0000-0002-8761-582X>),\nMichael Sweeting [ctb] (ORCID: <https://orcid.org/0000-0003-0980-8965>)",
  "Maintainer": "Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>",
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  "_user": "chjackson",
  "_type": "src",
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  "_created": "2026-05-09T08:14:30.000Z",
  "_published": "2026-06-02T20:14:22.397Z",
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    "message": "Don't try to calculate KM with continuous covariates (#16)\n",
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    "name": "Chris Jackson",
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    "dsurvmspline",
    "dsurvmspline_wane",
    "get_draws",
    "hazard",
    "hazard_ratio",
    "hrtime",
    "hsurvmspline",
    "Hsurvmspline",
    "hsurvmspline_wane",
    "Hsurvmspline_wane",
    "irmst",
    "mean_survmspline",
    "mean_survmspline_wane",
    "mspline_basis",
    "mspline_constant_coefs",
    "mspline_init",
    "mspline_list_init",
    "mspline_plotdata",
    "mspline_plotsetup",
    "mspline_spec",
    "msplinemodel_init",
    "p_beta",
    "p_gamma",
    "p_hr",
    "p_meansurv",
    "p_normal",
    "p_t",
    "plot_hazard",
    "plot_hazard_ratio",
    "plot_mspline",
    "plot_prior_hazard",
    "plot_survival",
    "print_priors",
    "prior_haz_const",
    "prior_haz_sd",
    "prior_hr",
    "prior_hr_sd",
    "prior_pred",
    "prior_sample",
    "prior_sample_hazard",
    "psurvmspline",
    "psurvmspline_wane",
    "qsurvmspline",
    "qsurvmspline_wane",
    "rmst",
    "rmst_survmspline",
    "rmst_survmspline_wane",
    "rsurvmspline",
    "rsurvmspline_wane",
    "standardise_to",
    "standardize_to",
    "survextrap",
    "survival"
  ],
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      "name": "cetux",
      "title": "Datasets for evaluation of cetuximab in head and neck cancer",
      "object": "cetux",
      "class": [
        "data.frame"
      ],
      "fields": [
        "months",
        "years",
        "d",
        "treat"
      ],
      "rows": 424,
      "table": true,
      "tojson": true
    },
    {
      "name": "cetux_bh",
      "title": "Datasets for evaluation of cetuximab in head and neck cancer",
      "object": "cetux_bh",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "hazard"
      ],
      "rows": 54,
      "table": true,
      "tojson": true
    },
    {
      "name": "cetux_seer",
      "title": "Datasets for evaluation of cetuximab in head and neck cancer",
      "object": "cetux_seer",
      "class": [
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      ],
      "fields": [
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        "stop",
        "r",
        "n",
        "treat",
        "haz",
        "haz_upper",
        "haz_lower"
      ],
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      "table": true,
      "tojson": true
    },
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      "object": "colons",
      "class": [
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        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
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        "study",
        "rx",
        "sex",
        "age",
        "obstruct",
        "perfor",
        "adhere",
        "nodes",
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        "extent",
        "surg",
        "node4",
        "time",
        "etype",
        "years"
      ],
      "rows": 191,
      "table": true,
      "tojson": true
    },
    {
      "name": "curedata",
      "title": "Simulated data for testing mixture cure models",
      "object": "curedata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "t",
        "status",
        "x"
      ],
      "rows": 200,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "survextrap-package",
      "title": "The 'survextrap' package.",
      "topics": [
        "survextrap-package"
      ]
    },
    {
      "page": "cetux",
      "title": "Datasets for evaluation of cetuximab in head and neck cancer",
      "topics": [
        "cetux",
        "cetux_bh",
        "cetux_seer"
      ]
    },
    {
      "page": "colons",
      "title": "Colon cancer survival data",
      "topics": [
        "colons"
      ]
    },
    {
      "page": "cumhaz",
      "title": "Estimates of cumulative hazard from a survextrap model",
      "topics": [
        "cumhaz"
      ]
    },
    {
      "page": "curedata",
      "title": "Simulated data for testing mixture cure models",
      "topics": [
        "curedata"
      ]
    },
    {
      "page": "get_draws",
      "title": "Posterior draws from a survextrap model",
      "topics": [
        "get_draws"
      ]
    },
    {
      "page": "hazard",
      "title": "Estimates of hazard from a 'survextrap' model",
      "topics": [
        "hazard"
      ]
    },
    {
      "page": "hazard_ratio",
      "title": "Hazard ratio against time in a survextrap model",
      "topics": [
        "hazard_ratio"
      ]
    },
    {
      "page": "hrtime",
      "title": "Hazard ratio between high and low values of the hazard over time",
      "topics": [
        "hrtime"
      ]
    },
    {
      "page": "irmst",
      "title": "Incremental restricted mean survival time",
      "topics": [
        "irmst"
      ]
    },
    {
      "page": "mean.survextrap",
      "title": "Mean survival time",
      "topics": [
        "mean.survextrap"
      ]
    },
    {
      "page": "mspline_basis",
      "title": "Evaluate an M-spline basis matrix at the specified times.",
      "topics": [
        "mspline_basis"
      ]
    },
    {
      "page": "mspline_constant_coefs",
      "title": "Determine M-spline basis coefficients which give a constant function.",
      "topics": [
        "mspline_constant_coefs"
      ]
    },
    {
      "page": "mspline_init",
      "title": "Create a default M-spline model structure",
      "topics": [
        "mspline_init"
      ]
    },
    {
      "page": "mspline_list_init",
      "title": "Validate an M-spline object supplied as a list, choosing defaults if needed.",
      "topics": [
        "mspline_list_init"
      ]
    },
    {
      "page": "mspline_plotdata",
      "title": "Data for plotting an M-spline function, showing how it is built up from its basis",
      "topics": [
        "mspline_plotdata"
      ]
    },
    {
      "page": "mspline_plotsetup",
      "title": "Get basis for an illustration of an M-spline with given knots.",
      "topics": [
        "mspline_plotsetup"
      ]
    },
    {
      "page": "mspline_spec",
      "title": "Make default M-spline knot specification given a survival dataset.",
      "topics": [
        "mspline_spec"
      ]
    },
    {
      "page": "msplinemodel_init",
      "title": "Create an M-spline survival model, both structure and parameters.",
      "topics": [
        "msplinemodel_init"
      ]
    },
    {
      "page": "p_hr",
      "title": "Derive a normal prior for the log hazard ratio parameter based on a guess at the hazard ratio",
      "topics": [
        "p_hr"
      ]
    },
    {
      "page": "p_meansurv",
      "title": "Derive a normal prior for the log hazard scale parameter based on a guess at survival times",
      "topics": [
        "p_meansurv"
      ]
    },
    {
      "page": "plot_hazard",
      "title": "Plot hazard curves from a survextrap model",
      "topics": [
        "plot_hazard"
      ]
    },
    {
      "page": "plot_hazard_ratio",
      "title": "Plot hazard ratio against time from a survextrap model",
      "topics": [
        "plot_hazard_ratio"
      ]
    },
    {
      "page": "plot_mspline",
      "title": "Plot a M-spline function, showing how it is built up from its basis",
      "topics": [
        "plot_mspline"
      ]
    },
    {
      "page": "plot_survival",
      "title": "Plot survival curves from a survextrap model",
      "topics": [
        "plot_survival"
      ]
    },
    {
      "page": "plot.survextrap",
      "title": "Plot method for survextrap model objects",
      "topics": [
        "plot.survextrap"
      ]
    },
    {
      "page": "print_priors",
      "title": "Print the priors used in a fitted survextrap model",
      "topics": [
        "print_priors"
      ]
    },
    {
      "page": "print.survextrap",
      "title": "Print a fitted survextrap model",
      "topics": [
        "print.survextrap"
      ]
    },
    {
      "page": "prior_haz",
      "title": "Determine priors for time-varying hazards and hazard ratios",
      "topics": [
        "prior_haz",
        "prior_haz_sd",
        "prior_hr_sd"
      ]
    },
    {
      "page": "prior_haz_const",
      "title": "Summarises the prior for the constant hazard implied by a particular prior on the hazard scale parameter and spline specification.",
      "topics": [
        "prior_haz_const"
      ]
    },
    {
      "page": "prior_hr",
      "title": "Summarises the prior for the hazard ratio implied by a particular prior on the log hazard ratio",
      "topics": [
        "prior_hr"
      ]
    },
    {
      "page": "prior_pred",
      "title": "Simulate a dataset from the prior predictive distribution of survival times in an M-spline survival model.",
      "topics": [
        "prior_pred"
      ]
    },
    {
      "page": "prior_sample",
      "title": "Sample from the joint prior of parameters in a survextrap model",
      "topics": [
        "prior_sample"
      ]
    },
    {
      "page": "prior_sample_hazard",
      "title": "Generate and/or plot a sample from the prior distribution of M-spline hazard curves",
      "topics": [
        "plot_prior_hazard",
        "prior_sample_hazard"
      ]
    },
    {
      "page": "priors",
      "title": "Prior distributions and options",
      "topics": [
        "priors",
        "p_beta",
        "p_gamma",
        "p_normal",
        "p_t"
      ]
    },
    {
      "page": "rmst",
      "title": "Restricted mean survival time",
      "topics": [
        "rmst"
      ]
    },
    {
      "page": "standardise_to",
      "title": "Constructor for a standardising population used for survextrap outputs",
      "topics": [
        "standardise_to",
        "standardize_to"
      ]
    },
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