{
  "_id": "6a1429b5acfb0bcc41d40712",
  "Package": "survcompare",
  "Title": "Nested Cross-Validation to Compare Cox-PH, Cox-Lasso, Survival\nRandom Forests",
  "Version": "0.3.0",
  "Date": "2025-06-25",
  "Authors@R": "c(\nperson(\"Diana\", \"Shamsutdinova\", , \"diana.shamsutdinova.github@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-2434-3641\")),\nperson(\"Daniel\", \"Stahl\", , \"daniel.r.stahl@kcl.ac.uk\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-7987-6619\"))\n)",
  "Description": "Performs repeated nested cross-validation for Cox\nProportionate Hazards, Cox Lasso, Survival Random Forest, and\ntheir ensemble. Returns internally validated concordance index,\ntime-dependent area under the curve, Brier score, calibration\nslope, and statistical testing of non-linear ensemble\noutperforming the baseline Cox model. In this, it helps\nresearchers to quantify the gain of using a more complex\nsurvival model, or justify its redundancy. Equally, it shows\nthe performance value of the non-linear and interaction terms,\nand may highlight the need of further feature transformation.\nFurther details can be found in Shamsutdinova, Stamate,\nRoberts, & Stahl (2022) \"Combining Cox Model and Tree-Based\nAlgorithms to Boost Performance and Preserve Interpretability\nfor Health Outcomes\" <doi:10.1007/978-3-031-08337-2_15>, where\nthe method is described as Ensemble 1.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
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  "VignetteBuilder": "knitr",
  "Maintainer": "Diana Shamsutdinova <diana.shamsutdinova.github@gmail.com>",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-25 10:47:35 UTC",
    "User": "root"
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  "Author": "Diana Shamsutdinova [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-2434-3641>), Daniel Stahl [aut]\n(ORCID: <https://orcid.org/0000-0001-7987-6619>)",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-06-25 15:40:51 UTC",
  "RemoteUrl": "https://github.com/cran/survcompare",
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  "_created": "2026-05-25T10:47:35.000Z",
  "_published": "2026-05-25T10:51:33.308Z",
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    "author": "Diana Shamsutdinova <diana.shamsutdinova.github@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.3.0\n",
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    "name": "Diana Shamsutdinova",
    "email": "diana.shamsutdinova.github@gmail.com",
    "orcid": "0000-0003-2434-3641"
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  "_dependencies": [
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    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
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  "_assets": [
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    "extra/citation.json",
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    },
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      "date": "2025-06-25"
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  "_exports": [
    "ml_hyperparams_srf",
    "simulate_crossterms",
    "simulate_linear",
    "simulate_nonlinear",
    "surv_validate",
    "survcompare",
    "survcompare2",
    "survcox_cv",
    "survcox_predict",
    "survcox_train",
    "survcoxlasso_train",
    "survsrf_cv",
    "survsrf_predict",
    "survsrf_train",
    "survsrfens_cv",
    "survsrfens_predict",
    "survsrfens_train",
    "survsrfstack_cv",
    "survsrfstack_predict",
    "survsrfstack_train"
  ],
  "_help": [
    {
      "page": "linear_beta",
      "title": "Auxiliary function for simulatedata functions",
      "topics": [
        "linear_beta"
      ]
    },
    {
      "page": "ml_hyperparams_srf",
      "title": "Internal function for getting grid of hyperparameters for random or grid search of size = max_grid_size",
      "topics": [
        "ml_hyperparams_srf"
      ]
    },
    {
      "page": "print.survcompare",
      "title": "Print survcompare object",
      "topics": [
        "print.survcompare"
      ]
    },
    {
      "page": "print.survensemble_cv",
      "title": "Prints trained survensemble object",
      "topics": [
        "print.survensemble_cv"
      ]
    },
    {
      "page": "simulate_crossterms",
      "title": "Simulated sample with survival outcomes with non-linear and cross-term dependencies",
      "topics": [
        "simulate_crossterms"
      ]
    },
    {
      "page": "simulate_linear",
      "title": "Simulated sample with survival outcomes with linear dependencies",
      "topics": [
        "simulate_linear"
      ]
    },
    {
      "page": "simulate_nonlinear",
      "title": "Simulated sample with survival outcomes with non-linear dependencies",
      "topics": [
        "simulate_nonlinear"
      ]
    },
    {
      "page": "summary.survcompare",
      "title": "Summary of survcompare results",
      "topics": [
        "summary.survcompare"
      ]
    },
    {
      "page": "summary.survensemble_cv",
      "title": "Prints summary of a trained survensemble_cv object",
      "topics": [
        "summary.survensemble_cv"
      ]
    },
    {
      "page": "surv_brierscore",
      "title": "Calculates time-dependent Brier Score",
      "topics": [
        "surv_brierscore"
      ]
    },
    {
      "page": "surv_validate",
      "title": "Computes performance statistics for a survival data given the predicted event probabilities",
      "topics": [
        "surv_validate"
      ]
    },
    {
      "page": "survcompare",
      "title": "Cross-validates and compares Cox Proportionate Hazards and Survival Random Forest models",
      "topics": [
        "\"_PACKAGE\"",
        "survcompare"
      ]
    },
    {
      "page": "survcompare2",
      "title": "Compares two cross-validated models using surv____cv functions of this package.",
      "topics": [
        "survcompare2"
      ]
    },
    {
      "page": "survcox_cv",
      "title": "Cross-validates Cox or CoxLasso model",
      "topics": [
        "survcox_cv"
      ]
    },
    {
      "page": "survcox_predict",
      "title": "Computes event probabilities from a trained cox model",
      "topics": [
        "survcox_predict"
      ]
    },
    {
      "page": "survcox_train",
      "title": "Trains CoxPH using survival package, or trains CoxLasso (cv.glmnet, lambda.min), and then re-trains survival:coxph on non-zero predictors",
      "topics": [
        "survcox_train"
      ]
    },
    {
      "page": "survcoxlasso_train",
      "title": "Trains CoxLasso, using cv.glmnet(s=\"lambda.min\")",
      "topics": [
        "survcoxlasso_train"
      ]
    },
    {
      "page": "survival_prob_km",
      "title": "Calculates survival probability estimated by Kaplan-Meier survival curve Uses polynomial extrapolation in survival function space, using poly(n=3)",
      "topics": [
        "survival_prob_km"
      ]
    },
    {
      "page": "survsrf_cv",
      "title": "Cross-validates Survival Random Forest",
      "topics": [
        "survsrf_cv"
      ]
    },
    {
      "page": "survsrf_predict",
      "title": "Predicts event probability by a trained Survival Random Forest",
      "topics": [
        "survsrf_predict"
      ]
    },
    {
      "page": "survsrf_train",
      "title": "Fits randomForestSRC, with tuning by mtry, nodedepth, and nodesize. Underlying model is by Ishwaran et al(2008) https://www.randomforestsrc.org/articles/survival.html Ishwaran H, Kogalur UB, Blackstone EH, Lauer MS. Random survival forests. The Annals of Applied Statistics. 2008;2:841–60.",
      "topics": [
        "survsrf_train"
      ]
    },
    {
      "page": "survsrf_tune",
      "title": "A repeated 3-fold CV over a hyperparameters grid",
      "topics": [
        "survsrf_tune"
      ]
    },
    {
      "page": "survsrf_tune_single",
      "title": "Internal function for survsrf_tune(), performs 1 CV",
      "topics": [
        "survsrf_tune_single"
      ]
    },
    {
      "page": "survsrfens_cv",
      "title": "Cross-validates predictive performance for SRF Ensemble",
      "topics": [
        "survsrfens_cv"
      ]
    },
    {
      "page": "survsrfens_predict",
      "title": "Predicts event probability by a trained sequential ensemble of Survival Random Forest and CoxPH",
      "topics": [
        "survsrfens_predict"
      ]
    },
    {
      "page": "survsrfens_train",
      "title": "Fits an ensemble of Cox-PH and Survival Random Forest (SRF) with internal CV to tune SRF hyperparameters.",
      "topics": [
        "survsrfens_train"
      ]
    },
    {
      "page": "survsrfstack_cv",
      "title": "Cross-validates stacked ensemble of the CoxPH and Survival Random Forest models",
      "topics": [
        "survsrfstack_cv"
      ]
    },
    {
      "page": "survsrfstack_predict",
      "title": "Predicts event probability by a trained stacked ensemble of Survival Random Forest and CoxPH",
      "topics": [
        "survsrfstack_predict"
      ]
    },
    {
      "page": "survsrfstack_train",
      "title": "Trains the stacked ensemble of the CoxPH and Survival Random Forest",
      "topics": [
        "survsrfstack_train"
      ]
    }
  ],
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      "filename": "survcompare_application.html",
      "title": "Survcompare_application",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Package background",
        "References:",
        "What can be inferred from the survcompare results?",
        "Why the CoxPH-SRF ensemble and not just SRF?",
        "Package installation",
        "Examples",
        "Example 1. Linear data",
        "Example 2. Non-linear data with interaction terms",
        "Example 3. Applying survcompare to GBSG data"
      ],
      "created": "2024-01-23 02:44:50",
      "modified": "2025-06-25 15:40:51",
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