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  "Title": "A Unified Framework for Machine Learning Ensembles in Survival\nAnalysis",
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  "Authors@R": "person(\"Yue\", \"Lyu\", email = \"yuelyu0521@gmail.com\", role = c(\"aut\", \"cre\"))",
  "Author": "Yue Lyu [aut, cre]",
  "Maintainer": "Yue Lyu <yuelyu0521@gmail.com>",
  "Description": "Implements a Super Learner framework for right-censored\nsurvival data. The package fits convex combinations of\nparametric, semiparametric, and machine learning survival\nlearners by minimizing cross-validated risk using inverse\nprobability of censoring weighting (IPCW). It provides tools\nfor automated hyperparameter grid search, high-dimensional\nvariable screening, and evaluation of prediction performance\nusing metrics such as the Brier score, Uno's C-index, and\ntime-dependent area under the curve (AUC). Additional utilities\nsupport model interpretation for survival ensembles, including\nShapley additive explanations (SHAP), and estimation of\ncovariate-adjusted restricted mean survival time (RMST)\ncontrasts. The methodology is related to treatment-specific\nsurvival curve estimation using machine learning described by\nWestling et al. (2024) <doi:10.1080/01621459.2023.2205060>, and\nthe unified ensemble framework described in Lyu et al. (2026)\n<doi:10.64898/2026.03.11.711010>.",
  "License": "MIT + file LICENSE",
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  "URL": "https://github.com/yuelyu21/SuperSurv,\nhttps://yuelyu21.github.io/SuperSurv/",
  "BugReports": "https://github.com/yuelyu21/SuperSurv/issues",
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  "Repository": "https://yuelyu21.r-universe.dev",
  "Date/Publication": "2026-05-04 06:44:24 UTC",
  "RemoteUrl": "https://github.com/yuelyu21/supersurv",
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  "_exports": [
    "censor_weights",
    "create_grid",
    "estimate_marginal_rmst",
    "eval_brier",
    "eval_cindex",
    "eval_summary",
    "eval_timeROC",
    "eval_times",
    "event_weights",
    "explain_kernel",
    "explain_survex",
    "learner_names",
    "list_wrappers",
    "plot_beeswarm",
    "plot_benchmark",
    "plot_calibration",
    "plot_dependence",
    "plot_global_importance",
    "plot_marginal_rmst_curve",
    "plot_patient_waterfall",
    "plot_predict",
    "plot_rmst_vs_obs",
    "plot_survival_heatmap",
    "screen.all",
    "screen.elasticnet",
    "screen.glmnet",
    "screen.marg",
    "screen.rfsrc",
    "screen.var",
    "selected_variables",
    "SuperSurv",
    "surv.aorsf",
    "surv.bart",
    "surv.coxboost",
    "surv.coxph",
    "surv.exponential",
    "surv.gam",
    "surv.gbm",
    "surv.glmnet",
    "surv.km",
    "surv.loglogistic",
    "surv.lognormal",
    "surv.parametric",
    "surv.ranger",
    "surv.rfsrc",
    "surv.ridge",
    "surv.rpart",
    "surv.svm",
    "surv.weibull",
    "surv.xgboost",
    "training_variables"
  ],
  "_datasets": [
    {
      "name": "metabric",
      "title": "METABRIC Breast Cancer Dataset",
      "object": "metabric",
      "class": [
        "data.frame"
      ],
      "fields": [
        "x0",
        "x1",
        "x2",
        "x3",
        "x4",
        "x5",
        "x6",
        "x7",
        "x8",
        "duration",
        "event"
      ],
      "rows": 1904,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "coef.SuperSurv",
      "title": "Extract SuperSurv ensemble coefficients",
      "topics": [
        "coef.SuperSurv"
      ]
    },
    {
      "page": "estimate_marginal_rmst",
      "title": "Estimate an Adjusted Marginal RMST Contrast",
      "topics": [
        "estimate_marginal_rmst"
      ]
    },
    {
      "page": "eval_brier",
      "title": "IPCW Brier Score and Integrated Brier Score (IBS)",
      "topics": [
        "eval_brier"
      ]
    },
    {
      "page": "eval_cindex",
      "title": "Calculate Concordance Index (Harrell's or Uno's)",
      "topics": [
        "eval_cindex"
      ]
    },
    {
      "page": "eval_summary",
      "title": "Evaluate SuperSurv predictions on test data",
      "topics": [
        "eval_summary"
      ]
    },
    {
      "page": "eval_timeROC",
      "title": "Time-Dependent AUC and Integrated AUC",
      "topics": [
        "eval_timeROC"
      ]
    },
    {
      "page": "eval_times",
      "title": "Access SuperSurv prediction evaluation times",
      "topics": [
        "eval_times",
        "eval_times.SuperSurv"
      ]
    },
    {
      "page": "event_weights",
      "title": "Access SuperSurv ensemble weights",
      "topics": [
        "censor_weights",
        "censor_weights.SuperSurv",
        "event_weights",
        "event_weights.SuperSurv"
      ]
    },
    {
      "page": "explain_kernel",
      "title": "Explain Predictions with Global SHAP (Kernel SHAP)",
      "topics": [
        "explain_kernel"
      ]
    },
    {
      "page": "explain_survex",
      "title": "Create a Time-Dependent Survex Explainer",
      "topics": [
        "explain_survex"
      ]
    },
    {
      "page": "learner_names",
      "title": "Access SuperSurv learner names",
      "topics": [
        "learner_names",
        "learner_names.SuperSurv"
      ]
    },
    {
      "page": "list_wrappers",
      "title": "List Available Wrappers and Screeners in SuperSurv",
      "topics": [
        "list_wrappers"
      ]
    },
    {
      "page": "metabric",
      "title": "METABRIC Breast Cancer Dataset",
      "topics": [
        "metabric"
      ]
    },
    {
      "page": "plot_beeswarm",
      "title": "Beeswarm Summary Plot for SuperSurv SHAP",
      "topics": [
        "plot_beeswarm"
      ]
    },
    {
      "page": "plot_benchmark",
      "title": "Plot Longitudinal Benchmark Metrics",
      "topics": [
        "plot_benchmark"
      ]
    },
    {
      "page": "plot_calibration",
      "title": "Plot Survival Calibration Curve",
      "topics": [
        "plot_calibration"
      ]
    },
    {
      "page": "plot_dependence",
      "title": "Plot SHAP Dependence for SuperSurv",
      "topics": [
        "plot_dependence"
      ]
    },
    {
      "page": "plot_global_importance",
      "title": "Plot Global Feature Importance for SuperSurv",
      "topics": [
        "plot_global_importance"
      ]
    },
    {
      "page": "plot_marginal_rmst_curve",
      "title": "Plot Adjusted Marginal RMST Contrast Over Time",
      "topics": [
        "plot_marginal_rmst_curve"
      ]
    },
    {
      "page": "plot_patient_waterfall",
      "title": "Waterfall Plot for an Individual Patient",
      "topics": [
        "plot_patient_waterfall"
      ]
    },
    {
      "page": "plot_predict",
      "title": "Plot Predicted Survival Curves",
      "topics": [
        "plot_predict"
      ]
    },
    {
      "page": "plot_rmst_vs_obs",
      "title": "Plot Predicted RMST vs. Observed Survival Times",
      "topics": [
        "plot_rmst_vs_obs"
      ]
    },
    {
      "page": "plot_survival_heatmap",
      "title": "Survival Probability Heatmap",
      "topics": [
        "plot_survival_heatmap"
      ]
    },
    {
      "page": "predict.SuperSurv",
      "title": "Predict method for SuperSurv fits",
      "topics": [
        "predict.SuperSurv"
      ]
    },
    {
      "page": "print.SuperSurv",
      "title": "Print a SuperSurv fit",
      "topics": [
        "print.SuperSurv"
      ]
    },
    {
      "page": "screen.all",
      "title": "Keep All Variables Screener",
      "topics": [
        "screen.all"
      ]
    },
    {
      "page": "screen.elasticnet",
      "title": "Elastic Net Screening Algorithm",
      "topics": [
        "screen.elasticnet"
      ]
    },
    {
      "page": "screen.glmnet",
      "title": "GLMNET (Lasso) Screening",
      "topics": [
        "screen.glmnet"
      ]
    },
    {
      "page": "screen.marg",
      "title": "Marginal Cox Regression Screening",
      "topics": [
        "screen.marg"
      ]
    },
    {
      "page": "screen.rfsrc",
      "title": "Random Survival Forest Screening Algorithm",
      "topics": [
        "screen.rfsrc"
      ]
    },
    {
      "page": "screen.var",
      "title": "High Variance Screening Algorithm (Unsupervised)",
      "topics": [
        "screen.var"
      ]
    },
    {
      "page": "selected_variables",
      "title": "Access variables selected by SuperSurv screeners",
      "topics": [
        "selected_variables",
        "selected_variables.SuperSurv"
      ]
    },
    {
      "page": "summary.SuperSurv",
      "title": "Summarize a SuperSurv fit",
      "topics": [
        "print.summary.SuperSurv",
        "summary.SuperSurv"
      ]
    },
    {
      "page": "SuperSurv",
      "title": "Super Learner for conditional survival functions",
      "topics": [
        "SuperSurv"
      ]
    },
    {
      "page": "surv.aorsf",
      "title": "Wrapper for AORSF (Oblique Random Survival Forest)",
      "topics": [
        "surv.aorsf"
      ]
    },
    {
      "page": "surv.bart",
      "title": "Wrapper for BART (Bayesian Additive Regression Trees)",
      "topics": [
        "surv.bart"
      ]
    },
    {
      "page": "surv.coxboost",
      "title": "Wrapper function for Component-Wise Boosting (CoxBoost)",
      "topics": [
        "surv.coxboost"
      ]
    },
    {
      "page": "surv.coxph",
      "title": "Wrapper for standard Cox Proportional Hazards",
      "topics": [
        "surv.coxph"
      ]
    },
    {
      "page": "surv.exponential",
      "title": "Parametric Survival Prediction Wrapper (Exponential)",
      "topics": [
        "surv.exponential"
      ]
    },
    {
      "page": "surv.gam",
      "title": "Wrapper for Generalized Additive Cox Regression (GAM)",
      "topics": [
        "surv.gam"
      ]
    },
    {
      "page": "surv.gbm",
      "title": "Wrapper function for Gradient Boosting (GBM) prediction algorithm",
      "topics": [
        "surv.gbm"
      ]
    },
    {
      "page": "surv.glmnet",
      "title": "Wrapper function for Penalized Cox Regression (GLMNET)",
      "topics": [
        "surv.glmnet"
      ]
    },
    {
      "page": "surv.km",
      "title": "Kaplan-Meier Prediction Algorithm",
      "topics": [
        "surv.km"
      ]
    },
    {
      "page": "surv.loglogistic",
      "title": "Parametric Survival Prediction Wrapper (Log-Logistic)",
      "topics": [
        "surv.loglogistic"
      ]
    },
    {
      "page": "surv.lognormal",
      "title": "Parametric Survival Prediction Wrapper (Log-Normal)",
      "topics": [
        "surv.lognormal"
      ]
    },
    {
      "page": "surv.parametric",
      "title": "Universal Parametric Survival Wrapper",
      "topics": [
        "surv.parametric"
      ]
    },
    {
      "page": "surv.ranger",
      "title": "Wrapper function for Ranger Random Survival Forest",
      "topics": [
        "surv.ranger"
      ]
    },
    {
      "page": "surv.rfsrc",
      "title": "Wrapper function for Random Survival Forests (RFSRC)",
      "topics": [
        "surv.rfsrc"
      ]
    },
    {
      "page": "surv.ridge",
      "title": "Wrapper for Ridge Regression (Penalized Cox)",
      "topics": [
        "surv.ridge"
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    },
    {
      "page": "surv.rpart",
      "title": "Wrapper for Survival Regression Trees (rpart)",
      "topics": [
        "surv.rpart"
      ]
    },
    {
      "page": "surv.svm",
      "title": "Wrapper for Survival Support Vector Machine (survivalsvm)",
      "topics": [
        "surv.svm"
      ]
    },
    {
      "page": "surv.weibull",
      "title": "Parametric Survival Prediction Wrapper (Weibull)",
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        "surv.weibull"
      ]
    },
    {
      "page": "surv.xgboost",
      "title": "Wrapper for XGBoost (Robust CV-Tuned + Safe Prediction)",
      "topics": [
        "surv.xgboost"
      ]
    },
    {
      "page": "training_variables",
      "title": "Access SuperSurv training variable names",
      "topics": [
        "training_variables",
        "training_variables.SuperSurv"
      ]
    }
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  "_rundeps": [
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    "globals",
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    "Matrix",
    "nnls",
    "parallelly",
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    "R6",
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    "utf8",
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  "_vignettes": [
    {
      "source": "installation.Rmd",
      "filename": "installation.html",
      "title": "Installation & Setup ",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Welcome to SuperSurv!",
        "Step 1: Install the Core Package",
        "Step 2: Install Base Learners (Optional but Recommended)",
        "Specialized Packages",
        "Step 3: You're Ready!",
        "References"
      ],
      "created": "2026-03-03 20:01:20",
      "modified": "2026-05-03 07:05:00",
      "commits": 3
    },
    {
      "source": "supersurv-ensemble.Rmd",
      "filename": "supersurv-ensemble.html",
      "title": "SuperSurv with Ensemble ",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1. Load Data & Prepare Matrices",
        "2. Define the Ensemble Library",
        "3. Train the SuperSurv Metalearner",
        "The Data Inputs",
        "The Model Libraries",
        "The Meta-Learner & Tuning",
        "4. Package Object Interface",
        "5. Inspect the Ensemble Weights and Risks",
        "How to Interpret This:",
        "6. Generating Predictions on New Data",
        "Understanding the Output Matrix:",
        "7. Visualizing Patient-Specific Predictions",
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