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  "Description": "Implementation of the following methods for event history\nanalysis. Risk regression models for survival endpoints also in\nthe presence of competing risks are fitted using binomial\nregression based on a time sequence of binary event status\nvariables. A formula interface for the Fine-Gray regression\nmodel and an interface for the combination of cause-specific\nCox regression models. A toolbox for assessing and comparing\nperformance of risk predictions (risk markers and risk\nprediction models). Prediction performance is measured by the\nBrier score and the area under the ROC curve for binary\npossibly time-dependent outcome. Inverse probability of\ncensoring weighting and pseudo values are used to deal with\nright censored data. Lists of risk markers and lists of risk\nmodels are assessed simultaneously. Cross-validation repeatedly\nsplits the data, trains the risk prediction models on one part\nof each split and then summarizes and compares the performance\nacross splits.",
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      ]
    },
    {
      "page": "calcSeCSC",
      "title": "Standard error of the absolute risk predicted from cause-specific Cox models",
      "topics": [
        "calcSeCSC"
      ]
    },
    {
      "page": "Cforest",
      "title": "S3-wrapper function for cforest from the party package",
      "topics": [
        "Cforest"
      ]
    },
    {
      "page": "coef.ate",
      "title": "Estimated Average Treatment Effect.",
      "topics": [
        "coef.ate"
      ]
    },
    {
      "page": "coef.CauseSpecificCox",
      "title": "Extract coefficients from a Cause-Specific Cox regression model",
      "topics": [
        "coef.CauseSpecificCox"
      ]
    },
    {
      "page": "coef.riskRegression",
      "title": "Extract coefficients from riskRegression model",
      "topics": [
        "coef.riskRegression"
      ]
    },
    {
      "page": "coef.wglm",
      "title": "Estimates from IPCW Logistic Regressions",
      "topics": [
        "coef.wglm"
      ]
    },
    {
      "page": "colCenter_cpp",
      "title": "Apply - by column",
      "topics": [
        "colCenter_cpp"
      ]
    },
    {
      "page": "colCumSum",
      "title": "Apply cumsum in each column",
      "topics": [
        "colCumSum"
      ]
    },
    {
      "page": "colMultiply_cpp",
      "title": "Apply * by column",
      "topics": [
        "colMultiply_cpp"
      ]
    },
    {
      "page": "colScale_cpp",
      "title": "Apply / by column",
      "topics": [
        "colScale_cpp"
      ]
    },
    {
      "page": "confint.ate",
      "title": "Confidence Intervals and Confidence Bands for the average treatment effect.",
      "topics": [
        "confint.ate"
      ]
    },
    {
      "page": "confint.influenceTest",
      "title": "Confidence Intervals and Confidence Bands for the Difference Between Two Estimates",
      "topics": [
        "confint.influenceTest"
      ]
    },
    {
      "page": "confint.predictCox",
      "title": "Confidence Intervals and Confidence Bands for the predicted Survival/Cumulative Hazard",
      "topics": [
        "confint.predictCox"
      ]
    },
    {
      "page": "confint.predictCSC",
      "title": "Confidence Intervals and Confidence Bands for the Predicted Absolute Risk (Cumulative Incidence Function)",
      "topics": [
        "confint.predictCSC"
      ]
    },
    {
      "page": "confint.wglm",
      "title": "Confidence intervals for Estimate from IPCW Logistic Regressions",
      "topics": [
        "confint.wglm"
      ]
    },
    {
      "page": "coxBaseEstimator",
      "title": "Extract the type of estimator for the baseline hazard",
      "topics": [
        "coxBaseEstimator",
        "coxBaseEstimator.coxph",
        "coxBaseEstimator.GLMnet",
        "coxBaseEstimator.phreg",
        "coxBaseEstimator.prodlim"
      ]
    },
    {
      "page": "coxCenter",
      "title": "Extract the mean value of the covariates",
      "topics": [
        "coxCenter",
        "coxCenter.coxph",
        "coxCenter.cph",
        "coxCenter.phreg"
      ]
    },
    {
      "page": "coxFormula",
      "title": "Extract the formula from a Cox model",
      "topics": [
        "coxFormula",
        "coxFormula.coxph",
        "coxFormula.cph",
        "coxFormula.glm",
        "coxFormula.GLMnet",
        "coxFormula.phreg",
        "coxFormula.prodlim"
      ]
    },
    {
      "page": "coxLP",
      "title": "Compute the linear predictor of a Cox model",
      "topics": [
        "coxLP",
        "coxLP.coxph",
        "coxLP.cph",
        "coxLP.GLMnet",
        "coxLP.phreg",
        "coxLP.prodlim"
      ]
    },
    {
      "page": "coxModelFrame",
      "title": "Extract the design matrix used to train a Cox model",
      "topics": [
        "coxModelFrame",
        "coxModelFrame.coxph",
        "coxModelFrame.cph",
        "coxModelFrame.GLMnet",
        "coxModelFrame.phreg",
        "coxModelFrame.prodlim"
      ]
    },
    {
      "page": "coxN",
      "title": "Extract the number of observations from a Cox model",
      "topics": [
        "coxN",
        "coxN.CauseSpecificCox",
        "coxN.coxph",
        "coxN.cph",
        "coxN.default",
        "coxN.glm",
        "coxN.GLMnet",
        "coxN.phreg",
        "coxN.prodlim"
      ]
    },
    {
      "page": "coxSpecial",
      "title": "Special characters in Cox model",
      "topics": [
        "coxSpecial",
        "coxSpecial.coxph",
        "coxSpecial.cph",
        "coxSpecial.GLMnet",
        "coxSpecial.phreg",
        "coxSpecial.prodlim"
      ]
    },
    {
      "page": "coxStrata",
      "title": "Define the strata for a new dataset",
      "topics": [
        "coxStrata",
        "coxStrata.coxph",
        "coxStrata.cph",
        "coxStrata.GLMnet",
        "coxStrata.phreg",
        "coxStrata.prodlim"
      ]
    },
    {
      "page": "coxStrataLevel",
      "title": "Returns the name of the strata in Cox model",
      "topics": [
        "coxStrataLevel",
        "coxStrataLevel.coxph",
        "coxStrataLevel.cph",
        "coxStrataLevel.phreg",
        "coxStrataLevel.prodlim"
      ]
    },
    {
      "page": "coxVarCov",
      "title": "Extract the variance covariance matrix of the beta from a Cox model",
      "topics": [
        "coxVarCov",
        "coxVarCov.coxph",
        "coxVarCov.cph",
        "coxVarCov.phreg",
        "coxVarCov.prodlim"
      ]
    },
    {
      "page": "coxVariableName",
      "title": "Extract variable names from a model",
      "topics": [
        "coxVariableName"
      ]
    },
    {
      "page": "CSC",
      "title": "Cause-specific Cox proportional hazard regression",
      "topics": [
        "CSC"
      ]
    },
    {
      "page": "Ctree",
      "title": "S3-Wrapper for ctree.",
      "topics": [
        "Ctree"
      ]
    },
    {
      "page": "dicreteRoot",
      "title": "Dichotomic search for monotone function",
      "topics": [
        "discreteRoot"
      ]
    },
    {
      "page": "drop1.IPWbox",
      "title": "Update Large IPW values",
      "topics": [
        "drop1.IPWbox"
      ]
    },
    {
      "page": "FGR",
      "title": "Formula wrapper for crr from cmprsk",
      "topics": [
        "FGR"
      ]
    },
    {
      "page": "getSplitMethod",
      "title": "Input for data splitting algorithms",
      "topics": [
        "getSplitMethod"
      ]
    },
    {
      "page": "GLMnet",
      "title": "Formula interface for glmnet",
      "topics": [
        "GLMnet"
      ]
    },
    {
      "page": "Hal9001",
      "title": "Fitting HAL for use with predictRisk",
      "topics": [
        "Hal9001"
      ]
    },
    {
      "page": "iid.wglm",
      "title": "IID for IPCW Logistic Regressions",
      "topics": [
        "iid.wglm"
      ]
    },
    {
      "page": "iidCox",
      "title": "Extract iid decomposition from a Cox model",
      "topics": [
        "iidCox",
        "iidCox.CauseSpecificCox",
        "iidCox.coxph",
        "iidCox.cph",
        "iidCox.phreg",
        "iidCox.prodlim"
      ]
    },
    {
      "page": "influenceTest",
      "title": "Influence test [Experimental!!]",
      "topics": [
        "influenceTest",
        "influenceTest.default",
        "influenceTest.list"
      ]
    },
    {
      "page": "information.wglm",
      "title": "Information for IPCW Logistic Regressions",
      "topics": [
        "information.wglm"
      ]
    },
    {
      "page": "IPA",
      "title": "Explained variation for settings with binary, survival and competing risk outcome",
      "topics": [
        "IPA",
        "IPA.CauseSpecificCox",
        "IPA.coxph",
        "IPA.default",
        "IPA.glm",
        "rsquared",
        "rsquared.CauseSpecificCox",
        "rsquared.coxph",
        "rsquared.default",
        "rsquared.glm"
      ]
    },
    {
      "page": "ipcw",
      "title": "Estimation of censoring probabilities",
      "topics": [
        "ipcw",
        "ipcw.aalen",
        "ipcw.cox",
        "ipcw.marginal",
        "ipcw.none",
        "ipcw.nonpar"
      ]
    },
    {
      "page": "IPWbox",
      "title": "Encapsulate Weights",
      "topics": [
        "IPWbox"
      ]
    },
    {
      "page": "is.iidCox",
      "title": "Check Computation of the Influence Function in a Cox Model",
      "topics": [
        "is.iidCox"
      ]
    },
    {
      "page": "Melanoma",
      "title": "Malignant melanoma data",
      "topics": [
        "Melanoma"
      ]
    },
    {
      "page": "model.matrix.cph",
      "title": "Extract design matrix for cph objects",
      "topics": [
        "model.matrix.cph"
      ]
    },
    {
      "page": "model.matrix.phreg",
      "title": "Extract design matrix for phreg objects",
      "topics": [
        "model.matrix.phreg"
      ]
    },
    {
      "page": "model.tables.ate",
      "title": "Statistical Inference for the Average Treatment Effect",
      "topics": [
        "model.tables.ate"
      ]
    },
    {
      "page": "model.tables.wglm",
      "title": "Statistical Inference for Estimate from IPCW Logistic Regressions",
      "topics": [
        "model.tables.wglm"
      ]
    },
    {
      "page": "Paquid",
      "title": "Paquid sample",
      "topics": [
        "Paquid"
      ]
    },
    {
      "page": "penalizedS3",
      "title": "S3-wrapper for S4 function penalized",
      "topics": [
        "penalizedS3"
      ]
    },
    {
      "page": "plot.riskRegression",
      "title": "Plotting predicted risk",
      "topics": [
        "plot.riskRegression"
      ]
    },
    {
      "page": "plotAUC",
      "title": "Plot of time-dependent AUC curves",
      "topics": [
        "plotAUC"
      ]
    },
    {
      "page": "plotBrier",
      "title": "Plot Brier curve",
      "topics": [
        "plotBrier"
      ]
    },
    {
      "page": "plotCalibration",
      "title": "Plot Calibration curve",
      "topics": [
        "plotCalibration"
      ]
    },
    {
      "page": "plotEffects",
      "title": "Plotting time-varying effects from a risk regression model.",
      "topics": [
        "plotEffects"
      ]
    },
    {
      "page": "plotPredictRisk",
      "title": "Plotting predicted risks curves.",
      "topics": [
        "plotPredictRisk"
      ]
    },
    {
      "page": "plotRisk",
      "title": "plot predicted risks",
      "topics": [
        "plotRisk"
      ]
    },
    {
      "page": "plotROC",
      "title": "Plot ROC curves",
      "topics": [
        "plotROC"
      ]
    },
    {
      "page": "predict.CauseSpecificCox",
      "title": "Predicting Absolute Risk from Cause-Specific Cox Models",
      "topics": [
        "predict.CauseSpecificCox",
        "predictBig.CauseSpecificCox"
      ]
    },
    {
      "page": "predict.FGR",
      "title": "Predict subject specific risks (cumulative incidence) based on Fine-Gray regression model",
      "topics": [
        "predict.FGR"
      ]
    },
    {
      "page": "predict.riskRegression",
      "title": "Predict individual risk.",
      "topics": [
        "predict.riskRegression"
      ]
    },
    {
      "page": "predictCox",
      "title": "Survival probabilities, hazards and cumulative hazards from Cox regression models",
      "topics": [
        "predictCox"
      ]
    },
    {
      "page": "predictCoxPL",
      "title": "Deprecated Function for Product Limit Estimation of Survival Probabilities .",
      "topics": [
        "predictCoxPL"
      ]
    },
    {
      "page": "predictRisk",
      "title": "Extrating predicting risks from regression models",
      "topics": [
        "predictRisk",
        "predictRisk.aalen",
        "predictRisk.ARR",
        "predictRisk.BinaryTree",
        "predictRisk.CauseSpecificCox",
        "predictRisk.comprisk",
        "predictRisk.cox.aalen",
        "predictRisk.CoxConfidential",
        "predictRisk.coxph",
        "predictRisk.coxph.penal",
        "predictRisk.cph",
        "predictRisk.default",
        "predictRisk.double",
        "predictRisk.factor",
        "predictRisk.FGR",
        "predictRisk.flexsurvreg",
        "predictRisk.formula",
        "predictRisk.gbm",
        "predictRisk.glm",
        "predictRisk.GLMnet",
        "predictRisk.Hal9001",
        "predictRisk.integer",
        "predictRisk.IPWbox",
        "predictRisk.lrm",
        "predictRisk.matrix",
        "predictRisk.multinom",
        "predictRisk.numeric",
        "predictRisk.pecCforest",
        "predictRisk.pecCtree",
        "predictRisk.penfitS3",
        "predictRisk.prodlim",
        "predictRisk.psm",
        "predictRisk.randomForest",
        "predictRisk.ranger",
        "predictRisk.rfsrc",
        "predictRisk.riskRegression",
        "predictRisk.rpart",
        "predictRisk.selectCox",
        "predictRisk.singleEventCB",
        "predictRisk.SuperPredictor",
        "predictRisk.survfit",
        "predictRisk.survreg",
        "predictRisk.wglm"
      ]
    },
    {
      "page": "print.ate",
      "title": "Print Average Treatment Effects",
      "topics": [
        "print.ate"
      ]
    },
    {
      "page": "print.CauseSpecificCox",
      "title": "Print of a Cause-Specific Cox regression model",
      "topics": [
        "print.CauseSpecificCox"
      ]
    },
    {
      "page": "print.FGR",
      "title": "Print of a Fine-Gray regression model",
      "topics": [
        "print.FGR"
      ]
    },
    {
      "page": "print.GLMnet",
      "title": "Print of a glmnet regression model",
      "topics": [
        "print.GLMnet"
      ]
    },
    {
      "page": "print.influenceTest",
      "title": "Output of the DIfference Between Two Estimates",
      "topics": [
        "print.influenceTest"
      ]
    },
    {
      "page": "print.IPA",
      "title": "Print IPA object",
      "topics": [
        "print.IPA"
      ]
    },
    {
      "page": "print.predictCox",
      "title": "Print Predictions From a Cox Model",
      "topics": [
        "print.predictCox"
      ]
    },
    {
      "page": "print.predictCSC",
      "title": "Print Predictions From a Cause-specific Cox Proportional Hazard Regression",
      "topics": [
        "print.predictCSC"
      ]
    },
    {
      "page": "print.riskRegression",
      "title": "Print function for riskRegression models",
      "topics": [
        "print.riskRegression"
      ]
    },
    {
      "page": "print.Score",
      "title": "Print Score object",
      "topics": [
        "print.Score"
      ]
    },
    {
      "page": "print.subjectWeights",
      "title": "Print subject weights",
      "topics": [
        "print.subjectWeights"
      ]
    },
    {
      "page": "print.synth_code",
      "title": "Print synthesized code",
      "topics": [
        "print.synth_code"
      ]
    },
    {
      "page": "reconstructData",
      "title": "Reconstruct the original dataset",
      "topics": [
        "reconstructData"
      ]
    },
    {
      "page": "riskLevelPlot",
      "title": "Level plots for risk prediction models",
      "topics": [
        "riskLevelPlot"
      ]
    },
    {
      "page": "riskRegression",
      "title": "Risk Regression Fits a regression model for the risk of an event - allowing for competing risks.",
      "topics": [
        "ARR",
        "LRR",
        "riskRegression"
      ]
    },
    {
      "page": "riskRegression.options",
      "title": "Global options for 'riskRegression'",
      "topics": [
        "riskRegression.options"
      ]
    },
    {
      "page": "rowCenter_cpp",
      "title": "Apply - by row",
      "topics": [
        "rowCenter_cpp"
      ]
    },
    {
      "page": "rowCumSum",
      "title": "Apply cumsum in each row",
      "topics": [
        "rowCumSum"
      ]
    },
    {
      "page": "rowMultiply_cpp",
      "title": "Apply * by row",
      "topics": [
        "rowMultiply_cpp"
      ]
    },
    {
      "page": "rowPaste",
      "title": "Collapse Rows of Characters.",
      "topics": [
        "rowPaste"
      ]
    },
    {
      "page": "rowScale_cpp",
      "title": "Apply / by row",
      "topics": [
        "rowScale_cpp"
      ]
    },
    {
      "page": "rowSumsCrossprod",
      "title": "Apply crossprod and rowSums",
      "topics": [
        "rowSumsCrossprod"
      ]
    },
    {
      "page": "sampleData",
      "title": "Simulate data with binary or time-to-event outcome",
      "topics": [
        "sampleData"
      ]
    },
    {
      "page": "saveCoxConfidential",
      "title": "Save confidential Cox objects",
      "topics": [
        "saveCoxConfidential"
      ]
    },
    {
      "page": "saveSynth",
      "title": "Export a 'synth' object.",
      "topics": [
        "saveSynth"
      ]
    },
    {
      "page": "Score",
      "title": "Score risk predictions",
      "topics": [
        "Score",
        "Score.list"
      ]
    },
    {
      "page": "score.wglm",
      "title": "Score for IPCW Logistic Regressions",
      "topics": [
        "score.wglm"
      ]
    },
    {
      "page": "selectCox",
      "title": "Backward variable selection in the Cox regression model",
      "topics": [
        "selectCox"
      ]
    },
    {
      "page": "selectJump",
      "title": "Evaluate the influence function at selected times",
      "topics": [
        "selectJump"
      ]
    },
    {
      "page": "simActiveSurveillance",
      "title": "Simulate data of a hypothetical active surveillance prostate cancer study",
      "topics": [
        "simActiveSurveillance"
      ]
    },
    {
      "page": "simMelanoma",
      "title": "Simulate data alike the Melanoma data",
      "topics": [
        "simMelanoma"
      ]
    },
    {
      "page": "simPBC",
      "title": "simulating data alike the pbc data",
      "topics": [
        "simPBC"
      ]
    },
    {
      "page": "simsynth",
      "title": "Simulating from a synthesized object",
      "topics": [
        "simsynth"
      ]
    },
    {
      "page": "SmcFcs",
      "title": "SmcFcs",
      "topics": [
        "SmcFcs"
      ]
    },
    {
      "page": "splitStrataVar",
      "title": "Reconstruct each of the strata variables",
      "topics": [
        "splitStrataVar"
      ]
    },
    {
      "page": "subjectWeights",
      "title": "Estimation of censoring probabilities at subject specific times",
      "topics": [
        "subjectWeights",
        "subjectWeights.aalen",
        "subjectWeights.cox",
        "subjectWeights.km",
        "subjectWeights.marginal",
        "subjectWeights.none",
        "subjectWeights.nonpar"
      ]
    },
    {
      "page": "subsetIndex",
      "title": "Extract Specific Elements From An Object",
      "topics": [
        "subsetIndex",
        "subsetIndex.default",
        "subsetIndex.matrix"
      ]
    },
    {
      "page": "summary.ate",
      "title": "Summary Average Treatment Effects",
      "topics": [
        "summary.ate"
      ]
    },
    {
      "page": "summary.FGR",
      "title": "Summary of a Fine-Gray regression model",
      "topics": [
        "summary.FGR"
      ]
    },
    {
      "page": "summary.riskRegression",
      "title": "Summary of a risk regression model",
      "topics": [
        "summary.riskRegression"
      ]
    },
    {
      "page": "summary.Score",
      "title": "Summary of prediction performance metrics",
      "topics": [
        "summary.Score"
      ]
    },
    {
      "page": "SuperPredictor",
      "title": "Formula interface for SuperLearner::SuperLearner",
      "topics": [
        "SuperPredictor"
      ]
    },
    {
      "page": "SurvResponseVar",
      "title": "Extract the time and event variable from a Cox model",
      "topics": [
        "SurvResponseVar"
      ]
    },
    {
      "page": "synthesize",
      "title": "Cooking and synthesizing survival data",
      "topics": [
        "synthesize",
        "synthesize.formula",
        "synthesize.lvm"
      ]
    },
    {
      "page": "terms.phreg",
      "title": "Extract terms for phreg objects",
      "topics": [
        "terms.phreg"
      ]
    },
    {
      "page": "transformCIBP",
      "title": "Compute Confidence Intervals/Bands and P-values After a Transformation",
      "topics": [
        "transformCIBP"
      ]
    },
    {
      "page": "vcov.ate",
      "title": "Variance-Covariance Matrix for the Average Treatment Effect.",
      "topics": [
        "vcov.ate"
      ]
    },
    {
      "page": "vcov.wglm",
      "title": "Variance-covariance for IPCW Logistic Regressions",
      "topics": [
        "vcov.wglm"
      ]
    },
    {
      "page": "weights.ate",
      "title": "Extract Inverse Probability Weights",
      "topics": [
        "weights.ate"
      ]
    },
    {
      "page": "weights.wglm",
      "title": "Extract IPCW Weights",
      "topics": [
        "weights.wglm"
      ]
    },
    {
      "page": "wglm",
      "title": "Logistic Regression Using IPCW",
      "topics": [
        "wglm"
      ]
    }
  ],
  "_readme": "https://github.com/tagteam/riskregression/raw/HEAD/README.md",
  "_rundeps": [
    "backports",
    "base64enc",
    "bslib",
    "cachem",
    "checkmate",
    "cli",
    "cluster",
    "cmprsk",
    "codetools",
    "colorspace",
    "cpp11",
    "data.table",
    "diagram",
    "digest",
    "doParallel",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "foreign",
    "Formula",
    "fs",
    "future",
    "future.apply",
    "ggplot2",
    "glmnet",
    "globals",
    "glue",
    "gridExtra",
    "gtable",
    "highr",
    "Hmisc",
    "htmlTable",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
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