| anova.ate | Risk Comparison Over Time |
| ARR | Risk Regression Fits a regression model for the risk of an event - allowing for competing risks. |
| as.data.table.ate | Turn ate Object Into a 'data.table' |
| as.data.table.influenceTest | Turn influenceTest Object Into a 'data.table' |
| as.data.table.predictCox | Turn predictCox Object Into a 'data.table' |
| as.data.table.predictCSC | Turn predictCSC Object Into a 'data.table' |
| ate | Average Treatment Effects Computation |
| autoplot.ate | Plot Average Risks |
| autoplot.predictCox | Plot Predictions From a Cox Model |
| autoplot.predictCSC | Plot Predictions From a Cause-specific Cox Proportional Hazard Regression |
| autoplot.Score | ggplot AUC curve |
| baseHaz_cpp | C++ Fast Baseline Hazard Estimation |
| boot2pvalue | Compute the p.value from the distribution under H1 |
| boxplot.Score | Boxplot risk quantiles |
| calcSeCox | Computation of standard errors for predictions |
| calcSeCSC | Standard error of the absolute risk predicted from cause-specific Cox models |
| Cforest | S3-wrapper function for cforest from the party package |
| coef.CauseSpecificCox | Extract coefficients from a Cause-Specific Cox regression model |
| coef.riskRegression | Extract coefficients from riskRegression model |
| colCenter_cpp | Apply - by column |
| colCumSum | Apply cumsum in each column |
| colMultiply_cpp | Apply * by column |
| colScale_cpp | Apply / by column |
| confint.ate | Confidence Intervals and Confidence Bands for the Predicted Absolute Risk (Cumulative Incidence Function) |
| confint.influenceTest | Confidence Intervals and Confidence Bands for the Difference Between Two Estimates |
| confint.predictCox | Confidence Intervals and Confidence Bands for the predicted Survival/Cumulative Hazard |
| confint.predictCSC | Confidence Intervals and Confidence Bands for the Predicted Absolute Risk (Cumulative Incidence Function) |
| coxBaseEstimator | Extract the type of estimator for the baseline hazard |
| coxBaseEstimator.coxph | Extract the type of estimator for the baseline hazard |
| coxBaseEstimator.phreg | Extract the type of estimator for the baseline hazard |
| coxCenter | Extract the mean value of the covariates |
| coxCenter.coxph | Extract the mean value of the covariates |
| coxCenter.cph | Extract the mean value of the covariates |
| coxCenter.phreg | Extract the mean value of the covariates |
| coxFormula | Extract the formula from a Cox model |
| coxFormula.coxph | Extract the formula from a Cox model |
| coxFormula.cph | Extract the formula from a Cox model |
| coxFormula.glm | Extract the formula from a Cox model |
| coxFormula.phreg | Extract the formula from a Cox model |
| coxLP | Compute the linear predictor of a Cox model |
| coxLP.coxph | Compute the linear predictor of a Cox model |
| coxLP.cph | Compute the linear predictor of a Cox model |
| coxLP.phreg | Compute the linear predictor of a Cox model |
| coxModelFrame | Extract the design matrix used to train a Cox model |
| coxModelFrame.coxph | Extract the design matrix used to train a Cox model |
| coxModelFrame.cph | Extract the design matrix used to train a Cox model |
| coxModelFrame.phreg | Extract the design matrix used to train a Cox model |
| coxN | Extract the number of observations from a Cox model |
| coxN.CauseSpecificCox | Extract the number of observations from a Cox model |
| coxN.coxph | Extract the number of observations from a Cox model |
| coxN.cph | Extract the number of observations from a Cox model |
| coxN.glm | Extract the number of observations from a Cox model |
| coxN.phreg | Extract the number of observations from a Cox model |
| coxSpecial | Special characters in Cox model |
| coxSpecial.coxph | Special characters in Cox model |
| coxSpecial.cph | Special characters in Cox model |
| coxSpecial.phreg | Special characters in Cox model |
| coxStrata | Define the strata for a new dataset |
| coxStrata.coxph | Define the strata for a new dataset |
| coxStrata.cph | Define the strata for a new dataset |
| coxStrata.phreg | Define the strata for a new dataset |
| coxStrataLevel | Returns the name of the strata in Cox model |
| coxStrataLevel.coxph | Returns the name of the strata in Cox model |
| coxStrataLevel.cph | Returns the name of the strata in Cox model |
| coxStrataLevel.phreg | Returns the name of the strata in Cox model |
| coxVarCov | Extract the variance covariance matrix of the beta from a Cox model |
| coxVarCov.coxph | Extract the variance covariance matrix of the beta from a Cox model |
| coxVarCov.cph | Extract the variance covariance matrix of the beta from a Cox model |
| coxVarCov.phreg | Extract the variance covariance matrix of the beta from a Cox model |
| coxVariableName | Extract variable names from a model |
| CSC | Cause-specific Cox proportional hazard regression |
| Ctree | S3-Wrapper for ctree. |
| discreteRoot | Dichotomic search for monotone function |
| FGR | Formula wrapper for crr from cmprsk |
| getSplitMethod | Input for data splitting algorithms |
| GLMnet | Fitting GLMnet for use with predictRisk |
| Hal9001 | Fitting HAL for use with predictRisk |
| iid.wglm | IID for IPCW Logistic Regressions |
| iidCox | Extract iid decomposition from a Cox model |
| iidCox.CauseSpecificCox | Extract iid decomposition from a Cox model |
| iidCox.coxph | Extract iid decomposition from a Cox model |
| iidCox.cph | Extract iid decomposition from a Cox model |
| iidCox.phreg | Extract iid decomposition from a Cox model |
| influenceTest | Influence test [Experimental!!] |
| influenceTest.default | Influence test [Experimental!!] |
| influenceTest.list | Influence test [Experimental!!] |
| information.wglm | Information for IPCW Logistic Regressions |
| IPA | Explained variation for settings with binary, survival and competing risk outcome |
| IPA.CauseSpecificCox | Explained variation for settings with binary, survival and competing risk outcome |
| IPA.coxph | Explained variation for settings with binary, survival and competing risk outcome |
| IPA.default | Explained variation for settings with binary, survival and competing risk outcome |
| IPA.glm | Explained variation for settings with binary, survival and competing risk outcome |
| ipcw | Estimation of censoring probabilities |
| ipcw.aalen | Estimation of censoring probabilities |
| ipcw.cox | Estimation of censoring probabilities |
| ipcw.marginal | Estimation of censoring probabilities |
| ipcw.none | Estimation of censoring probabilities |
| ipcw.nonpar | Estimation of censoring probabilities |
| LRR | Risk Regression Fits a regression model for the risk of an event - allowing for competing risks. |
| Melanoma | Malignant melanoma data |
| model.matrix.cph | Extract design matrix for cph objects |
| model.matrix.phreg | Extract design matrix for phreg objects |
| Paquid | Paquid sample |
| penalizedS3 | S3-wrapper for S4 function penalized |
| plot.riskRegression | Plotting predicted risk |
| plotAUC | Plot of time-dependent AUC curves |
| plotBrier | Plot Brier curve |
| plotCalibration | Plot Calibration curve |
| plotEffects | Plotting time-varying effects from a risk regression model. |
| plotPredictRisk | Plotting predicted risks curves. |
| plotRisk | plot predicted risks |
| plotROC | Plot ROC curves |
| predict.CauseSpecificCox | Predicting Absolute Risk from Cause-Specific Cox Models |
| predict.FGR | Predict subject specific risks (cumulative incidence) based on Fine-Gray regression model |
| predict.riskRegression | Predict individual risk. |
| predictBig.CauseSpecificCox | Predicting Absolute Risk from Cause-Specific Cox Models |
| predictCox | Fast computation of survival probabilities, hazards and cumulative hazards from Cox regression models |
| predictCoxPL | Computation of survival probabilities from Cox regression models using the product limit estimator. |
| predictRisk | Extrating predicting risks from regression models |
| predictRisk.aalen | Extrating predicting risks from regression models |
| predictRisk.ARR | Extrating predicting risks from regression models |
| predictRisk.BinaryTree | Extrating predicting risks from regression models |
| predictRisk.CauseSpecificCox | Extrating predicting risks from regression models |
| predictRisk.comprisk | Extrating predicting risks from regression models |
| predictRisk.cox.aalen | Extrating predicting risks from regression models |
| predictRisk.coxph | Extrating predicting risks from regression models |
| predictRisk.coxph.penal | Extrating predicting risks from regression models |
| predictRisk.coxphTD | Extrating predicting risks from regression models |
| predictRisk.cph | Extrating predicting risks from regression models |
| predictRisk.CSCTD | Extrating predicting risks from regression models |
| predictRisk.default | Extrating predicting risks from regression models |
| predictRisk.double | Extrating predicting risks from regression models |
| predictRisk.factor | Extrating predicting risks from regression models |
| predictRisk.FGR | Extrating predicting risks from regression models |
| predictRisk.flexsurvreg | Extrating predicting risks from regression models |
| predictRisk.formula | Extrating predicting risks from regression models |
| predictRisk.gbm | Extrating predicting risks from regression models |
| predictRisk.glm | Extrating predicting risks from regression models |
| predictRisk.GLMnet | Extrating predicting risks from regression models |
| predictRisk.Hal9001 | Extrating predicting risks from regression models |
| predictRisk.integer | Extrating predicting risks from regression models |
| predictRisk.lrm | Extrating predicting risks from regression models |
| predictRisk.matrix | Extrating predicting risks from regression models |
| predictRisk.numeric | Extrating predicting risks from regression models |
| predictRisk.pecCforest | Extrating predicting risks from regression models |
| predictRisk.pecCtree | Extrating predicting risks from regression models |
| predictRisk.penfitS3 | Extrating predicting risks from regression models |
| predictRisk.prodlim | Extrating predicting risks from regression models |
| predictRisk.psm | Extrating predicting risks from regression models |
| predictRisk.randomForest | Extrating predicting risks from regression models |
| predictRisk.ranger | Extrating predicting risks from regression models |
| predictRisk.rfsrc | Extrating predicting risks from regression models |
| predictRisk.riskRegression | Extrating predicting risks from regression models |
| predictRisk.rpart | Extrating predicting risks from regression models |
| predictRisk.selectCox | Extrating predicting risks from regression models |
| predictRisk.singleEventCB | Extrating predicting risks from regression models |
| predictRisk.SuperPredictor | Extrating predicting risks from regression models |
| predictRisk.survfit | Extrating predicting risks from regression models |
| predictRisk.wglm | Extrating predicting risks from regression models |
| print.ate | Print Average Treatment Effects |
| print.CauseSpecificCox | Print of a Cause-Specific Cox regression model |
| print.FGR | Print of a Fine-Gray regression model |
| print.influenceTest | Output of the DIfference Between Two Estimates |
| print.IPA | Print IPA object |
| print.predictCox | Print Predictions From a Cox Model |
| print.predictCSC | Print Predictions From a Cause-specific Cox Proportional Hazard Regression |
| print.riskRegression | Print function for riskRegression models |
| print.Score | Print Score object |
| print.subjectWeights | Print subject weights |
| reconstructData | Reconstruct the original dataset |
| riskLevelPlot | Level plots for risk prediction models |
| riskRegression | Risk Regression Fits a regression model for the risk of an event - allowing for competing risks. |
| riskRegression.options | Global options for 'riskRegression' |
| rowCenter_cpp | Apply - by row |
| rowCumSum | Apply cumsum in each row |
| rowMultiply_cpp | Apply * by row |
| rowPaste | Collapse Rows of Characters. |
| rowScale_cpp | Apply / by row |
| rowSumsCrossprod | Apply crossprod and rowSums |
| rsquared | Explained variation for settings with binary, survival and competing risk outcome |
| rsquared.CauseSpecificCox | Explained variation for settings with binary, survival and competing risk outcome |
| rsquared.coxph | Explained variation for settings with binary, survival and competing risk outcome |
| rsquared.default | Explained variation for settings with binary, survival and competing risk outcome |
| rsquared.glm | Explained variation for settings with binary, survival and competing risk outcome |
| sampleData | Simulate data with binary or time-to-event outcome |
| sampleDataTD | Simulate data with binary or time-to-event outcome |
| Score | Score risk predictions |
| Score.list | Score risk predictions |
| score.wglm | Score for IPCW Logistic Regressions |
| selectCox | Backward variable selection in the Cox regression model |
| selectJump | Evaluate the influence function at selected times |
| simActiveSurveillance | Simulate data of a hypothetical active surveillance prostate cancer study |
| simMelanoma | Simulate data alike the Melanoma data |
| simPBC | simulating data alike the pbc data |
| simsynth | Simulating from a synthesized object |
| SmcFcs | SmcFcs |
| splitStrataVar | Reconstruct each of the strata variables |
| subjectWeights | Estimation of censoring probabilities at subject specific times |
| subjectWeights.aalen | Estimation of censoring probabilities at subject specific times |
| subjectWeights.cox | Estimation of censoring probabilities at subject specific times |
| subjectWeights.km | Estimation of censoring probabilities at subject specific times |
| subjectWeights.marginal | Estimation of censoring probabilities at subject specific times |
| subjectWeights.none | Estimation of censoring probabilities at subject specific times |
| subjectWeights.nonpar | Estimation of censoring probabilities at subject specific times |
| subsetIndex | Extract Specific Elements From An Object |
| subsetIndex.default | Extract Specific Elements From An Object |
| subsetIndex.matrix | Extract Specific Elements From An Object |
| summary.ate | Summary Average Treatment Effects |
| summary.FGR | Summary of a Fine-Gray regression model |
| summary.riskRegression | Summary of a risk regression model |
| summary.Score | Summary of prediction performance metrics |
| SuperPredictor | Formula interface for SuperLearner::SuperLearner |
| SurvResponseVar | Extract the time and event variable from a Cox model |
| synthesize | Cooking and synthesizing survival data |
| synthesize.formula | Cooking and synthesizing survival data |
| synthesize.lvm | Cooking and synthesizing survival data |
| terms.phreg | Extract terms for phreg objects |
| transformCIBP | Compute Confidence Intervals/Bands and P-values After a Transformation |
| wglm | Logistic Regression Using IPCW |