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