Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

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Documentation for package ‘riskRegression’ version 2019.01.29

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A B C D F G I L M P R S T

-- A --

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.ateRobust 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 Compute the Average Treatment Effects Via the G-formula
ateRobust Average Treatment Effects (ATE) for survival outcome (with competing risks) using doubly robust estimating equations
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

-- B --

boot2pvalue Compute the p.value from the distribution under H1
boxplot.Score Boxplot risk quantiles

-- C --

calcSeCox Computation of standard errors for predictions
calcSeCSC Standard error of the absolute risk predicted from cause-specific Cox models
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
colSumsCrossprod Apply crossprod and colSums
confBandCox Compute quantiles of a gaussian process
confint.ate Confidence Intervals and Confidence Bands for the Predicted Absolute Risk (Cumulative Incidence Function)
confint.ateRobust Confidence Intervals for the Average Treatment Effect
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.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.coxph Extract the number of observations from a Cox model
coxN.cph 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

-- D --

discreteRoot Dichotomic search for monotone function

-- F --

FGR Formula wrapper for crr from cmprsk

-- G --

getSplitMethod Input for data splitting algorithms

-- I --

iidCox Extract i.i.d. decomposition from a Cox model
influenceTest Influence test [Experimental!!]
influenceTest.default Influence test [Experimental!!]
influenceTest.list Influence test [Experimental!!]
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

-- L --

LRR Risk Regression Fits a regression model for the risk of an event - allowing for competing risks.

-- M --

Melanoma Malignant melanoma data
model.matrix.cph Extract design matrix for cph objects
model.matrix.phreg Extract design matrix for phreg objects

-- P --

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.
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.
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.CauseSpecificCox Extrating predicting risks from regression models
predictRisk.cox.aalen Extrating predicting risks from regression models
predictRisk.coxph Extrating predicting risks from regression models
predictRisk.cph Extrating predicting risks from regression models
predictRisk.default Extrating predicting risks from regression models
predictRisk.FGR Extrating predicting risks from regression models
predictRisk.glm Extrating predicting risks from regression models
predictRisk.lrm Extrating predicting risks from regression models
predictRisk.matrix Extrating predicting risks from regression models
predictRisk.pecCforest Extrating predicting risks from regression models
predictRisk.pecCtree 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.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.survfit Extrating predicting risks from regression models
predictSurv Compute Event-Free Survival From a CSC Object
print.ate Print Average Treatment Effects
print.ateRobust Print Average Treatment Effect
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.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

-- R --

reconstructData Reconstruct the original dataset
riskRegression Risk Regression Fits a regression model for the risk of an event - allowing for competing risks.
rowCenter_cpp Apply - by row
rowCumSum Apply cumsum in each row
rowMultiply_cpp Apply * by row
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

-- S --

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
selectCox Backward variable selection in the Cox regression model
selectJump Evaluate the influence function at selected times
simMelanoma Simulate data alike the Melanoma data
sliceMultiplyPointer_cpp Apply * by slice
sliceMultiply_cpp Apply * by slice
sliceScalePointer_cpp Apply / by slice
sliceScale_cpp Apply / by slice
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
summary.FGR Summary of a Fine-Gray regression model
summary.riskRegression Summary of a risk regression model
SurvResponseVar Extract the time and event variable from a Cox model

-- T --

terms.phreg Extract terms for phreg objects
transformCI Compute Confidence Intervals using a transformation
transformCIBP Compute Confidence Intervals/Bands and P-values After a Transformation
transformIID Compute Influence Functions after Transformation
transformP Compute P-values After a Transformation
transformSE Compute Standard Errors after Transformation