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

Documentation for package ‘riskRegression’ version 2023.12.21

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-- A --

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

-- B --

baseHaz_cpp	C++ Fast Baseline Hazard Estimation
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
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.

-- D --

discreteRoot

Dichotomic search for monotone function

-- F --

FGR	Formula wrapper for crr from cmprsk

-- G --

getSplitMethod	Input for data splitting algorithms
GLMnet	Fitting GLMnet for use with predictRisk

-- H --

Hal9001

Fitting HAL for use with predictRisk

-- I --

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

-- 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.
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.CoxConfidential	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.multinom	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

-- R --

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

-- S --

sampleData	Simulate data with binary or time-to-event outcome
sampleDataTD	Simulate data with binary or time-to-event outcome
saveCoxConfidential	Save confidential Cox objects
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

-- T --

terms.phreg	Extract terms for phreg objects
transformCIBP	Compute Confidence Intervals/Bands and P-values After a Transformation

-- W --

wglm	Logistic Regression Using IPCW