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

Documentation for package ‘riskRegression’ version 1.3.7

DESCRIPTION file.

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-- A --

ARR	Risk Regression Fits a regression model for the risk of an event - allowing for competing risks.
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 effect using CSC.

-- B --

boxplot.Score

Boxplot risk quantiles

-- C --

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
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
CoxDesign	Extract the design matrix used to train a Cox model
CoxDesign.coxph	Extract the design matrix used to train a Cox model
CoxDesign.phreg	Extract the design matrix used to train a Cox model
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
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
CoxSpecialStrata	Special character for strata in Cox model
CoxSpecialStrata.coxph	Special character for strata in Cox model
CoxSpecialStrata.cph	Special character for strata in Cox model
CoxSpecialStrata.phreg	Special character for strata 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
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

-- E --

extractStrata

Extract the information about the strata

-- F --

FGR	Formula wrapper for crr from cmprsk
findP1	Compute the p.value from the distribution under H1

-- I --

IClambda2hazard	Evaluate the influence function for the hazard based on the one of the baseline hazard##'
iid	Extract i.i.d. decomposition from a Cox model
iidCox	Extract i.i.d. decomposition from a Cox model
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.phreg	Extract design matrix for phreg objects

-- P --

penalizedS3	S3-wrapper for S4 function penalized
plot.predictCSC	Plot predictions from a Cause-specific Cox proportional hazard regression
plot.riskRegression	Plotting predicted risk
plotAUC	Plot AUC curve
plotBrier	Plot Brier curve
plotCalibration	Plot Calibration curve
plotEffects	Plotting time-varying effects from a risk regression model.
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
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
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.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

-- Q --

qplot.predictCox	Plot predictions from a Cox model
qplot.predictCSC	Plot predictions from a Cause-specific Cox proportional hazard regression
qplotAUC	Plot AUC curve

-- R --

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

-- S --

sampleData	Simulate data with binary or time-to-event outcome
Score	Score risk predictions
Score.list	Score risk predictions
seCSC	Standard error of the absolute risk predicted from cause-specific Cox models
selectJump	Evaluate the influence function at selected times
seRobustCox	Computation of standard errors for predictions
simMelanoma	Simulate data alike the Melanoma data
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