Package CPE. R topics documented: February 19, 2015
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1 Package CPE February 19, 2015 Title Concordance Probability Estimates in Survival Analysis Version Depends R (>= ),survival,rms Author Qianxing Mo, Mithat Gonen and Glenn Heller Maintainer Qianxing Mo <qmo@bcm.edu> Description Functions to calculate concordance probability estimates in survival analysis LazyData no License GPL (>= 2) Repository CRAN Date/Publication :21:46 NeedsCompilation yes R topics documented: phcpe phcpe Index 5 phcpe Gonen \& Heller Concordance Probability Estimate for the Cox Proportional Hazards model Description Usage A function to calculate Gonen \& Heller concordance probability estimate (CPE) for the Cox proportional hazards model. phcpe(coxfit, =FALSE,out.ties=FALSE) 1
2 2 phcpe Arguments coxfit out.ties A coxph or cph object A logical value indicating whether the standard error of the CPE should be calculated If out.ties is set to FALSE,pairs of observations tied on covariates will be used to calculate the CPE. Otherwise, they will not be used. Value CPE Concordance Probability Estimate the Standard Error of the Concordance Probability Estimate Author(s) Qianxing Mo, Mithat Gonen and Glenn Heller; <qmo@bcm.edu> References Mithat Gonen and Glenn Heller. (2005). Concordance probability and discriminatory power in proportional hazards regression. Biometrika, 92, 4, pp Examples ### create a simple data set for testing set.seed(199) nn < time <- rexp(nn) status <- sample(0:1, nn, replace=true) covar <- matrix(rnorm(3*nn), ncol=3) survd <- data.frame(time, status, covar) names(survd) <- c("time","status","x1","x2","x3") coxph.fit <- coxph(surv(time,status)~x1+x2+x3,data=survd) phcpe(coxph.fit) phcpe(coxph.fit,out.ties=true) #result is identical because the covariates are not tied # ### Calculate CPE and phcpe(coxph.fit, =TRUE) phcpe(coxph.fit, =TRUE,out.ties=TRUE) #*** For unknown reason, coxph.fit may need to be removed before running cph()*** rm(coxph.fit) cph.fit <- cph(surv(time, status)~x1+x2+x3, data=survd,method="breslow")
3 phcpe2 3 phcpe(cph.fit) phcpe(cph.fit,out.ties=true) ### Calculate CPE and phcpe(cph.fit, =TRUE) phcpe(cph.fit, =TRUE,out.ties=TRUE) phcpe2 Gonen \& Heller Concordance Probability Estimate for the Cox Proportional Hazards model Description A function to calculate Gonen \& Heller concordance probability estimate (CPE) for the Cox proportional hazards model. Usage phcpe2(coef,coef.var,design, =FALSE,out.ties=FALSE) Arguments coef coef.var design out.ties The coefficients of the Cox model. The covariance matrix of the coefficients of the Cox model. A design matrix for covariates. The rows correspond to subjects, and the columns correspond to covariates. A logical value indicating whether the standard error of the CPE should be calculated If out.ties is set to FALSE,pairs of observations tied on covariates will be used to calculate the CPE. Otherwise, they will not be used. Value CPE Concordance Probability Estimate the Standard Error of the Concordance Probability Estimate Author(s) Qianxing Mo, Mithat Gonen and Glenn Heller; <qmo@bcm.edu> References Mithat Gonen and Glenn Heller. (2005). Concordance probability and discriminatory power in proportional hazards regression. Biometrika, 92, 4, pp
4 4 phcpe2 Examples ### create a simple data set for testing set.seed(199) nn < time <- rexp(nn) status <- sample(0:1, nn, replace=true) covar <- matrix(rnorm(3*nn), ncol=3) survd <- data.frame(time, status, covar) names(survd) <- c("time","status","x1","x2","x3") coxph.fit <- coxph(surv(time,status)~x1+x2+x3,data=survd) phcpe(coxph.fit,=true) phcpe2(coef=coxph.fit$coefficients,coef.var=coxph.fit$var,design=model.matrix(coxph.fit)) #*** For unknown reason, coxph.fit may need to be removed before running cph()*** rm(coxph.fit) cph.fit <- cph(surv(time, status)~x1+x2+x3, data=survd,method="breslow") phcpe2(cph.fit$coefficients,coef.var=cph.fit$var,design=model.matrix(cph.fit),=true)
5 Index Topic survival phcpe, 1 phcpe2, 3 phcpe, 1 phcpe2, 3 5
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