[R] R survAUC Package

[David Winsemius]

On Dec 4, 2013, at 7:49 AM, kevinod wrote:

> I have a concern about the survAUC package option AUC.cd.  
> 

So shouldn't you be sending this to the package authors? They may or may not be regular readers of R help. It's apackage I have never heard of.

> I am exploring package functionality, specifically AUC statistics for Cox
> Regression, for a small academic project
> 
> When utilizing this package on the ovarian data set within that package I
> obtain an AUC statistic of 0.3322928.  When AUC calculations use a
> dichotomous outcome such as this, see included R code, the result should lie
> between 0.5 and 1, not 0.33.
> 
> Please explain this, I am not certain that the algorithm that is being
> utilized for this package is correct.
> 
> Thank you
> 
> Kevin O’Donnell, MS Work Environment, MS Env Eng.,  MS Const Project Mgmt
> Graduate Student
> Department of Biostatistics
> Boston University School of Public Health
> 715 Albany Street Boston, MA
> 
> 617-480-1677
> 
> x11(h=8,w=11)
> fit = survfit(Surv(futime,fustat) ~ rx)
> plot(fit, mark.time=FALSE, xscale=365.25,main="Plot of Survival Curves by
> Prescription Status",
>        xlab='Length of Survival', ylab='Proportion of Individuals who have
> Survived')
> lines(fit[1], lwd=3,lty=2:3, xscale=365.24,col=2)
> lines(fit[2], lwd=2,lty=2:2, xscale=365.24,col=3)
> legend(.2,.2, c("No treatment", "treatment"), lwd=3,lty = 2:3) 
> 
> 
> TR2 = ovarian[1:16,]
> TE2 = ovarian[17:26,]
> train.fit2  = coxph(Surv(futime, fustat) ~ rx,
>                    x=TRUE, y=TRUE, method="efron", data=TR)
> lp2 = predict(train.fit) 
> lpnew2 = predict(train.fit2, newdata=TE2)
> Surv.rsp2 = Surv(TR2$futime, TR2$fustat)
> Surv.rsp.new2 = Surv(TE2$futime, TE2$fustat)
> times2 = seq(10, 1000, 10)                  
> 
> AUC_CD2 = AUC.cd(Surv.rsp2, Surv.rsp.new2, lp2, lpnew2, times2)
> 
> 
> AUC_hc2 = AUC.hc(Surv.rsp2, Surv.rsp.new2, lpnew2, times2)
> 
> 
> AUC_sh2 = AUC.sh(Surv.rsp2, Surv.rsp.new2, lp2, lpnew2, times2)
> 
> 
> AUC_Uno2 = AUC.uno(Surv.rsp2, Surv.rsp.new2, lpnew2, times2)
> 
> 
> 
> 
> --
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> 
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David Winsemius
Alameda, CA, USA