From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>

Date: Sun, 02 Mar 2008 23:49:57 +0100

Date: Sun, 02 Mar 2008 23:49:57 +0100

Calum wrote:

> OK this is bound to be something silly as I'm completely new to R -

*> having started using it yesterday. However I am already warming to its
**> lack of 'proper' GUI... I like being able to rerun a command by editing
**> one parameter easily... try and do that in a Excel Chart Wizzard!
**>
**> I eventually want to use it to analyse some chemotherapy response /
**> survival data. That data will not be mature and so my interest is in
**> using it to deliver predictions of what mature data may produce by using
**> Weibull Regression
**>
**> However for now I've borrowed a dataset from the BMJ (CSV tabs seperated
**> version here:
**> http://www.wittongilbert.free-online.co.uk/HepatitisData.csv ) and am
**> trying to plot some curves.
**>
**> I've succeeded in plotting a Kaplan-Meier Survival Curve by using the
**> following:
**>
**> > my_var.bygroup <- survfit(Surv (Survival, Censored==0) ~
**> TreatmentGroup, data=TestData)
**> > plot(my_var.bygroup, conf.int=FALSE, col=c("black","grey"), lty=1:2,
**> legend.text=c("Placebo","Prednisolone"), main="dKaplan-Meier Survival
**> Curve", xlab="Time (months)", ylab="Probability of Survival")
**>
**> That produces this: http://www.wittongilbert.free-online.co.uk/RGraph.jpg
**>
**> All of that is very nice so far. The I followed bits and pieces of
**> other peoples posts in the past to plot on a weibull regression...
**>
**> > my_curve.Plac <- survreg( Surv(Survival, Censored==0)~
**> TreatmentGroup, subset=TreatmentGroup=="Placebo", data=TestData,
**> dist='weibull')
**> > curve(pweibull(x, scale=exp(coef(my_curve.Plac)),
**> shape=1/my_curve.Plac$scale, lower.tail=FALSE),from=0, col="black",
**> to=max(TestData$Survival), add=TRUE)
**> > my_curve.Pred <- survreg( Surv(Survival, Censored==0)~
**> TreatmentGroup, subset=TreatmentGroup=="Prednisolone", data=TestData,
**> dist='weibull')
**> > curve(pweibull(x, scale=exp(coef(my_curve.Pred)),
**> shape=1/my_curve.Pred$scale, lower.tail=FALSE),from=0, col="grey",
**> to=max(TestData$Survival), add=TRUE)
**>
**> This is where I have my problem - and I know its going to be something
**> really silly! Look at my output:
**> http://www.wittongilbert.free-online.co.uk/RGraph2.jpg the trend line is
**> zig-zagging between y=0 and the value it should be. If you draw a line
**> along the tips of the zig-zags I guess thats a reasonable trendline...
**>
**> Anyone able to help me on this?
**>
*

I'd take a hard look at the pweibull(...) bit. Is "scale" really what
you want it to be? If coef(my_curve.Pred) is not a scalar, then it gets
recycled, which could easily cause oscillations.

> Also is it possible to get an R-squared type value for the fit of this

*> curve from someplace?
**>
**> Finally (three questions in one!) the first two censored data points (1
**> in each group) are actually lost to follow-ups. Should they be marked
**> differently from censored?
**>
*

Customarily they are not. (I'm sure it is possible to speculate at
length about it, though.)

> Sorry I know thats a mamoth post - and have a horrible feeling someone's

*> going to say 'You are trying to do something thats statistically wrong!'
**> - feel free!
**>
*

Nothing spectacularly incompetent this far... (I'm not happy with R^2
measures outside of linear models, or even within linear models, but
several well-reputed people do find them useful, so who am I to bicker?)

-- O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard_at_biostat.ku.dk) FAX: (+45) 35327907 ______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.Received on Sun 02 Mar 2008 - 22:52:31 GMT

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