From: Calum <stats_at_wittongilbert.free-online.co.uk>

Date: Sun, 02 Mar 2008 22:14:57 +0000

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 - 22:18:15 GMT

Date: Sun, 02 Mar 2008 22:14:57 +0000

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!

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?

Also is it possible to get an R-squared type value for the fit of this curve from someplace?

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!

Many thanks

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 - 22:18:15 GMT

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