R help - Mar 2008 - Problem plotting curve on survival curve (something silly?)

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?

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?

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

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             ?ster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
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~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)              FAX: (+45) 35327907