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 ~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 ______________________________________________ R-help@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.
