[R] "prodlim" problem with censor ticks in stratified KM plot

[David Winsemius]

On Dec 8, 2009, at 11:49 AM, bnorth wrote:

>
> I am having a problem with the censor tick marks with plot and prodlim
> I am using the example code from ?prodlim but I have added  
> mark.time=T to
> the plot command to get tick marks at censor times.
> The problem is the tick marks occur at exactly the same point in  
> each of the
> arms.
> This seems wrong as the censorings do not occur at the same times in  
> each
> arm.
>
> pfit.edema <- prodlim(Surv(time,status)~edema,data=pbc)

I get an error here, I think because status has three values and Surv  
expects two but possibly because my efforts to work around the Design  
overlays to the survival package were not correct. I tried a few other  
approaches to getting the code to work, but failed.

I did notice that pbc$status is numeric rather than a factor, and  
wondered if that three level categorical variable might be treated  
differently by the various functions you are using because of its R  
class. Perhaps if you created a factor pbc$stat2, it might work  
correctly?

-- 
David

> summary(pfit.edema)
> summary(pfit.edema,intervals=TRUE)
> plot(pfit.edema,mark.time=T)
>
> Here is my sessionInfo
>
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets   
> methods
> [8] base
>
> other attached packages:
> [1] prodlim_1.0.5      survival_2.35-7    KernSmooth_2.22-22
>
>
> many many thanks to anyone who can spot my error
> -- 
> View this message in context: http://n4.nabble.com/prodlim-problem-with-censor-ticks-in-stratified-KM-plot-tp955433p955433.html
> Sent from the R help mailing list archive at Nabble.com.
>
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT