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

[David Winsemius]

On Dec 8, 2009, at 12:17 PM, David Winsemius wrote:

>
> 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?
>

Meant to say that pbc$edema was numeric. Got success in reproducing  
the problem using a Hist object instead of a Surv object and, ... no,  
changing edema to a factor variable does not solve the problem. How  
about sending an email to the author?


> -- 
> 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.
>>
>> ______________________________________________
>> 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.
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
> ______________________________________________
> 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.

David Winsemius, MD
Heritage Laboratories
West Hartford, CT