R help - Mar 2009 - error message obtained when plotting survival curves (error not previously obtained)

Hello,

I now receive an error message when obtaining a survival plot, which 
was not previously received with the same code. I recently updated 
all my packages. It does not seem to be a peculiarity of my data as I 
receive the error using data available in R. A plot is produced but I 
am uncertain regarding the error message.



 > library(surv2sample)
 > data(gastric)
 > fit <- survfit(Surv(time, event) ~ treatment, data = gastric)
Error in get(x, envir = ns, inherits = FALSE) :
   variable "survfit.km" was not found
 > #Default plot:
 > plot(fit)


regards

Bob Green

I cannot reproduce the error:

 > sessionInfo()
R version 2.8.1 Patched (2009-01-19 r47650)
i386-apple-darwin9.6.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets   
methods   base

other attached packages:
[1] surv2sample_0.1-2 lattice_0.17-20   Design_2.1-2       
survival_2.34-1   Hmisc_3.5-2
[6] boot_1.2-35

loaded via a namespace (and not attached):
[1] cluster_1.11.12 grid_2.8.1      tools_2.8.1

Be on notice that survfit in Design masks survfit in survival, but no  
error re-appears after detaching Design and Hmisc.

-- 
David Winsemius


On Mar 31, 2009, at 5:14 PM, Bob Green wrote:
>
> Hello,
>
> I now receive an error message when obtaining a survival plot, which  
> was not previously received with the same code. I recently updated  
> all my packages. It does not seem to be a peculiarity of my data as  
> I receive the error using data available in R. A plot is produced  
> but I am uncertain regarding the error message.
>
>
>
> > library(surv2sample)
> > data(gastric)
> > fit <- survfit(Surv(time, event) ~ treatment, data = gastric)
> Error in get(x, envir = ns, inherits = FALSE) :
>  variable "survfit.km" was not found
> > #Default plot:
> > plot(fit)
>
>
> regards
>
> Bob Green
>
> ______________________________________________
> 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

On Wed, 1 Apr 2009, Bob Green wrote:
>
> Hello,
>
> I now receive an error message when obtaining a survival plot, which was
not
> previously received with the same code. I recently updated all my packages.
It
> does not seem to be a peculiarity of my data as I receive the error using
data
> available in R. A plot is produced but I am uncertain regarding the error 
> message.
>
>
>
>> library(surv2sample)
>> data(gastric)
>> fit <- survfit(Surv(time, event) ~ treatment, data = gastric)
> Error in get(x, envir = ns, inherits = FALSE) :
>  variable "survfit.km" was not found
>> #Default plot:
>> plot(fit)
>
You don't show what packages you have loaded.  My guess would be that you
are calling Design::survfit rather than survival::survfit, and the problem is
due to the incompatibility between the most recent versions of Design and
survival. Frank Harrell and the folks at Vanderbilt are working on a new version
of Design.

       -thomas

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle