[R] ctree and survival problem

[Achim Zeileis]

On Thu, 28 Apr 2011, moleps wrote:

> sessionInfo yields the following:

OK, the "Design" package causes the problem here. When you load the Design 
package, it provides a new Surv() and related methods. This clashes with 
the computations of ctree() based on Surv(). So it's better not to load 
both packages simultaneously...
Z

>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats4    tcltk     splines   grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ipred_0.8-8        class_7.3-3        mlbench_2.1-0      rpart_3.1-46       party_0.9-99991    vcd_1.2-9          colorspace_1.0-1   strucchange_1.4-3  coin_1.0-18        mvtnorm_0.9-95
> [11] modeltools_0.2-17  Design_2.3-0       car_2.0-8          nnet_7.3-1         sandwich_2.2-6     boot_1.2-43        Amelia_1.2-18      lmtest_0.9-27      zoo_1.6-4          MASS_7.3-7
> [21] mgcv_1.7-2         cem_1.0.142        randomForest_4.6-2 lattice_0.19-17    nlme_3.1-97        rgl_0.92.798       Hmisc_3.8-3        survival_2.36-2    ggplot2_0.8.9      proto_0.3-8
> [31] reshape_0.8.3      plyr_1.4           foreign_0.8-41
>
> loaded via a namespace (and not attached):
> [1] cluster_1.13.2     digest_0.4.2       Matrix_0.999375-46 tools_2.11.1
>
>
> As i described in the original post I ran
>
>> example(ctree)
>
> and the following part yields an error:
>
>
>  if (require("ipred")) {
>        data("GBSG2", package = "ipred")
>        GBSG2ct <- ctree(Surv(time, cens) ~ .,data = GBSG2)
>        plot(GBSG2ct)
>        treeresponse(GBSG2ct, newdata = GBSG2[1:2,])
>    }
>
> Error in Summary.Surv(c(1814, 2018, 712, 1807, 772, 448, 2172, 2161, 471,  :
>  Invalid operation on a survival time
>
>
> //M
>
>
>
>
>
> On 28. apr. 2011, at 14.19, Jonathan Daily wrote:
>
>> It would help people who know more about R's guts than me if you
>> posted your sessionInfo() output and exactly what commands produced
>> your error.
>>
>> It is also recommended that you try simply upgrading R to the latest
>> version and see if you get an error with the latest version of
>> 'party'. My guess is that the error will go away.
>>
>> On Wed, Apr 27, 2011 at 3:40 PM, moleps <moleps2 at gmail.com> wrote:
>>> Forgot to mention that the ctree command is from the party library.
>>> //M
>>>
>>> ______________________________________________
>>> 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.
>>>
>>
>>
>>
>> --
>> ===============================================
>> Jon Daily
>> Technician
>> ===============================================
>> #!/usr/bin/env outside
>> # It's great, trust me.
>
> ______________________________________________
> 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.
>