[R] ctree and survival problem
moleps
moleps2 at gmail.com
Thu Apr 28 20:31:10 CEST 2011
Yup, thats the culprit. Thx.
//M
On 28. apr. 2011, at 18.36, Achim Zeileis wrote:
> 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.
>>
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