ctree and survival problem

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ctree and survival problem

Moleps
Forgot to mention that the ctree command is from the party library.
//M

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Re: ctree and survival problem

Jonathan Daily
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 <[hidden email]> wrote:
> Forgot to mention that the ctree command is from the party library.
> //M
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
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Re: ctree and survival problem

Moleps
sessionInfo yields the following:

> 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 <[hidden email]> wrote:
>> Forgot to mention that the ctree command is from the party library.
>> //M
>>
>> ______________________________________________
>> [hidden email] 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.

______________________________________________
[hidden email] 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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Re: ctree and survival problem

Achim Zeileis-4
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 <[hidden email]> wrote:
>>> Forgot to mention that the ctree command is from the party library.
>>> //M
>>>
>>> ______________________________________________
>>> [hidden email] 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.
>
> ______________________________________________
> [hidden email] 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.
>

______________________________________________
[hidden email] 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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Re: ctree and survival problem

Moleps
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 <[hidden email]> wrote:
>>>> Forgot to mention that the ctree command is from the party library.
>>>> //M
>>>>
>>>> ______________________________________________
>>>> [hidden email] 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.
>>
>> ______________________________________________
>> [hidden email] 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.
>>

______________________________________________
[hidden email] 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.