R help - Jul 2004 - rpart and TREE, can be the same?

Hi, all,

I am wondering if it is possible to set parameters of 'rpart' and
'tree'
such that they will produce the exact same tree? Thanks.

Auston Wei
Statistical Analyst
Department of Biostatistics and Applied Mathematics
The University of Texas MD Anderson Cancer Center
Tel: 713-563-4281
Email: wwei@mdanderson.org
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I guess if you define the splitting criterion in rpart so that it matches
the one used in tree(), that's possible.  However, I believe the two also
differ in how they handle NAs.

Andy
> From:  WWei at mdanderson.org
> 
> Hi, all,
> 
> I am wondering if it is possible to set parameters of 'rpart' 
> and 'tree' 
> such that they will produce the exact same tree? Thanks.
> 
> Auston Wei
> Statistical Analyst
> Department of Biostatistics and Applied Mathematics
> The University of Texas MD Anderson Cancer Center
> Tel: 713-563-4281
> Email: wwei at mdanderson.org
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
> 
>

Hi, Andy,

Thank you again for your help. Tree( ) does have an option split='gini'
in
my version, which I recently downloaded from CRAN. The question is the 
tree.control only controls over mindev, no option for gini. Or maybe there 
is a way to specify a 'cp' like parameter when using gini index in tree(
)?

Thanks,
Auston






"Liaw, Andy" <andy_liaw@merck.com>

07/16/2004 02:04 PM



 

To:
"'WWei@mdanderson.org'" <WWei@mdanderson.org>
cc:





Subject:
RE: [R] rpart and TREE, can be the same?



Auston,
 
tree() does not use Gini as splitting criterion, AFAIK.  It uses deviance. 
 You can try to see if the various splitting criteria available in rpart 
is described in Terry's tech report (available on the Mayo Clinic web 
site).
 
Andy
-----Original Message-----
From: WWei@mdanderson.org [mailto:WWei@mdanderson.org] 
Sent: Friday, July 16, 2004 2:15 PM
To: Liaw, Andy
Subject: RE: [R] rpart and TREE, can be the same?


Thank you, Andy. Well, I tried 'gini' for both of them and my data has
no
NAs, but they still don't match. BTW, what is exactly the splitting 
criterion 'information' used in rpart? Thanks. 

Auston 





"Liaw, Andy" <andy_liaw@merck.com> 
Sent by: r-help-bounces@stat.math.ethz.ch 
07/16/2004 01:01 PM 



 

To: 
"'WWei@mdanderson.org'" <WWei@mdanderson.org>,
r-help@stat.math.ethz.ch
cc: 





Subject: 
RE: [R] rpart and TREE, can be the same?




I guess if you define the splitting criterion in rpart so that it matches
the one used in tree(), that's possible.  However, I believe the two also
differ in how they handle NAs.

Andy
> From:  WWei@mdanderson.org
> 
> Hi, all,
> 
> I am wondering if it is possible to set parameters of 'rpart' 
> and 'tree' 
> such that they will produce the exact same tree? Thanks.
> 
> Auston Wei
> Statistical Analyst
> Department of Biostatistics and Applied Mathematics
> The University of Texas MD Anderson Cancer Center
> Tel: 713-563-4281
> Email: wwei@mdanderson.org
>                  [[alternative HTML version deleted]]


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They are substantially different, even if I used 'gini' for both of them
and set feature parameters to 0's. Seems to me there is something more 
than splitting rule that governs the growth of tree. What could that be, 
other than sizes?
Thank you,
Auston






"Liaw, Andy" <andy_liaw@merck.com>

07/19/2004 09:38 AM



 

To:
"'WWei@mdanderson.org'" <WWei@mdanderson.org>
cc:





Subject:
RE: [R] rpart and TREE, can be the same?



Auston,
 
I see that now.  Have you tried setting mindev=0 in tree() and cp=0 in 
rpart(), to see if the unpruned trees are identical?  If so, you can 
probably try pruning the trees back using other tools in those packages. 
 
Cheers,
Andy


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