[R] Random Forest - partial dependence plot

Carlos M. Zambrana-Torrelio cmzambranat at gmail.com
Tue Oct 20 22:24:24 CEST 2009

Thanks Andy,

I'm sorry, I didn't clear myself. I was talking about the y-axis, so
your explanation was very helpful.

On Tue, Oct 20, 2009 at 9:39 AM, Liaw, Andy <andy_liaw at merck.com> wrote:
> Are you talking about the y-axis or the x-axis?  If you're talking about
> the y-axis, that range isn't really very meaningful.  The partial
> dependence function basically gives you the "average" trend of that
> variable (integrating out all others in the model).  It's the shape of
> that trend that is "important".  You may interpret the relative range of
> these plots from different predictor variables, but not the absolute
> range.  Hope that helps.
> Andy
>> -----Original Message-----
>> From: r-help-bounces at r-project.org
>> [mailto:r-help-bounces at r-project.org] On Behalf Of Carlos M.
>> Zambrana-Torrelio
>> Sent: Monday, October 19, 2009 3:47 PM
>> To: r-help at r-project.org
>> Subject: [R] Random Forest - partial dependence plot
>> Hi everybody,
>> I used random forest regression to explain the patterns of species
>> richness and a bunch of climate variables (e.g. Temperature,
>> precipitation, etc.) All are continuos variables. My results are
>> really interesting and my model explained 96,7% of the variance.
>> Now I am  trying to take advantage of the  importance variable
>> function and depicts the observed patterns using partial dependence
>> plots.
>> However, I found a really strange (at least for me...) behavior: the
>> species number ranges between 1 to 150, but when I make the partial
>> plot the graphic only represent values between 43 to 50!!
>> I  use the following code to get the partial plot:
>> partialPlot(ampric.rf, amp.data, "Temp")
>> where ampric.rf is the random forest object; amp.data are the data and
>> Temp is the variable I am interested.
>> How I can have partial plot explaining all species number
>> (from 1 to 150)??
>> Also, I read the RF documentation and I was wondering what its the
>> meaning of "marginal effect of a variable"
>> Thanks for your help
>> Carlos
>>  I found really interesting
>> --
>> Carlos M. Zambrana-Torrelio
>> Department of Biology
>> University of Puerto Rico - RP
>> PO BOX 23360
>> San Juan, PR 00931-3360
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Carlos M. Zambrana-Torrelio
Department of Biology
University of Puerto Rico - RP
PO BOX 23360
San Juan, PR 00931-3360

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