R help - Oct 2009 - 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

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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