[R] Random Forest - partial dependence plot

Carlos M. Zambrana-Torrelio cmzambranat at gmail.com
Mon Oct 19 21:46:50 CEST 2009

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

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


 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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