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_l...@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-boun...@r-project.org >> [mailto:r-help-boun...@r-project.org] On Behalf Of Carlos M. >> Zambrana-Torrelio >> Sent: Monday, October 19, 2009 3:47 PM >> To: r-help@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 >> >> ______________________________________________ >> R-help@r-project.org 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. >> > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates (which may be known > outside the United States as Merck Frosst, Merck Sharp & Dohme or > MSD and in Japan, as Banyu - direct contact information for affiliates is > available at http://www.merck.com/contact/contacts.html) that may be > confidential, proprietary copyrighted and/or legally privileged. It is > intended solely for the use of the individual or entity named on this > message. If you are not the intended recipient, and have received this > message in error, please notify us immediately by reply e-mail and > then delete it from your system. > > -- Carlos M. Zambrana-Torrelio Department of Biology University of Puerto Rico - RP PO BOX 23360 San Juan, PR 00931-3360 ______________________________________________ R-help@r-project.org 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.
