[R] randomForest partial dependence plots

Liaw, Andy andy_liaw at merck.com
Wed Sep 10 15:26:30 CEST 2008

The partial dependence at X1=x is simply the average of predicted
response at all data points, holding X1=x.  No additional
`normalization' is done.

That web link says the image does not exist.


From: Christopher Schwalm
> Hello ALL,
> I'm unsure how to interpret partial dependence plots and had 
> 2 questions:
> Does the randomForest library scale partial dependence plots 
> such that zero 
> on the y axis is mean(y)? I am also unclear as to why the 
> range of y on 
> these plots is smaller than what is in the dataset.
> Also I have noticed that partial dependence plots cluster 
> around the mean 
> response. That is, if I'm looking at the partial dependence 
> plot of y given 
> x1, x2, x3 and I standardize the x's (so they scale sensibly to be 
> displayed on one graph) then everything seems to meet at mean(y) and 
> z-score of 0 for all x's. The match is not exact but is close 
> and shows up 
> in all partial dependence plots I've looked at for this 
> particular project. 
> A sample graph of this is here:
> img213 imagevenue com/img php?image=48746_partial_plot_122_538lo jpg
> [replace spaces with dots, this bounces otherwise]
> I am unsure if this means anything or if it's built in (like 
> a SLR going 
> thru the mean of x an y). I should note that for this example I have 
> assumed that the y-axis is not scaled somehow (see first question).
> Any insight appreciated. Thanks for your time.
> Christopher
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