[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.
Andy
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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