[R] interpretation of MDS plot in random forest

[mbressan at arpa.veneto.it]

thanks andy

it's a real honour form me to get a reply by you;
I'm still a bit faraway from a proper grasp of the purpose of the plot...

may I ask you for a more technical (trivial) issue?
is it possible to add a legend in the MDS plot?
my problem is to link the color points in the chart to the factor that was
used as response to train rf, how to?

best

max

> Yes, that's part of the intention anyway.  One can also use them to do
> clustering.
>
> Best,
> Andy
>
> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
> On Behalf Of Massimo Bressan
> Sent: Monday, December 02, 2013 6:34 AM
> To: r-help at r-project.org
> Subject: [R] interpretation of MDS plot in random forest
>
> Given this general example:
>
> set.seed(1)
>
> data(iris)
>
> iris.rf <- randomForest(Species ~ ., iris, proximity=TRUE,
> keep.forest=TRUE)
>
> #varImpPlot(iris.rf)
>
> #varUsed(iris.rf)
>
> MDSplot(iris.rf, iris$Species)
>
> I’ve been reading the documentation about random forest (at best of my -
> poor - knowledge) but I’m in trouble with the correct interpretation of
> the MDS plot and I hope someone can give me some clues
>
> What is intended for “the scaling coordinates of the proximity matrix”?
>
>
> I think to understand that the objective is here to present the distance
> among species in a parsimonious and visual way (of lower dimensionality)
>
> Is therefore a parallelism to what are intended the principal components
> in a classical PCA?
>
> Are the scaling coordinates DIM 1 and DIM2 the eigenvectors of the
> proximity matrix?
>
> If that is correct, how would you find the eigenvalues for that
> eigenvectors? And what are the eigenvalues repreenting?
>
>
> What are saying these two dimensions in the plot about the different
> iris species? Their relative distance in terms of proximity within the
> space DIM1 and DIM2?
>
> How to choose for the k parameter (number of dimensions for the scaling
> coordinates)?
>
> And finally how would you explain the plot in simple terms?
>
> Thank you for any feedback
> Best regards
>
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