Hi everyone,

    I have another "Random Forest" package question:

   - my (presumably incorrect) understanding of the varImpPlot is that it
   should plot the "% increase in MSE" and "IncNodePurity" exactly as can be
   found from the "importance" section of the model results.
      - However, the plot does not, in fact, match the "importance" section
      of the random forest model.

    E.g., if you use the example given in the ?randomForest, you will see
the plot showing the highest few "%IncMSE" values around 17 or 18%.  But if
you look at the $importance, it is 9.7, 9.4, 7.7, and 7.3.  Perhaps more
importantly, for the plot, it will show "wt" is highest %MSE, then "disp",
then "cyl", then "hp"; whereas the $importance will show "wt", then "disp",
then "hp", then "cyl".  And the ratios look somewhat different, too.
    Here is the code for that example:

set.seed(4543)
data(mtcars)
mtcars.rf <- randomForest(mpg ~ ., data=mtcars, ntree=1000,
keep.forest=FALSE,
importance=TRUE)
varImpPlot(mtcars.rf)

    I am using version 2.11.1 of 'R' and version 4.5-35 of Random Forest.

    I don't really care or need for the varImpPlot to work just right.  But
I am not sure which is accurate:  the varImpPlot or the $importance
section.  Which should I trust more, especially when they disagree
appreciably?

                                             Thanks!
                                                     Mike



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Some x-ray slides, a music score, Minard's Napoleanic war:
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  -- xkcd

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