[R] Surprising randomForest Results

[Rodney Barnett]

For the sake of anyone else asking this question....as Andy Liaw explained
to me, yes, this is expected because predict() uses all the trees in the
forest, including the ones based on any particular item in the input data
frame.

Rodney

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Rodney Barnett
Sent: Wednesday, October 01, 2008 10:01 AM
To: r-help at r-project.org
Subject: [R] Surprising randomForest Results

Is it expected that predict.randomForest() produces the response vector when
given the same data frame as provided to randomForest()?  See below.

Thanks.

Rodney

> rf <- randomForest (Species ~ ., iris)
> pc <- predict (rf, iris)
> confusion (pc, iris$Species)
            true
object       setosa versicolor virginica
  setosa         50          0         0
  versicolor      0         50         0
  virginica       0          0        50
attr(,"error")
[1] 0
> confusion (rf$predicted, iris$Species)
            true
object       setosa versicolor virginica
  setosa         50          0         0
  versicolor      0         47         3
  virginica       0          3        47
attr(,"error")
[1] 0.04
> rf$confusion
           setosa versicolor virginica class.error
setosa         50          0         0        0.00
versicolor      0         47         3        0.06
virginica       0          3        47        0.06
>

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