Hi Andy,

It worked for classification, but not regression. For example:

> iris1 <- iris[-(1:5),]
> iris2 <- iris[(1:5),]
> iris2[1,3] <- NA
> iris2[3,1] <- NA
> iris_sum <- sum (iris$Sepal.Length + iris$Sepa.Width + iris$Petal.Length 
+ iris$Petal.Width)
> iris_sum1 <-  iris_sum[-(1:5)]
> iris_sum2 <-  iris_sum[(1:5)]
> iris_sum.rf <- randomForest (iris_sum1 ~ ., iris1[,c(1:4)])
>   predict (iris_sum.rf, iris2[-5])
>   predict (iris_sum.rf, iris2[-5])
[1]  9.556591  9.589573 10.104155

# Just to be clear I was hoping for behavior like the linear model has:

> iris_sum.lm <- lm (iris_sum1 ~ ., iris1[,c(1:4)])
>  predict (iris_sum.lm, iris2[-5])
   1    2    3    4    5 
  NA  9.5   NA  9.4 10.2 

In the event that this is not available in the regression part of 
randomForest, is a work around possible?



thanks,

Clayton




"Liaw, Andy" <andy_liaw@merck.com> 
04/25/2007 09:59 AM

To
clayton.springer@novartis.com, r-help@stat.math.ethz.ch
cc

Subject
RE: [R] NA and NaN randomForest






Hi Clayton,

If you use the formula interface, then it should do what you want:

R> library(randomForest)
randomForest 4.5-18 
Type rfNews() to see new features/changes/bug fixes.
R> iris1 <- iris[-(1:5),]
R> iris2 <- iris[1:5,]
R> iris2[1, 3] <- NA
R> iris2[3, 1] <- NA
R> iris.rf <- randomForest(Species ~ ., iris1)
R> predict(iris.rf, iris2[-5])
[1] <NA>   setosa <NA>   setosa setosa
Levels: setosa versicolor virginica

The problem, of course, is that the formula interface is not suitable
for data with large number of variables.  I'll look into doing the same
thing in the default method.

Andy


From: clayton.springer@novartis.com
> 
> Dear R-help,
> 
> This is about randomForest's handling of NA and NaNs in test set data.
> Currently, if the test set data contains an NA or NaN then 
> predict.randomForest will skip that row in the output.
> 
> I would like to change that behavior to outputting an NA.
> 
> Can this be done with flags to randomForest?
> If not can some sort of wrapper be built to put the NAs back in?
> 
> thanks,
> 
> Clayton
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