[R] sampsize in Random Forests

[Liaw, Andy]

Are you sure there are 100 sites in your data?  Here's an example:

R> library(randomForest)
randomForest 4.5-23
Type rfNews() to see new features/changes/bug fixes.
R> f <- factor(sample(1:4, nrow(iris), replace=TRUE))
R> rf1 <- randomForest(iris[1:4], iris[[5]], strata=f, sampsize=rep(5,
nlevels(f)))
R> rf1

Call:
 randomForest(x = iris[1:4], y = iris[[5]], strata = f, sampsize =
rep(5,      nlevels(f))) 
               Type of random forest: classification
                     Number of trees: 500
No. of variables tried at each split: 2

        OOB estimate of  error rate: 4.67%
Confusion matrix:
           setosa versicolor virginica class.error
setosa         50          0         0        0.00
versicolor      0         47         3        0.06
virginica       0          4        46        0.08
 

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Naiara Pinto
> Sent: Sunday, March 09, 2008 5:19 PM
> To: r-help at r-project.org
> Subject: [R] sampsize in Random Forests
> 
> Hi all,
> 
> I have a dataset where each point is assigned to a class A, B, C, or
> D. Each point is also assigned to a study site. Each study site is
> coded with a number ranging between 1-100. This information is stored
> in the vector studySites.
> 
> I want to run randomForests using stratified sampling, so I 
> chose the option
> strata = factor(studySites)
> 
> But I am not sure how to control the number of samples taken from each
> study site. I tried to use 10 points from each study site:
> mySampSize = rep(10, 100)
> 
> So my function call looks like:
> RF = randomForest(myClass~., data=myData, mtry=5, importance=TRUE,
> strata = factor(studySites), sampsize=mySampSize)
> 
> But randomForest gives me the following error:
> Error in randomForest.default(m, y, ...) :
> sampsize can not be larger than class frequency
> 
> Does anybody have any idea why this happens?
> 
> Thank you very much,
> 
> Naiara.
> 
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> 
> 
> 


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