[R] randomForest

[Weiwei Shi]

Hi there:
I have a question on random foresst:

recently i helped a friend with her random forest and i came with this problem:
her dataset has 6 classes and since the sample size is pretty small:
264 and the class distr is like this (Diag is the response variable)
sample.size <- lapply(1:6, function(i) sum(Diag==i))
> sample.size
[[1]]
[1] 36

[[2]]
[1] 12

[[3]]
[1] 120

[[4]]
[1] 36

[[5]]
[1] 30

[[6]]
[1] 30

I assigned this sample.size to sampsz for a stratiefied sampling
purpose and i got the following error:
Error in sum(..., na.rm = na.rm) : invalid 'mode' of argument

if I use sampsz=c(36, 12, 120, 36, 30, 30), then it is fine. Could you
tell me why?
btw, as to classification problem for this with uneven class number
situation, do u have some suggestions to improve its accuracy?  I
tried to use c() way to make the sampsz works but the result is
similar.

Thanks,

weiwei

On 6/30/05, Liaw, Andy <andy_liaw at merck.com> wrote:
> The limitation comes from the way categorical splits are represented in the
> code:  For a categorical variable with k categories, the split is
> represented by k binary digits: 0=right, 1=left.  So it takes k bits to
> store each split on k categories.  To save storage, this is `packed' into a
> 4-byte integer (32-bit), thus the limit of 32 categories.
> 
> The current Fortran code (version 5.x) by Breiman and Cutler gets around
> this limitation by storing the split in an integer array.  While this lifts
> the 32-category limit, it takes much more memory to store the splits.  I'm
> still trying to figure out a more memory efficient way of storing the splits
> without imposing the 32-category limit.  If anyone has suggestions, I'm all
> ears.
> 
> Best,
> Andy
> 
> > From: Arne.Muller at sanofi-aventis.com
> >
> > Hello,
> >
> > I'm using the random forest package. One of my factors in the
> > data set contains 41 levels (I can't code this as a numeric
> > value - in terms of linear models this would be a random
> > factor). The randomForest call comes back with an error
> > telling me that the limit is 32 categories.
> >
> > Is there any reason for this particular limit? Maybe it's
> > possible to recompile the module with a different cutoff?
> >
> >       thanks a  lot for your help,
> >       kind regards,
> >
> >
> >       Arne
> >
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> >
> >
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-- 
Weiwei Shi, Ph.D

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