Andrew,
Thanks for the suggestion!  This seems to have fixed things.  I was wondering if you could explain why this works and what was wrong.  If I issue the command 

>my.boot<-boot(dataframe,cs,R=999)  

and in order to what effect the command you told me use has I then do something like

>dataframe[my.boot$weights,]

my.boot$weights looks to be a vector where element is 1/sample size.R reports that 

[1] var1    var2   var3   var4 var5
<0 rows> (or 0-length row.names)

 Which indicates to me that I then have a dataframe with no data in it! (Am I wrong about this?)  What is going on here?  Why did this work?  Sorry for the basic questions.

Ben


-------------------------------
Benjamin Ridenhour
School of Biological Sciences
Washigton State University
P.O. Box 644236
Pullman, WA 99164-4236
Phone (509)335-7218
-------------------------------- 
"Nothing in biology makes sense except in the light of evolution."
-T. Dobzhansky


----- Original Message ----
From: Andrew Robinson <A.Robinson@ms.unimelb.edu.au>

Cc: r-help@stat.math.ethz.ch
Sent: Tue Jan 17 22:20:55 2006
Subject: Re: [R] Bootstrapping help

The first thing you are doing wrong is that you are not including a
copy of cs for us to see ;).

Based on what you have written, I speculate that cs does not use the
index correctly.  if so then a simple, although inefficient,
workaround is to rewrite cs:

cs <- function(dataframe, index) {
    dataframe <- dataframe[index,]
    ...
}

Good luck, 

Andrew

On Tue, Jan 17, 2006 at 10:02:49PM -0800, Ben Ridenhour wrote:
> Hello,
>  I am new to using R and I am having problems get boot() to work properly.  Here is what I am trying to do:
>  
>  I have statistic called "cs".  cs takes a data matrix (154 x 5) and calculates 12 different scores for me.  cs outputs the data as a vector (12 x 1).  cs doesn't really use weights, per se, however I have included this as one of the 2 arguments cs can take.
>  
>  I try performing a bootstrap by issuing: 
>  myout<-boot(data, cs,R=999) 
>  I have tried other versions where I specify stype="w", etc...
>  
>  The problem I get is that the dataset does not seem to be resampled.  I end up with 999 replicates that have the exact same value of the output of cs.
>  
>  In the end I have something like
>  
>  Bootstrap Statistics :
>           original        bias    std. error
>  t1*   0.865122275  1.698641e-14           0
>  t2*  -0.005248414 -9.627715e-17           0
>  t3*  -0.052833740 -8.812395e-16           0
>  t4*   0.807040121  1.287859e-14           0
>  t5*   0.542082588 -9.103829e-15           0
>  t6*  -0.018617838 -7.285839e-17           0
>  t7*   0.006409704  1.422473e-16           0
>  t8*   0.529874453  8.104628e-15           0
>  t9*   0.074804390  2.359224e-16           0
>  t10* -0.007153634  1.301043e-16           0
>  t11* -0.018241243 -2.359224e-16           0
>  t12*  0.049409513 -1.200429e-15           0
>  
>  Clearly the bootstrap is not working.  What am I doing wrong?
>  
>  Thanks,
>  Ben
>  
>    
> -------------------------------
> Benjamin Ridenhour
> School of Biological Sciences
> Washigton State University
> P.O. Box 644236
> Pullman, WA 99164-4236
> Phone (509)335-7218
> -------------------------------- 
> "Nothing in biology makes sense except in the light of evolution."
> -T. Dobzhansky
> 
> 
> 
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> 
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-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
Email: a.robinson@ms.unimelb.edu.au         http://www.ms.unimelb.edu.au




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