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
[[alternative HTML version deleted]]
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
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
--
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 at ms.unimelb.edu.au http://www.ms.unimelb.edu.au
Hi, R users: I have a data.frame (not a matrix), I got a vector with the same length as the number of records (rows) of the data frame, and each element of that vector is the column number (in a specific range of columns) of the corresponding record that I must set to zero. How can I do this without a "for" loop? Thank you for your help. Kenneth
try:
DF2 <- as.data.frame(matrix(vec, nr=nrow(DF),nc=ncol(DF))=
matrix(1:ncol(DF),nr=nrow(DF),nc=ncol(DF),byrow=T))
DF3 <- data.frame(mapply(function(z,x,y) { x[y] <- 0 ; x },
names(DF), DF, DF2, SIMPLIFY=F))
but there must be an easier way...
Kenneth Cabrera a ??crit :
> Hi, R users:
>
> I have a data.frame (not a matrix), I got a vector with the same
> length as the
> number of records (rows) of the data frame, and each element of
> that vector is the column number (in a specific range of columns) of
> the corresponding
> record that I must set to zero.
>
> How can I do this without a "for" loop?
>
> Thank you for your help.
>
> Kenneth
>
>------------------------------------------------------------------------
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>
Hi eg. your data frame has 35 rows and 6 columns a<-sample(1:6, 35, replace=T) b<-1:35 vec<-rep(0,35*6) vec[a+6*(b-1)]<-1 This shall do the replacement your.d.f[matrix(vec,35,6, byrow=T)==1] <- 0 But I am not sure if it is quicker than a loop. HTH Petr On 18 Jan 2006 at 2:35, Kenneth Cabrera wrote: Date sent: Wed, 18 Jan 2006 02:35:35 -0500 From: Kenneth Cabrera <krcabrer at epm.net.co> To: r-help at stat.math.ethz.ch Subject: [R] Data frame index?> Hi, R users: > > I have a data.frame (not a matrix), I got a vector with the same > length as the number of records (rows) of the data frame, and each > element of that vector is the column number (in a specific range of > columns) of the corresponding record that I must set to zero. > > How can I do this without a "for" loop? > > Thank you for your help. > > Kenneth > >Petr Pikal petr.pikal at precheza.cz
you could try something like the following:
dat <- data.frame(matrix(rnorm(200), 20, 10))
index <- sample(10, 20, TRUE)
###############
mat.ind <- matrix(FALSE, nrow(dat), length(dat))
mat.ind[cbind(seq(along = index), index)] <- TRUE
dat[mat.ind] <- 0
index
dat
I hope it helps.
Best,
Dimitris
----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://www.med.kuleuven.be/biostat/
http://www.student.kuleuven.be/~m0390867/dimitris.htm
----- Original Message -----
From: "Kenneth Cabrera" <krcabrer at epm.net.co>
To: <r-help at stat.math.ethz.ch>
Sent: Wednesday, January 18, 2006 8:35 AM
Subject: [R] Data frame index?
> Hi, R users:
>
> I have a data.frame (not a matrix), I got a vector with the same
> length
> as the
> number of records (rows) of the data frame, and each element of
> that vector is the column number (in a specific range of columns) of
> the
> corresponding
> record that I must set to zero.
>
> How can I do this without a "for" loop?
>
> Thank you for your help.
>
> Kenneth
>
>
--------------------------------------------------------------------------------
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
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