[R] boot.ci error with large data sets
Dear List
I have run into some problems with boot.ci from package boot. When I
try to obtain a confidence interval of type bca, boot.ci() returns the
following error when the data set i large:
Error in bca.ci(boot.out, conf, index[1L], L = L, t = t.o, t0 =
t0.o, :
estimated adjustment 'a' is NA
Below is an example that produces the above mentioned error on my
machine.
library(boot)
#The wrapper function:
w.mean <- function(x, d) {
E <- x[d,]
return(weighted.mean(E$A, E$B))}
#Some fake data:
test <- data.frame(rnorm(1000, 5), rnorm(1000, 3))
test1 <- data.frame(rnorm(1, 5), rnorm(1, 3))
names(test) <- c("A", "B")
names(test1) <- c("A", "B")
# Getting the boot object and the CI, seem to works fine
bootout <- boot(test, w.mean, R=1000, stype="i")
(bootci <- boot.ci(bootout, conf = 0.95, type = "bca"))
# Now with a bigger data set, boot.ci returns an error.
bootout1 <- boot(test1, w.mean, R=1000, stype="i")
(bootci1 <- boot.ci(bootout1, conf = 0.95, type = "bca"))
Does anyone have an idea as to why this happens? (Session info below)
Best,
Lars
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] da_DK.UTF-8/da_DK.UTF-8/C/C/da_DK.UTF-8/da_DK.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] boot_1.2-43
loaded via a namespace (and not attached):
[1] tools_2.12.1
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Re: [R] Odd crash with tcl/tk
Hi Peter
Spot on! You where absolutely right. After installing the tcltk bits
it worked just fine.
Thank you very much!
Lars
On Aug 17, 4:36 pm, peter dalgaard wrote:
> Sorry to chime in late (for some reason, I was not at the Mac when this came
> in originally).
>
> I can't reproduce the situation. One guess is that you haven't installed the
> tcltk bits, as indicated on thehttp://cran.at.r-project.org/bin/macosx/page.
>
> -pd
>
> On Aug 17, 2010, at 4:12 PM, Lars Dalby wrote:
>
>
>
>
>
> > Hi
>
> > @ Andrew: Did you get this problem solved?
> > I am having similar problems and have tried to work around it using
> > options(gsubfn.engine = "R") as suggested by Gabor.
> > However, this don't solve on my machine. R just freezes up trying to
> > execute read.csv.sql()
>
> > On OSX 10.6.4, R 2.11.1 (2010-05-31) 64bit
>
> > Any help is much appreciated!
>
> > Lars
>
> > On Jul 28, 9:41 pm, Gabor Grothendieck
> > wrote:
> >> On Wed, Jul 28, 2010 at 10:06 AM, AndrewPage wrote:
>
> >>> Hi,
>
> >>> Recently, I've been trying to use packages in R that require loading the
> >>> Tcl/Tk interface. However, I get a strange result and a crash that I
> >>> haven't been able to find discussion about on these boards (or any
> >>> others).
>
> >>> When I enter library(tcltk), it reads "Loading Tcl/Tk interface ... ", but
> >>> then never says "done" or displays some sort of error message. Looks like
> >>> this:
>
> >>>> x11()
> >>>> library(tcltk)
> >>> Loading Tcl/Tk interface ...
>
> >>> Now you can type additional commands in, at your peril! For example, if I
> >>> type in the text "library", nothing happens, but "library(" causes R to
> >>> freeze up irreparably, with "executing:
> >>> try(gsub('\\s+','',paste(capture.output(print(args(library,collapse="))
> >>> ,silent=TRUE)"
> >>> displayed at the bottom. When this happens, there's nothing you can do
> >>> but
> >>> restart R because it's completely frozen.
>
> >>> I'm running R version 2.11.1 Patched (2010-07-27 r52627)
>
> >>> [R.app GUI 1.35 (5603) i386-apple-darwin9.8.0]
>
> >>> with XQuartz 2.3.5 (xorg-server 1.4.2-apple53)
>
> >>> on a mac (snow leopard)
>
> >>> Thanks for any help/suggestions in advance,
>
> >>> Andrew
>
> >> One thought is that if this is to use gsubfn or sqldf (which uses
> >> gsubfn) then you can get them to not use thetcltkcode but use R code
> >> instead by either of these two means:
>
> >> 1. issue the command:
> >> options(gsubfn.engine = "R")
> >> before issuing your library(sqldf) or library(gsubfn) command. You
> >> can put the options command in your .Rprofile if you like and then you
> >> will have it on every session.
>
> >> or
>
> >> 2. use a build of R that has notcltkin it. In that case it will
> >> recognize it and switch to using R. I believe one such build exists
> >> for the Mac.
>
> >> __
> >> r-h...@r-project.org mailing
> >> listhttps://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
>
> > __
> > r-h...@r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> Peter Dalgaard
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd@cbs.dk Priv: pda...@gmail.com
>
> __
> r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd crash with tcl/tk
Hi
@ Andrew: Did you get this problem solved?
I am having similar problems and have tried to work around it using
options(gsubfn.engine = "R") as suggested by Gabor.
However, this don't solve on my machine. R just freezes up trying to
execute read.csv.sql()
On OSX 10.6.4, R 2.11.1 (2010-05-31) 64bit
Any help is much appreciated!
Lars
On Jul 28, 9:41 pm, Gabor Grothendieck
wrote:
> On Wed, Jul 28, 2010 at 10:06 AM, AndrewPage wrote:
>
> > Hi,
>
> > Recently, I've been trying to use packages in R that require loading the
> > Tcl/Tk interface. However, I get a strange result and a crash that I
> > haven't been able to find discussion about on these boards (or any others).
>
> > When I enter library(tcltk), it reads "Loading Tcl/Tk interface ... ", but
> > then never says "done" or displays some sort of error message. Looks like
> > this:
>
> >> x11()
> >> library(tcltk)
> > Loading Tcl/Tk interface ...
>
> > Now you can type additional commands in, at your peril! For example, if I
> > type in the text "library", nothing happens, but "library(" causes R to
> > freeze up irreparably, with "executing:
> > try(gsub('\\s+','',paste(capture.output(print(args(library,collapse="))
> > ,silent=TRUE)"
> > displayed at the bottom. When this happens, there's nothing you can do but
> > restart R because it's completely frozen.
>
> > I'm running R version 2.11.1 Patched (2010-07-27 r52627)
>
> > [R.app GUI 1.35 (5603) i386-apple-darwin9.8.0]
>
> > with XQuartz 2.3.5 (xorg-server 1.4.2-apple53)
>
> > on a mac (snow leopard)
>
> > Thanks for any help/suggestions in advance,
>
> > Andrew
>
> One thought is that if this is to use gsubfn or sqldf (which uses
> gsubfn) then you can get them to not use thetcltkcode but use R code
> instead by either of these two means:
>
> 1. issue the command:
> options(gsubfn.engine = "R")
> before issuing your library(sqldf) or library(gsubfn) command. You
> can put the options command in your .Rprofile if you like and then you
> will have it on every session.
>
> or
>
> 2. use a build of R that has notcltkin it. In that case it will
> recognize it and switch to using R. I believe one such build exists
> for the Mac.
>
> __
> r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
