Re: [R] Font Encodings --- some work, some don't
Are you talking about the pdf() device? You never say so, but you do say The font encoding error does not appear in the postscript device driver, and it works fine. This report is far too vague: what did you do and what reported the file was corrupt? (Note that Acrobat reader is famous for mis-rendering files which meet the Adobe PDF specification.) Please do read the posting guide and restate your problem following the guidelines there. Finally, I don't see any claim that arbitrary font encodings would produce a valid PDF file, so what did you read to suggest that? On Tue, 30 Aug 2005, ivo welch wrote: Dear R wizards: I believe some more font encoding info. some of the font encodings work, others do not: IsoLatin1, MacRoman, WinAnsi, and PDFDoc seem fine. AdobeStd, AdobeSym, ISOLatin2, ISOLatin9, and TeXtext seem broken, in that the resulting output file is silently corrupt. The font encoding error does not appear in the postscript device driver, and it works fine. It would be nice if R gave an error message, instead of producing corrupt .pdf files. Just a suggestion... Regards, /iaw --- ivo welch __ R-help@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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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
Re: [R] R binaries
On Wed, 31 Aug 2005, Berwin A Turlach wrote: G'day Nam-Ky, NKN == Nam-Ky Nguyen [EMAIL PROTECTED] writes: NKN I intend to burn some R CDs to colleagues in Vietnam. I want NKN to put all binary files for base as well as contributed NKN packages (for both Windows and Linux). I don't believe that precompiled binary files for Linux exist, since they would depend very much on which flavour of Linux you are running. NKN It is very time consuming if I download files by files. Is NKN there a place a can buy a CD with all the mentioned files? Not that I am aware off. But I would do the following for easy download of all contributed files: Issue from an R session the following commands (mostly untested): options(repos=c(CRAN=http://cran.au.r-project.org/;)) tmp - available.packages() # Or just use CRAN.packages() ?? ## To download all source files download.packages(tmp, destdir=.) ## To download all windows binary download.packages(tmp, destdir=., type=win.binary) If you do it from a Windows machine, you may have to adapt the destdir argument in those commands. Also, if you sit behind a proxy, then you might have to first issue an appropriate 'Sys.putenv(http_proxy=put your proxy here)' command. available.packages() does not seem to have a type argument according to its documentation, so I guess that even if it is run under Windows that it returns a list of all source packages available in contrib. Depends on what contriburl is set to, but the default under Windows is binary packages. See my article in the current R-Newsletter. The default argument is contrb.url(getOption(repos)), and contrib.url does have a type argument (and its default is getOption(pkgType) ). If some of those are not available as a precompiled windows binary, the download.packages() command will probably fail with an error, so you have to do the download in bits and pieces, removing offending entries from `tmp' -- but that should be still faster than downloading file by file (presumably by clicking in a web browser?). (The development version of R should now be more robust (Thanks again, Brian) when downloading and just continue downloading the remaining files if it encounters an error. But I don't know where you run (or what to run) R-devel ;-) ). Hope this helps. Cheers, Berwin == Full address Berwin A Turlach Tel.: +61 (8) 6488 3338 (secr) School of Mathematics and Statistics+61 (8) 6488 3383 (self) The University of Western Australia FAX : +61 (8) 6488 1028 35 Stirling Highway Crawley WA 6009e-mail: [EMAIL PROTECTED] Australiahttp://www.maths.uwa.edu.au/~berwin __ R-help@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 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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
Re: [R] R binaries
G'day Brian, BDR == Prof Brian Ripley [EMAIL PROTECTED] writes: BDR On Wed, 31 Aug 2005, Berwin A Turlach wrote: available.packages() does not seem to have a type argument according to its documentation, so I guess that even if it is run under Windows that it returns a list of all source packages available in contrib. BDR Depends on what contriburl is set to, but the default under BDR Windows is binary packages. See my article in the current BDR R-Newsletter. BDR The default argument is contrb.url(getOption(repos)), and BDR contrib.url does have a type argument (and its default is BDR getOption(pkgType) ). Thanks for pointing this out; seems as if I didn't read the documentation in sufficient details. Thus, since Nam-Ky works on a Linux box (private e-mail) the commands should be options(repos=c(CRAN=http://cran.au.r-project.org/;), + pkgType=source) download.packages(available.packages(), destdir=.) to download all the source files; followed by options(pkgType=win.binary) download.packages(available.packages(), destdir=.) to download all contributed binary packages for Windows. Cheers, Berwin __ R-help@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
Re: [R] R binaries
Berwin A Turlach [EMAIL PROTECTED] writes: Thus, since Nam-Ky works on a Linux box (private e-mail) the commands should be On a Linux box, I would rather suggest using wget on the appropriate CRAN directories (wget -r --no-parent http://etc.etc.etc/...) - unless of course it is the download speed that is the issue. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
[R] Distributional characteristics
Hi all I've a continuous variable and I want to test (graphically, plotting observed and theoretical distr, qqplot) whether it follows some formal distribution. (some thing close to Ricci document : Fitting distributions with R, Feb05). The distribution I want to fit is a truncated Gamma at 1 (the minimal value is 1), P(x)=Pgamma(rate,x)/(1-Pgamma(rate,x1)) NB : changing the variable (x-1,ln(x)) didn't get satisfying results Best Naji __ R-help@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
Re: [R] R binaries
Nam-Ky Nguyen schrieb: Dear Rexperts, I intend to burn some R CDs to colleagues in Vietnam. I want to put all binary files for base as well as contributed packages (for both Windows and Linux). It is very time consuming if I download files by files. Is there a place a can buy a CD with all the mentioned files? Regards, There are many methods to download several files at once, either text based using an ftp or http client (e.g. wget) or GUI based. Some GUI's: - the downTHEMall! plugin for Mozilla Firefox - Total Commander (Shareware, Windows) is a very nice universal file manager with an effective built-in ftp client. - KDE on a recent LINUX distribution: the file manager konqueror has built-in http and ftp support and is able to copy complete directory trees. As an example to copy some documentation simply type ftp://cran.r-project.org/pub/R/doc (please select your cran mirror near you) into the address line, then select the required directory (e.g. Rnews) and press the right mouse button, but be careful if you select huge directory tries. Thomas P. __ R-help@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
Re: [R] Installation help
On Tue, 30 Aug 2005, b wrote: Solved the problem with the 'R' installation! One of the processes that loads up on startup was conflicting with it. It was a program called Gameutil.exe which seems to enhance games by altering display modes. For some reason a conflict existed. Anyhow I dont really need the Gameutil.exe, so I'm as happy as Larry R works! Was this on Windows? If so, such programs are covered by the rw-FAQ, see the posting guide. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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
Re: [R] PLSR: model notation and reliabilities
On Mon, Aug 29, 2005 at 08:08:53AM +0200, Bj?rn-Helge Mevik wrote: It seems to me that what you are looking for, is some sort of structured equation models (? la Lisrel). The pls package implements partial least squares regression and principal component regression, which is something different. I quess you could still use plsr for the outer model (path model), but you would have to build the inner model (the constructs) with other tools, such as prcomp/princomp or other factor analyses (see e.g. ?factanal and ?varimax). Alternatively, there is an R package sem that implements structured equation models. You might want to take a look at that. Thank you very much for your hints. I actually tried factanal to construct the latent variables, and both the reliabilties and the explained variance seem to be ok, but I'm afraid that this is not my case. I thought that plsr should be used to perform this task, and that PLS is prefered under conditions on non-normality and small to medium sample sizes where you do not assume error free measurement (Chin et all, 1996, p25). Also Wold suggests using PLS or PC scores in each level of hierarchical PLS models (Wold et al, 2004, p17). It is obvious to me how I should use plsr to perform the final regression between the constructs, but I'm missing the procedure I have to use in order to construct the factors (constructs) from the observed indicators. Any hints will be much appreciatted. Rgrds References: Chin et al, 1996, A PARTIAL LEAST SQUARES LATENT VARIABLE MODELING APPROACH FOR MEASURING INTERACTION EFFECTS: RESULTS FROM A MONTE CARLO SIMULATION STUDY AND VOICE MAIL EMOTION/ADOPTION STUDY, Available: http://disc-nt.cba.uh.edu/chin/plsfaq/http/disc-nt.cba.uh.edu/chin/icis96.pdf Wold et al, 2004, The PLS method -- partial least squares projections to latent structures -- and its applications in industrial RDP, Available: http://www.umetrics.com/pdfs/events/prague%200408%20__%20PLS_text_wold.pdf Ioannis Ioannou __ R-help@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
[R] Gamma for ordinal trends
Dear list, Are there any functions for calculating gamma (and its standard error), which measures the association of ordinal factors in I x J contingency table. I did a RSiteSearch but did not find any clues... Thanks, Wuming __ R-help@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
[R] tcl/tk return problem
Hello,
I'm very new in working with tcl/tk in R and have a problem which will
probably
sound silly to most of you.
Here is the code I have problems with:
readcelfiles - function()
{
require(tcltk)
tt - tktoplevel()
tkgrid(tklabel(tt,text=Choose a directory!))
OnOK - function()
{
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
#return(data.raw)
}
OK.but - tkbutton(tt,text=OK,command=OnOK)
tkgrid(OK.but)
tkfocus(tt)
}
So after clicking on my OK button, I choose my directory and read the
cel-files.
But now I want to return the object to my workspace ... return doesn't
work here.
Could anyone give me a hint?
Thank you very much,
Daniela
__
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Re: [R] Gamma for ordinal trends
On 08/31/05 17:46, Wuming Gong wrote: Dear list, Are there any functions for calculating gamma (and its standard error), which measures the association of ordinal factors in I x J contingency table. I did a RSiteSearch but did not find any clues... You have to look for Goodman-Kruskal gamma. It is a bit obscure. It is rcorr.cens in the Hmisc package. The significance test is the same as for Kendall's tau, according to some books. I don't know about standard error. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ R-help@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
Re: [R] tcl/tk return problem
deggle wrote:
Hello,
I'm very new in working with tcl/tk in R and have a problem which will
probably
sound silly to most of you.
Here is the code I have problems with:
readcelfiles - function()
{
require(tcltk)
tt - tktoplevel()
tkgrid(tklabel(tt,text=Choose a directory!))
OnOK - function()
{
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
#return(data.raw)
}
OK.but - tkbutton(tt,text=OK,command=OnOK)
tkgrid(OK.but)
tkfocus(tt)
}
So after clicking on my OK button, I choose my directory and read the
cel-files.
But now I want to return the object to my workspace ... return doesn't
work here.
I suppose you mean in the User Workspace. Your OnOK function should look
like that:
OnOK - function() {
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
}
Note that the function overwrites any existing 'data.raw', so this could
be dangerous. Writting directly in the User Workspace is not advised
from inside a function, but here, it is the simplest way to return a
result from a tk widget action.
Best
Philippe Grosjean
Could anyone give me a hint?
Thank you very much,
Daniela
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] tcl/tk return problem
On Wed, 31 Aug 2005, Philippe Grosjean wrote:
deggle wrote:
Hello,
I'm very new in working with tcl/tk in R and have a problem which will
probably
sound silly to most of you.
Here is the code I have problems with:
readcelfiles - function()
{
require(tcltk)
tt - tktoplevel()
tkgrid(tklabel(tt,text=Choose a directory!))
OnOK - function()
{
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
#return(data.raw)
}
OK.but - tkbutton(tt,text=OK,command=OnOK)
tkgrid(OK.but)
tkfocus(tt)
}
So after clicking on my OK button, I choose my directory and read the
cel-files.
But now I want to return the object to my workspace ... return doesn't
work here.
I suppose you mean in the User Workspace. Your OnOK function should look
like that:
OnOK - function() {
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
}
Note that the function overwrites any existing 'data.raw', so this could
be dangerous. Writting directly in the User Workspace is not advised
from inside a function, but here, it is the simplest way to return a
result from a tk widget action.
Maybe simplest, but not a very good way. See
R_SOURCES/src/library/tcltk/R/utils.R for ideas on how to write a modal
dialog box that returns the value selected.
One problem with - is that it does not necessarily write in the
workspace. You need
assign(data.raw, ReadAffy(celfile.path=fileDir), envir=.GlobalEnv)
to be sure of that. (The example code I quote does use - but in a
controlled way.)
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272860 (secr)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@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
Re: [R] Gamma for ordinal trends
Jonathan Baron [EMAIL PROTECTED] writes: On 08/31/05 17:46, Wuming Gong wrote: Dear list, Are there any functions for calculating gamma (and its standard error), which measures the association of ordinal factors in I x J contingency table. I did a RSiteSearch but did not find any clues... You have to look for Goodman-Kruskal gamma. It is a bit obscure. It is rcorr.cens in the Hmisc package. The significance test is the same as for Kendall's tau, according to some books. Well, it would be if we handled ties in Kendall's tau correctly... I don't know about standard error. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
Re: [R] Gamma for ordinal trends
Is it possible to use delta method to evaluate the standard error of Goodman-Kruskal gamma and then Wald test to evaluate the significance of association? Wuming On 31 Aug 2005 13:42:27 +0200, Peter Dalgaard [EMAIL PROTECTED] wrote: Jonathan Baron [EMAIL PROTECTED] writes: On 08/31/05 17:46, Wuming Gong wrote: Dear list, Are there any functions for calculating gamma (and its standard error), which measures the association of ordinal factors in I x J contingency table. I did a RSiteSearch but did not find any clues... You have to look for Goodman-Kruskal gamma. It is a bit obscure. It is rcorr.cens in the Hmisc package. The significance test is the same as for Kendall's tau, according to some books. Well, it would be if we handled ties in Kendall's tau correctly... I don't know about standard error. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
Re: [R] tcl/tk return problem
Prof Brian Ripley wrote:
On Wed, 31 Aug 2005, Philippe Grosjean wrote:
deggle wrote:
Hello,
I'm very new in working with tcl/tk in R and have a problem which will
probably
sound silly to most of you.
Here is the code I have problems with:
readcelfiles - function()
{
require(tcltk)
tt - tktoplevel()
tkgrid(tklabel(tt,text=Choose a directory!))
OnOK - function()
{
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
#return(data.raw)
}
OK.but - tkbutton(tt,text=OK,command=OnOK)
tkgrid(OK.but)
tkfocus(tt)
}
So after clicking on my OK button, I choose my directory and read the
cel-files.
But now I want to return the object to my workspace ... return doesn't
work here.
I suppose you mean in the User Workspace. Your OnOK function should look
like that:
OnOK - function() {
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
}
Note that the function overwrites any existing 'data.raw', so this could
be dangerous. Writting directly in the User Workspace is not advised
from inside a function, but here, it is the simplest way to return a
result from a tk widget action.
Maybe simplest, but not a very good way. See
R_SOURCES/src/library/tcltk/R/utils.R for ideas on how to write a modal
dialog box that returns the value selected.
One problem with - is that it does not necessarily write in the
workspace. You need
assign(data.raw, ReadAffy(celfile.path=fileDir), envir=.GlobalEnv)
to be sure of that. (The example code I quote does use - but in a
controlled way.)
This works, and you weren't suggesting it as a good style, but I'd like
to say it's really a bad style to write to .GlobalEnv. The controlled
use of - as in tk_select.list from the file you quoted is really the
best way to solve this problem. As a general rule, you shouldn't stomp
on something you don't own, and functions don't own variables in
.GlobalEnv.
What tk_select.list does is define OnOK locally, and use - to write to
the tk_select.list environment. Then the result can be manipulated and
returned politely, without stomping on anything anywhere.
Duncan Murdoch
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] tcl/tk return problem
On Wed, 31 Aug 2005, Duncan Murdoch wrote:
Prof Brian Ripley wrote:
On Wed, 31 Aug 2005, Philippe Grosjean wrote:
deggle wrote:
Hello,
I'm very new in working with tcl/tk in R and have a problem which will
probably
sound silly to most of you.
Here is the code I have problems with:
readcelfiles - function()
{
require(tcltk)
tt - tktoplevel()
tkgrid(tklabel(tt,text=Choose a directory!))
OnOK - function()
{
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
#return(data.raw)
}
OK.but - tkbutton(tt,text=OK,command=OnOK)
tkgrid(OK.but)
tkfocus(tt)
}
So after clicking on my OK button, I choose my directory and read the
cel-files.
But now I want to return the object to my workspace ... return doesn't
work here.
I suppose you mean in the User Workspace. Your OnOK function should look
like that:
OnOK - function() {
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
}
Note that the function overwrites any existing 'data.raw', so this could
be dangerous. Writting directly in the User Workspace is not advised
from inside a function, but here, it is the simplest way to return a
result from a tk widget action.
Maybe simplest, but not a very good way. See
R_SOURCES/src/library/tcltk/R/utils.R for ideas on how to write a modal
dialog box that returns the value selected.
One problem with - is that it does not necessarily write in the
workspace. You need
assign(data.raw, ReadAffy(celfile.path=fileDir), envir=.GlobalEnv)
to be sure of that. (The example code I quote does use - but in a
controlled way.)
This works, and you weren't suggesting it as a good style, but I'd like
to say it's really a bad style to write to .GlobalEnv.
It was the question asked! If you use a non-modal tcltk dialog you
have little choice, as the parent function will have returned and vanished
long ago. Now, having a widget firing off R commands independently of the
command line is not a great idea (R's evaluator is not multithreaded and
this could be interspersed in another computation) so there is a lot to be
said for using dialog boxes modally.
The controlled use of - as in tk_select.list from the file you
quoted is really the best way to solve this problem. As a general
rule, you shouldn't stomp on something you don't own, and functions
don't own variables in .GlobalEnv.
One could argue the user who pressed the button does: it is the user
workspace.
What tk_select.list does is define OnOK locally, and use - to write to
the tk_select.list environment. Then the result can be manipulated and
returned politely, without stomping on anything anywhere.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272860 (secr)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@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
Re: [R] tcl/tk return problem
On 8/31/2005 8:57 AM, Prof Brian Ripley wrote:
On Wed, 31 Aug 2005, Duncan Murdoch wrote:
Prof Brian Ripley wrote:
On Wed, 31 Aug 2005, Philippe Grosjean wrote:
deggle wrote:
Hello,
I'm very new in working with tcl/tk in R and have a problem which will
probably
sound silly to most of you.
Here is the code I have problems with:
readcelfiles - function()
{
require(tcltk)
tt - tktoplevel()
tkgrid(tklabel(tt,text=Choose a directory!))
OnOK - function()
{
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
#return(data.raw)
}
OK.but - tkbutton(tt,text=OK,command=OnOK)
tkgrid(OK.but)
tkfocus(tt)
}
So after clicking on my OK button, I choose my directory and read the
cel-files.
But now I want to return the object to my workspace ... return doesn't
work here.
I suppose you mean in the User Workspace. Your OnOK function should look
like that:
OnOK - function() {
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
}
Note that the function overwrites any existing 'data.raw', so this could
be dangerous. Writting directly in the User Workspace is not advised
from inside a function, but here, it is the simplest way to return a
result from a tk widget action.
Maybe simplest, but not a very good way. See
R_SOURCES/src/library/tcltk/R/utils.R for ideas on how to write a modal
dialog box that returns the value selected.
One problem with - is that it does not necessarily write in the
workspace. You need
assign(data.raw, ReadAffy(celfile.path=fileDir), envir=.GlobalEnv)
to be sure of that. (The example code I quote does use - but in a
controlled way.)
This works, and you weren't suggesting it as a good style, but I'd like
to say it's really a bad style to write to .GlobalEnv.
It was the question asked!
Yes, I agree, but I was pointing out that it is probably the wrong question.
Duncan Murdoch
If you use a non-modal tcltk dialog you
have little choice, as the parent function will have returned and vanished
long ago. Now, having a widget firing off R commands independently of the
command line is not a great idea (R's evaluator is not multithreaded and
this could be interspersed in another computation) so there is a lot to be
said for using dialog boxes modally.
The controlled use of - as in tk_select.list from the file you
quoted is really the best way to solve this problem. As a general
rule, you shouldn't stomp on something you don't own, and functions
don't own variables in .GlobalEnv.
One could argue the user who pressed the button does: it is the user
workspace.
What tk_select.list does is define OnOK locally, and use - to write to
the tk_select.list environment. Then the result can be manipulated and
returned politely, without stomping on anything anywhere.
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Re: [R] problem with certain data sets when using randomForest
I've been trying to play catch-up on R-help since DSC2005. This one must have slipped through... This is what I'd do: iris.sub - subset(iris, Species %in% c(setosa, virginica)) iris.sub$Species - factor(iris.sub$Species) That last line drops the empty level in the factor. You can then run randomForest with that data. HTH, Andy From: Martin Lam Hi, Since I've had no replies on my previous post about my problem I am posting it again in the hope someone notice it. The problem is that the randomForest function doesn't take datasets which has instances only containing a subset of all the classes. So the dataset with instances that either belong to class a or b from the levels a, b and c doesn't work because there is no instance that has class c. Is there any way to solve this problem? library(randomForest) # load the iris plant data set dataset - iris numberarray - array(1:nrow(dataset), nrow(dataset), 1) # include only instances with Species = setosa or virginica indices - t(numberarray[(dataset$Species == setosa | dataset$Species == virginica) == TRUE]) finaldataset - dataset[indices,] # just to let you see the 3 classes levels(finaldataset$Species) # create the random forest randomForest(formula = Species ~ ., data = finaldataset, ntree = 5) # The error message I get Error in randomForest.default(m, y, ...) : Can't have empty classes in y. #The problem is that the finaldataset doesn't contain #any instances of versicolor, so I think the only way #to solve this problem is by changing the levels the #Species have to only setosa and virginica, # correct me if I'm wrong. # So I tried to change the levels but I got stuck: # get the possible unique classes uniqueItems - unique(levels(finaldataset$Species)) # the problem! newlevels - list(uniqueItems[1] = c(uniqueItems[1], uniqueItems[2]), uniqueItems[3] = uniqueItems[3]) # Error message Error: syntax error # In the help they use constant names to rename the #levels, so this works (but that's not what I want #because I don't want to change the code every time I #use another data set): newlevels - list(setosa = c(uniqueItems[1], uniqueItems[2]), virginica = uniqueItems[3]) levels(finaldataset$Species) - newlevels levels(finaldataset$Species) finaldataset$Species --- Thanks in advance, Martin __ R-help@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 __ R-help@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
[R] Bioconductor and R-devel
Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools Welcome to 'simpleaffy' V 2.1.3 Produced by The Paterson Institute for Cancer Research and funded by CANCER RESEARCH UK. http://bioinformatics.picr.man.ac.uk/simpleaffy mailto: [EMAIL PROTECTED] Background correcting Retrieving data from AffyBatch...done. Computing expression calls... .done. scaling to a TGT of 100 ... Scale factor for: 0203_YH10_H_MCF7_r1.CEL 0.291660289301555 Scale factor for: 0203_YH11_H_MCF10A_r1.CEL 0.42025300545212 Scale factor for: 0203_YH12_H_a100MCF7_r1.CEL 0.287589038746987 Scale factor for: 0203_YH13_H_a100MCF10A_r1.CEL 0.451200408584071 Scale factor for: 0203_YH14_H_a10MCF7_r1.CEL 0.385462078301135 Scale factor for: 0203_YH15_H_a100MCF7_r2.CEL 0.284974495993646 Scale factor for: 0203_YH16_H_a100MCF7_r3.CEL 0.376484877281483 Scale factor for: 0203_YH17_H_a100MCF10A_r2.CEL 0.374087365857816 Scale factor for: 0203_YH18_H_a100MCF10A_r3.CEL 0.487207458237659 Scale factor for: 0203_YH19_H_a10MCF7_r2.CEL 0.413217979158927 Scale factor for: 0203_YH20_H_a10MCF7_r3.CEL 0.482703032325383 Scale factor for: 0203_YH21_H_a10MCF10A_r1.CEL 0.945369712044904 Scale factor for: 0203_YH22_H_a10MCF10A_r2.CEL 1.96143996386198 Scale factor for: 0203_YH23_H_a10MCF10A_r3_rescan.CEL 0.841535915879218 Scale factor for: 0203_YH24_H_MCF7_r2.CEL 0.347795838770919 Scale factor for: 0203_YH25_H_MCF7_r3.CEL 0.318539156900791 Scale factor for: 0203_YH26_H_MCF10A_r2.CEL 0.578922233010316 Scale factor for: 0203_YH27_H_MCF10A_r3.CEL 0.394833650209601 Scale factor for: 0403_YH34_H_a10MCF10A_r4.CEL 1.06804698986081 Scale factor for: 0403_YH35_H_a1MCF7_r1_2.CEL 3.5923019165673 Scale factor for: 0403_YH36_H_a1MCF7_r2.CEL 3.16130786066591 Scale factor for: 0403_YH37_H_a1MCF7_r3_2.CEL 2.01330391697437 Scale factor for: 0403_YH38_H_a1MCF10A_r1.CEL 0.923881702153984 Scale factor for: 0403_YH39_H_a1MCF10A_r2_2.CEL 2.29265379531566 Scale factor for: 0403_YH40_H_a1MCF10A_r3.CEL 4.02474777803345 Getting probe level data... Computing p-values Doing PMA Calls TEST 1 : time Elapsed = 0 1 20 Background correcting Retrieving data from AffyBatch...done. Computing expression calls... .Error in FUN(X[[9]], ...) : Expecting 22283 unique probesets, found 22284 Can anyone advise me on how to fix this problem? I was able to run the same data set with gcc-compiled R2.1.1 and BioConductor 1.6 successfully. Here is the code that I ran, if it helps to diagnose the problems. library(simpleaffy); library(affy); ampli.data - ReadAffy() # normalize the data using call.exprs and mas5 ampli.eset - call.exprs(ampli.data, mas5) # see what data is stored in [EMAIL PROTECTED]@preprocssing names([EMAIL PROTECTED]@preprocessing) # acess each piece of information within [EMAIL PROTECTED]@preprocessing scale factors [EMAIL PROTECTED]@preprocessing$sfs # filenames so that the scale factors can be related to their chips [EMAIL PROTECTED]@preprocessing$filenames # tgt is the target intensity each chip was scaled to [EMAIL PROTECTED]@preprocessing$tgt # which version of the affy package was used [EMAIL PROTECTED]@preprocessing$affyversion qc.data - qc(ampli.data, ampli.eset); slotNames(qc.data); # scale.factors contains a list of scale factors applied to each chip; [EMAIL PROTECTED] # target is the target intensity that each chip was scaled to [EMAIL PROTECTED] # percent.present is a list of the percentage of probesets called present on each chip; [EMAIL PROTECTED] # average.background, minimum.background, maximum.background are all lists detailing # the average, minimum and maximum background for each chip; [EMAIL PROTECTED] # spikes is a matrix containing normalized values for each of the spike controls colnames([EMAIL PROTECTED]) Thanks, Jennifer __ R-help@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
Re: [R] tcl/tk return problem
Duncan Murdoch wrote:
On 8/31/2005 8:57 AM, Prof Brian Ripley wrote:
On Wed, 31 Aug 2005, Duncan Murdoch wrote:
Prof Brian Ripley wrote:
On Wed, 31 Aug 2005, Philippe Grosjean wrote:
deggle wrote:
Hello,
I'm very new in working with tcl/tk in R and have a problem which
will
probably
sound silly to most of you.
Here is the code I have problems with:
readcelfiles - function()
{
require(tcltk)
tt - tktoplevel()
tkgrid(tklabel(tt,text=Choose a directory!))
OnOK - function()
{
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
#return(data.raw)
}
OK.but - tkbutton(tt,text=OK,command=OnOK)
tkgrid(OK.but)
tkfocus(tt)
}
So after clicking on my OK button, I choose my directory and
read the
cel-files.
But now I want to return the object to my workspace ... return
doesn't
work here.
I suppose you mean in the User Workspace. Your OnOK function should
look
like that:
OnOK - function() {
fileDir-tclvalue(tkchooseDirectory())
data.raw - ReadAffy(celfile.path=fileDir)
}
Note that the function overwrites any existing 'data.raw', so this
could
be dangerous. Writting directly in the User Workspace is not advised
from inside a function, but here, it is the simplest way to return a
result from a tk widget action.
Maybe simplest, but not a very good way. See
R_SOURCES/src/library/tcltk/R/utils.R for ideas on how to write a
modal
dialog box that returns the value selected.
One problem with - is that it does not necessarily write in the
workspace. You need
assign(data.raw, ReadAffy(celfile.path=fileDir),
envir=.GlobalEnv)
to be sure of that. (The example code I quote does use - but in a
controlled way.)
This works, and you weren't suggesting it as a good style, but I'd like
to say it's really a bad style to write to .GlobalEnv.
It was the question asked!
Yes, I agree, but I was pointing out that it is probably the wrong
question.
Duncan Murdoch
This was to provide a direct answer to the question. I think I said it
is not a good practice. For storing temporary variables for a GUI, I
prefer to use a dedicated workspace. The very simple functions
assignTemp(), getTemp() and rmTemp() in the svMisc package (SciViews
bundle) ease its use. 'TempEnv' is used in SciViews-R, and, after a
suggestion, John Fox included it also in R Commander (called 'RcmdrEnv'
there).
May be a modal Tk dialog box is all what is needed here... Although
since we are speaking about good and bad questions, I wonder if the
whole stuff is of any value:
1°) Draw a Tk dialog just with a Choose a directory! and an OK
button is totally useless. Why not to display tkchooseDirectory()
directly? After all, the 'Cancel' button is there in case the user does
not want to proceed. This error in GUI design is to place in the same
bag as Do you want to quit? - Do you really want to quit? - Are
you really sure you really want to quit? !!!
2°) However, if the initial idea is to place other info in the Tk
dialog, it then makes sense. Now, if this is the case, it is not
necessary to put tkchooseDirectory() in the OnOK() function. The
following code is doing the job without all the problems mentioned:
# This is because I don't have the ReadAffy() function...
ReadAffy - function(celfile.path) return(celfile.path)
readcelfiles - function() {
require(tcltk)
tt - tktoplevel()
tkgrid(tklabel(tt, text = Choose a directory!))
tkgrid(tkbutton(tt, text = OK,
command = function() tkdestroy(tt)))
tkfocus(tt)
tkwait.window(tt)
fileDir-tclvalue(tkchooseDirectory())
return(ReadAffy(celfile.path = fileDir))
}
readcelfiles()
So... perhaps the wrong question is not where one think it is ;-)
Best,
Philippe
If you use a non-modal tcltk dialog you
have little choice, as the parent function will have returned and
vanished
long ago. Now, having a widget firing off R commands independently of
the
command line is not a great idea (R's evaluator is not multithreaded and
this could be interspersed in another computation) so there is a lot
to be
said for using dialog boxes modally.
The controlled use of - as in tk_select.list from the file you
quoted is really the best way to solve this problem. As a general
rule, you shouldn't stomp on something you don't own, and functions
don't own variables in .GlobalEnv.
One could argue the user who pressed the button does: it is the user
workspace.
What tk_select.list does is define OnOK locally, and use - to write to
the tk_select.list environment. Then the result can be manipulated and
returned politely, without stomping on anything anywhere.
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[R] Cases as Variables in Principal Component Analysis?
Dear R users, I have a data set of 25 cases with 150-160 explanatory variables(the number of which depends on what I choose from 200 odd digitalized spectrum strength numbers) and one dependent variable(a sensory test result). My natural choice is to work on a principal component analysis using the explanatory variables, thus enabling to characterize and describe the data space, and make a regression of the dependent variable on the principal components. But a colleague of mine transposed the data matrix and, using the cases as the independent variables, explained the dependent variable in terms of the principal components he had. He changed obviously the score for the rotation. The analysis gave a plausible story. But I can't be sure of the physical meaning of it. My colleague says that this method is common in the image analysis proper, which he specializes in. Is there anyone who can comment on this matter. Venables Ripley says something to the effect that either method will do, but the authors do not seem to give a specific example. In my trade(chemistry), the data is commonly analyzed by the PLS(Partial Least Suare) method, which seems to give more or less the same result. Only the contribution of the PC's seems to be different. I would appreciate any help. Thank you. -- Yukihiro Ishii [EMAIL PROTECTED] __ R-help@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
Re: [R] Bioconductor and R-devel
Hi Jennifer, I'm moving this over to the bioconductor mail list since we are discussing Bioconductor packages, that would be the best place for the discussion at this point. Please subscribe and reply there. A couple quick comments: 1. You do realize BioC 1.7 is the current devel version, right? 2. After you see the error, try traceback() to get a better idea of where things are going wrong. Then you can use debug(someFunc) to debug in the place where the error occurs. I'm sure the package maintainers will be most receptive to any bug fixes. Best, + seth On 31 Aug 2005, [EMAIL PROTECTED] wrote: Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools Welcome to 'simpleaffy' V 2.1.3 Produced by The Paterson Institute for Cancer Research and funded by CANCER RESEARCH UK. http://bioinformatics.picr.man.ac.uk/simpleaffy mailto: [EMAIL PROTECTED] Background correcting Retrieving data from AffyBatch...done. Computing expression calls... .done. scaling to a TGT of 100 ... Scale factor for: 0203_YH10_H_MCF7_r1.CEL 0.291660289301555 Scale factor for: 0203_YH11_H_MCF10A_r1.CEL 0.42025300545212 Scale factor for: 0203_YH12_H_a100MCF7_r1.CEL 0.287589038746987 Scale factor for: 0203_YH13_H_a100MCF10A_r1.CEL 0.451200408584071 Scale factor for: 0203_YH14_H_a10MCF7_r1.CEL 0.385462078301135 Scale factor for: 0203_YH15_H_a100MCF7_r2.CEL 0.284974495993646 Scale factor for: 0203_YH16_H_a100MCF7_r3.CEL 0.376484877281483 Scale factor for: 0203_YH17_H_a100MCF10A_r2.CEL 0.374087365857816 Scale factor for: 0203_YH18_H_a100MCF10A_r3.CEL 0.487207458237659 Scale factor for: 0203_YH19_H_a10MCF7_r2.CEL 0.413217979158927 Scale factor for: 0203_YH20_H_a10MCF7_r3.CEL 0.482703032325383 Scale factor for: 0203_YH21_H_a10MCF10A_r1.CEL 0.945369712044904 Scale factor for: 0203_YH22_H_a10MCF10A_r2.CEL 1.96143996386198 Scale factor for: 0203_YH23_H_a10MCF10A_r3_rescan.CEL 0.841535915879218 Scale factor for: 0203_YH24_H_MCF7_r2.CEL 0.347795838770919 Scale factor for: 0203_YH25_H_MCF7_r3.CEL 0.318539156900791 Scale factor for: 0203_YH26_H_MCF10A_r2.CEL 0.578922233010316 Scale factor for: 0203_YH27_H_MCF10A_r3.CEL 0.394833650209601 Scale factor for: 0403_YH34_H_a10MCF10A_r4.CEL 1.06804698986081 Scale factor for: 0403_YH35_H_a1MCF7_r1_2.CEL 3.5923019165673 Scale factor for: 0403_YH36_H_a1MCF7_r2.CEL 3.16130786066591 Scale factor for: 0403_YH37_H_a1MCF7_r3_2.CEL 2.01330391697437 Scale factor for: 0403_YH38_H_a1MCF10A_r1.CEL 0.923881702153984 Scale factor for: 0403_YH39_H_a1MCF10A_r2_2.CEL 2.29265379531566 Scale factor for: 0403_YH40_H_a1MCF10A_r3.CEL 4.02474777803345 Getting probe level data... Computing p-values Doing PMA Calls TEST 1 : time Elapsed = 0 1 20 Background correcting Retrieving data from AffyBatch...done. Computing expression calls... .Error in FUN(X[[9]], ...) : Expecting 22283 unique probesets, found 22284 Can anyone advise me on how to fix this problem? I was able to run the same data set with gcc-compiled R2.1.1 and BioConductor 1.6 successfully. Here is the code that I ran, if it helps to diagnose the problems. library(simpleaffy); library(affy); ampli.data - ReadAffy() # normalize the data using call.exprs and mas5 ampli.eset - call.exprs(ampli.data, mas5) # see what data is stored in [EMAIL PROTECTED]@preprocssing names([EMAIL PROTECTED]@preprocessing) # acess each piece of information within [EMAIL PROTECTED]@preprocessing scale factors [EMAIL PROTECTED]@preprocessing$sfs # filenames so that the scale factors can be related to their chips [EMAIL PROTECTED]@preprocessing$filenames # tgt is the target intensity each chip was scaled to [EMAIL PROTECTED]@preprocessing$tgt # which version of the affy package was used [EMAIL PROTECTED]@preprocessing$affyversion qc.data - qc(ampli.data, ampli.eset); slotNames(qc.data); # scale.factors contains a list of scale factors applied to each # chip; [EMAIL PROTECTED] # target is the target intensity that each chip was scaled to [EMAIL PROTECTED] # percent.present is a list of the percentage of probesets called present on each chip; [EMAIL PROTECTED] # average.background, minimum.background, maximum.background are all lists detailing # the average, minimum and maximum background for each chip; [EMAIL PROTECTED] # spikes is a matrix containing normalized values for each of the # spike controls colnames([EMAIL PROTECTED]) Thanks, Jennifer __
Re: [R] xtable
You do have to load optional packages in each R session. See ?require But you can automate the loading; see ?Startup -Don At 6:46 PM +0200 8/30/05, Mag. Ferri Leberl wrote: I have installed package xtable with su -c 'R CMD INSTALL xtable' and got this promising feedback: * Installing *source* package 'xtable' ... ** R ** data ** help Building/Updating help pages for package 'xtable' Formats: text html latex example * DONE (xtable) Despite that, R returns: Error: couldn't find function print.xtable Execution halted when I call that function. What have I done wrong? Do I have to activate the package everytime when I start R? Thank you in advance! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] loop
I was wondering why this loop doesn't work! for (i in 1:k) fnTr[i] - function (p) 0.5* sum ( n*log(2*pi) - log(sd(i)^2) +(logitp(i)-p)^2/sd(i)^2 ) outTr[i]- nlm (fnTr[i],p=c(10),hessian=TRUE) minimumTr[i] - outTr[i]$minimum valueTr[i] - outTr[i]$estimate list (minimumTr[i],valueTr[i]) Has anyone can help me? Thank you very much Hathaikan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] loop
Hathaikan Chootrakool wrote:
I was wondering why this loop doesn't work!
for (i in 1:k)
fnTr[i] - function (p) 0.5* sum ( n*log(2*pi) - log(sd(i)^2)
+(logitp(i)-p)^2/sd(i)^2 )
outTr[i]- nlm (fnTr[i],p=c(10),hessian=TRUE)
minimumTr[i] - outTr[i]$minimum
valueTr[i] - outTr[i]$estimate
list (minimumTr[i],valueTr[i])
Has anyone can help me?
Thank you very much
Hathaikan
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missing {} on your code block
for(...){
...
}
EJ
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[R] extrating BLUP values from linear mixed models
Hello, I wish to learn how to extract best linear unbiased predictor values from a linear mixed model of repeated measures on individuals which has a random error structure (random =~ 1|individual). Thanks for your time, Kind regards Matt -- Matt Robinson Institute of Evolutionary Biology University of Edinburgh __ R-help@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
Re: [R] extrating BLUP values from linear mixed models
Use the ranef() command ranef(fm1, level=1) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Matt Robinson Sent: Wednesday, August 31, 2005 12:26 PM To: r-help@stat.math.ethz.ch Subject: [R] extrating BLUP values from linear mixed models Hello, I wish to learn how to extract best linear unbiased predictor values from a linear mixed model of repeated measures on individuals which has a random error structure (random =~ 1|individual). Thanks for your time, Kind regards Matt -- Matt Robinson Institute of Evolutionary Biology University of Edinburgh __ R-help@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 __ R-help@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
[R] best c++ matrix library?
Hi folks, I am planning to write some more time-consuming matrix manipulations in c++. What is the experience with the existing c++ matrix libraries? Do you have some recommendations? Are some libraries more compatible with R than the others? All suggestions welcome! Best, Ott __ R-help@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
[R] sinput for Windows
Hi, I'm trying to latex part of my R- code and don't know where to find the sinput package to include in my version of miktex (I have the LINUX version handy, but need also the Windows one) Any idea? (sorry it is not really a R question) Thanks Isotta - [[alternative HTML version deleted]] __ R-help@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
[R] Block-Diagonal Matrix and Multivariate Skew Normal
Dear R-users, Does anybody know how to construct a block-diagonal matrix (with the blocks being different matrixs, concerning the dimension and the values) ? I would like to know also if there is any package that generates values from a multivariate skew normal distribution. Thanks all, Caio - [[alternative HTML version deleted]] __ R-help@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
[R] En: Block-Diagonal Matrix and Multivariate Skew Normal
Dear R-users, Does anybody know how to construct a block-diagonal matrix (with the blocks being different matrixs, concerning the dimension and the values) ? I would like to know also if there is any package that generates values from a multivariate skew normal distribution. Thanks all, Caio - __ [[alternative HTML version deleted]] __ R-help@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
[R] Reading numeric data in Excel as character data in R using RODBC
The Excel 'database' I am pulling from mixes multiple character indicators for different kinds of non-numeric results in the same column as the numeric values. A simple sqlFetch turns all of the character indicators into NAs. I would like to pull in all of the Excel data as character so that I can split the column into multiple types of vectors and control the type conversion within R. Can anyone provide clues as to how I go about getting RODBC to bring in data containing some numbers without running a numeric conversion? The simple code I use to pull data directly from Excel is generally something like the following: prj-'C:/data' library(RODBC) channel - odbcConnectExcel(paste(prj,/intermediate/datafile.xls,sep='')) r - sqlTables(channel) ifn.display - sqlFetch(channel, SHEET1) il2.display - sqlFetch(channel, SHEET2) pl.display - sqlFetch(channel, SHEET3) odbcClose(channel) Background: The current problem is small enough to solve with read.csv but I expect to get larger problems in the future. My clients generally give me data in Excel format. Sometimes I get multiple character indicators for different kinds of non-numeric results. Sometimes I get 40+ sheets in a single file where all of the sheets are formatted alike. I'd like to be ready to run a reasonably automated data conversion whenever a client decides to give me both at once. Thanks for your time. Chuck __ R-help@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
Re: [R] best c++ matrix library?
Hi, I used Meschach: http://www.math.uiowa.edu/~dstewart/meschach/ However, it is written in C. The API is strong. I used the same API and trimmed down the functionality, as well. Both worked for me. IBM Developworks has an article on the subject Matrix libraries for C and C++: http://www-128.ibm.com/developerworks/linux/library/l-matrix.html It has also a comparison for some libraries. I wonder if there is another library... --vst Ott Toomet wrote: Hi folks, I am planning to write some more time-consuming matrix manipulations in c++. What is the experience with the existing c++ matrix libraries? Do you have some recommendations? Are some libraries more compatible with R than the others? All suggestions welcome! Best, Ott __ R-help@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 __ R-help@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
Re: [R] sinput for Windows
On 8/31/2005 12:57 PM, Isotta Felli wrote: Hi, I'm trying to latex part of my R- code and don't know where to find the sinput package to include in my version of miktex (I have the LINUX version handy, but need also the Windows one) Any idea? (sorry it is not really a R question) If you have it on Linux, just grab a copy, install it in your localtexmf folder, and rebuild the indices. miktex uses the same format for packages as other TeX implementations. Duncan Murdoch __ R-help@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
Re: [R] Block-Diagonal Matrix and Multivariate Skew Normal
For your first question, here's a function originally posted by Ben Bolker,
with modification by Rich Raubertas:
blockdiag - function (x, ...)
{
if (!is.list(x))
x - list(x)
args - list(...)
if (length(args) 0)
args - c(x, args)
else args - x
idx - which(!sapply(args, is.matrix))
if (length(idx) 0)
for (i in idx) args[[i]] - as.matrix(args[[i]])
if (length(args) == 1)
return(args[[1]])
nr - sapply(args, nrow)
nc - sapply(args, ncol)
cumnc - cumsum(nc)
NR - sum(nr)
NC - sum(nc)
rowfun - function(m, zbefore, zafter) {
cbind(matrix(0, ncol = zbefore, nrow = nrow(m)), m, matrix(0,
ncol = zafter, nrow = nrow(m)))
}
ret - rowfun(args[[1]], 0, NC - ncol(args[[1]]))
for (i in 2:length(args)) {
ret - rbind(ret, rowfun(args[[i]], cumnc[i - 1], NC -
cumnc[i]))
}
ret
}
Andy
From: Caio Lucidius Naberezny Azevedo
Dear R-users,
Does anybody know how to construct a block-diagonal matrix
(with the blocks being different matrixs, concerning the
dimension and the values) ?
I would like to know also if there is any package that
generates values from a multivariate skew normal distribution.
Thanks all,
Caio
-
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Re: [R] Advice about system for installing updating all R packa ge in a Linux Lab?
If you have several different versions of R installed, you might want to use
a script like this one, which should work on (at least) 1.9.1 and newer.
script
#!/bin/sh
echo ##
echo ## This script will attempt to install all available R packages
echo ## from the package repositories:
echo ##
echo ## - CRAN: http://cran.r-project.org/;
echo ## - BioCondictor: http://www.bioconductor.org;
echo ##
echo ## As well as Pfizer custom packages
echo ##
echo ## - Rlsf: ~warneg/src/R/Rlsf
echo ## - AffyTool: nlvfs016:rstat-data/
echo ## ExpressionAnalysis/StandardAffyAnalysis/AffyTool
echo ##
echo ##
echo ##
if [ -z '$1' ]; then
RCMD=R
echo ## Parameter 1 : R Command Name = $RCMD (Default)
else
RCMD=$1
echo ## Parameter 1 : R Command Name = $RCMD
fi
export RCMD
echo $RCMD
echo ##
echo ##
echo ##
echo ## Starting R ...
echo ##
$RCMD --vanilla EOF
##
## Update installed packages
##
update.packages (repos =http://cran.r-project.org,ask = FALSE,
installWithVers=TRUE )
##
## Install New Packages from CRAN
##
#
if (exists(new.packages,mode=function))
{
options(repos=http://cran.r-project.org;)
new.list - new.packages(ask=FALSE)
} else
{
CRAN.list - CRAN.packages()[,1]
here.list - installed.packages()[,1]
new.list - CRAN.list[ ! CRAN.list %in% here.list ]
}
install.packages(pkgs=new.list, dependencies=TRUE, installWithVers=TRUE )
##
## Install (New) Bioconductor Packages
##
source(http://www.bioconductor.org/getBioC.R;)
getBioC(groupName=all)
y
EOF
echo ##
echo ## All Done!
echo ##
echo ## *Check the log for failed package installs*
echo ##
echo ##
/script
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Prof
Brian Ripley
Sent: Saturday, August 20, 2005 1:28 AM
To: Paul Johnson
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Advice about system for installing updating all R
package in a Linux Lab?
This is based on the pre-2.1.0 ideas. Try
update.packages(ask=FALSE)
install.packages(new.packages(), dependencies=TRUE)
However, I would suggest that you set up each student with a
library, say
~/R/library, and point R_LIBS at it (set in Renviron.site).
That's what
we do for Windows, and it seems successful. (We have other
reasons to
want very complete central Linux setups, one being that we
run more than
one archtecture where personal libraries are a little harder
to manage.)
On Fri, 19 Aug 2005, Paul Johnson wrote:
Good day:
I'm administering 6 linux systems (FC4) in a student lab
and worry that
users may want packages that are not installed. I get
tired of adding
them one by one. Then I happened upon this page
http://support.stat.ucla.edu/view.php?supportid=30
Many of the commands there are now or about to be deprecated. See my
article in the current R-News.
about installing all R packages from CRAN. That did not
run as it was,
but after some fiddling I arrived at the following script,
which does
run and it builds many packages and reports failures on the rest:
#R_installAll.R
options(repos = http://lib.stat.cmu.edu/R/CRAN/;)
update.packages(ask=F)
x -
packageStatus(repositories=http://cran.r-project.org/src/contrib;)
st - x$avai[Status]
install.packages(rownames(st)[which(st$Status==not installed)],
dependencies=T)
If I run that in batch mode (as root, of course)
R CMD BATCH R_installAll.R
It produces some informative output. Some packages don't
build because
they are for Windows. As Prof Ripley mentioned recently,
some packages
don't build because of gcc-4.0.1. Some fail because I don't
have some
requisite libraries installed. I try to deduce which FC
packages may be
used to fix that and iterate the process now and then.
But, for the most part, the packages to be OK (as far as I
can tell).
The output of a recent update is posted on the net here, in
case you are
interested to see (this lists the ones that don't build plus the
successful updates):
http://lark.cc.ku.edu/~pauljohn/software/R/R_installAll.Rout
I can't see how this does any damage, since the packages that don't
build are very graceful about erasing themselves, and the
ones that do
build are automatically available for the users.
Can you see any downside to scheduling this process to run as a cron
job, say once per week, to keep packages up to date?
None at all. We do something similar (but based on
new.packages and with
a stoplist of packages that we know will not install).
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
[R] b1 function in ch 12 scripts of MASS
Dear list,
I have been trying to reproduce the scripts of the MASS library and I have
found a problem when trying to reproduce the code in 12.4, with the use of
neural networks and the function b1:
b1 - function(Z, ...)
{
zp - Z[,3] - pmax(Z[,2], Z[,1])
contour(xp/log(10), yp/log(10), matrix(zp, np),
add=T, levels=0, labex=0, ...)
zp - Z[,1] - pmax(Z[,3], Z[,2])
contour(xp/log(10), yp/log(10), matrix(zp, np),
add=T, levels=0, labex=0, ...)
}
Using this function, the contours appear in a much reduced zone of the
chart. Instead, if I use
b1 - function(Z, ...)
{
zp - Z[,3] - pmax(Z[,2], Z[,1])
contour(exp(xp), exp(yp), matrix(zp, np),
add=T, levels=0, labex=0, ...)
zp - Z[,1] - pmax(Z[,3], Z[,2])
contour(exp(xp), exp(yp), matrix(zp, np),
add=T, levels=0, labex=0, ...)
}
I get similar panels to the ones in the book. Also, this choice would be
consistent with the functions predplot and cushplot.
Am I doing something wrong?
Regards
Jordi
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[R] label *on the side* in conditional lattice plots?
I'm doing bwplot(x ~ y | z, ...) with lattice, but would like the z-labels to appear to the *side* of each bwplot, rather than on top... is this possible? The main reason is that my bwplots are horizontal, and as such can be nicely squished in the vertical axis (big space-saver when including in papers), but the labels get in the way, look too large in comparison, while I have all this empty space to the side of the plots which is being wasted instead... -- Maciej Kalisiak [EMAIL PROTECTED] http://www.dgp.toronto.edu/~mac __ R-help@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
Re: [R] best c++ matrix library?
* Ott Toomet [EMAIL PROTECTED] [2005-08-31 19:53]: I am planning to write some more time-consuming matrix manipulations in c++. What is the experience with the existing c++ matrix libraries? Do you have some recommendations? Are some libraries more compatible with R than the others? Liboctave is a quite powerful C++ matrix library. It is part of Octave (www.octave.org), but you can write standalone applications with it. Since liboctave links against standard Fortran and C libraries (lapack, odepack, minpack, quadpack, slatec, fftw, etc), you have access to all matrix algorithms of Octave. Attached below is an example, showing eigenvalue computation (via the lapack routine). Also attached is the compilation command and the output of the program (in my Debian sarge box). I do not know how liboctave compares with the other libraries as regards speed. As far as I know, there is no efforts for gluing liboctave into R. -- Rafael Laboissiere $ g++ -I/usr/include/octave eig.cc -o eig -L/usr/lib/octave-2.1.69/ -loctave $ LD_LIBRARY_PATH=/usr/lib/octave-2.1.69/ ./eig Original Matrix 3 2 2 0 Eigen Vectors (0.447214,0) (-0.894427,0) (-0.894427,0) (-0.447214,0) Eigen Values (-1,0) (4,0) Recomposed Matrix (3,0) (2,0) (2,0) (-9.92587e-17,0) __ R-help@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
Re: [R] label *on the side* in conditional lattice plots?
I think you might be able to use the horizontal argument to lattice to rotate all your plots and squish them in the other dimension. (Though I don't know whether you consider that a good outcome ...) Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Maciej Kalisiak Sent: Wednesday, August 31, 2005 4:21 PM To: r-help@stat.math.ethz.ch Subject: [R] label *on the side* in conditional lattice plots? I'm doing bwplot(x ~ y | z, ...) with lattice, but would like the z-labels to appear to the *side* of each bwplot, rather than on top... is this possible? The main reason is that my bwplots are horizontal, and as such can be nicely squished in the vertical axis (big space-saver when including in papers), but the labels get in the way, look too large in comparison, while I have all this empty space to the side of the plots which is being wasted instead... -- Maciej Kalisiak [EMAIL PROTECTED] http://www.dgp.toronto.edu/~mac __ R-help@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 __ R-help@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
[R] Imputation using Pan in R
Hi, I've tried to run the multiple imputation for longitudinal data using Pan in R. The trimmed data consist 10 individuals across 4 time points. Following the example in panex.R, I imputated the model with one y variable and only random intercept. It worked well. The next step for me is to imputate a model with one y variable and both random intercept and slope. The program ran well, but did not imputate any of my missing values. I attached my codes in the following. Did I do anything wrong in the codes? I am confused with the setting of xcol and zcol (and of course the pred). Do anyone know how to set these matrices when including both random intercept and slope or when having 2 or more y's? Any suggestions would be appreciated. Thanks! Yi-fu library(pan) y - c(5,8,NA,10, +2,NA,NA,NA, +10,10,8,NA, +NA,10,4,NA, +2,8,NA,9, +NA,NA,NA,NA, +8,6,NA,5, +6,NA,NA,NA, +10,2,NA,NA, +6,8,NA,2) subj - c(1,1,1,1, + 2,2,2,2, + 3,3,3,3, + 4,4,4,4, + 5,5,5,5, + 6,6,6,6, + 7,7,7,7, + 8,8,8,8, + 9,9,9,9, + 10,10,10,10) pred - cbind(int=rep(1,40), +dummy1=rep(c(1,0,0,0),10), +dummy2=rep(c(0,1,0,0),10), +dummy3=rep(c(0,0,1,0),10), +dummy4=rep(c(0,2,4,6),10)) xcol - 1:4 zcol - c(1,5) a - array (2,dim=c(2,2)) prior - list(a=1,Binv=1,c=2,Dinv=a) result - pan(y,subj,pred,xcol,zcol,prior,seed=25679,iter=5000) result$y [1] 5 8 NaN 10 2 NaN NaN NaN 10 10 8 NaN NaN 10 4 NaN 2 8 NaN [20] 9 NaN NaN NaN NaN 8 6 NaN 5 6 NaN NaN NaN 10 2 NaN NaN 6 8 [39] NaN 2 [[alternative HTML version deleted]] __ R-help@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
[R] eigen-decomposition of symmetric BCCB matrices
Hi, Can anyone please point to how to decompose BCCB (Block-Circulant-Circulant-Block) matrices? I am interested in the derivations: I do know that this can be numerically done using 2-dimensional FFTs. Many thanks and best wishes! __ R-help@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
Re: [R] best c++ matrix library?
Ott Toomet otoomet at ut.ee writes: I am planning to write some more time-consuming matrix manipulations in c++. What is the experience with the existing c++ matrix libraries? Do you have some recommendations? Are some libraries more compatible with R than the others? A lng time ago, I used to use the newmat C++ library by Robert Davies -- see http://www.robertnz.net/nm_intro.htm which states This C++ library is intended for scientists and engineers who need to manipulate a variety of types of matrices using standard matrix operations. Emphasis is on the kind of operations needed in statistical calculations such as least squares, linear equation solve and eigenvalues. In fact, my use even lead to a short review about newmat and g++ for the Journal of Applied Econometrics (http://dirk.eddelbuettel.com/papers/gccnewmat.ps.gz). Robert has continued to maintain, support and extend newmat. I would probably start there if I needed a C++ Matrix library as newmat is (in no order of preference) -- fairly small (unlike Boost) -- as I recall, doesn't depend on anything else -- well documented -- well tested -- pretty clean conceptually Moreover, Robert really is a statistician so there may be interest on his side in tieing newmat to R if were to provide some prototypes. But this really is a question of programming style and preferences, and mine certainly changed in the meantime so take this with the usual spoon of salt. Hope this helps, Dirk __ R-help@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
Re: [R] loop
just one more thing. Why are you defining the function over and over again... On Wed, 31 Aug 2005, Hathaikan Chootrakool wrote: I was wondering why this loop doesn't work! for (i in 1:k) fnTr[i] - function (p) 0.5* sum ( n*log(2*pi) - log(sd(i)^2) +(logitp(i)-p)^2/sd(i)^2 ) outTr[i]- nlm (fnTr[i],p=c(10),hessian=TRUE) minimumTr[i] - outTr[i]$minimum valueTr[i] - outTr[i]$estimate list (minimumTr[i],valueTr[i]) Has anyone can help me? Thank you very much Hathaikan __ R-help@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 __ R-help@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
[R] R environment
This is probably a weird question but I need to know if there is a way... I run an R batch job without saving the variables at each step to the disk. Is there a way to invoke another session of R and link it to the same environment for read only. The problem is that I am running optim with every step getting the parameters into the global env using - However, I forgot to issue a save(list=ls(),...) right after so I can load and see how the parameters are changing. It's been couple of days and it is still running so I am hoping that I can invoke another session of R and link it to the environment of the batch session. Does this sound totally ridiculous ? it is a debian machine with R 2.1.1 Thanks Jean __ R-help@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
[R] R binaries, platform independent and Design of Experiments
Dear Rexpert, I would like to thank those who spend time answering my email on the burning of a CD with all R binary files for Windows and Linux. I have tried a couple of suggestions but have not been successful. I will pass these suggestions to our system administrator and I am sure that he can sort them out. I hope that the future version of R will be written in Java so that it is platform independent. This means there will be a single binary file for each new version of R. At the moment there are files for Windows, Mac OS, Fedora 1, 2, 3, 4, SUSE 9.1, 9.2, 9.3, etc. I also hope that the future of version of R include more DOE (Design of Experiments) modules. R will be more useful if it is not only a language and environment for statistical computing and graphics, but also for design of experiments. I am toying with the idea of adding to R some modules of my Gendex DOE toolkit (http://designcomputing.net/gendex/). I learn from an Rexpert that the first step for this exercise is to convert my java code to C++. As I do not know C++ (and life is short) please let me know whether there is an alternative way without this conversion and whether you can actively help me in this exercise. Regards, -- Nam-Ky Nguyen, Senior Lecturer School of Mathematics, Statistics and Computer Science University of New England, Armidale NSW 2351 Australia [EMAIL PROTECTED] Tel: +612 6773 2763 http://turing.une.edu.au/~nkn Fax: +612 6773 3312 Please convert Word files into PDF files before sending them to me. See http://www.gnu.org/philosophy/no-word-attachments.html __ R-help@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
Re: [R] label *on the side* in conditional lattice plots?
On 8/31/05, Wiener, Matthew [EMAIL PROTECTED] wrote: I think you might be able to use the horizontal argument to lattice to rotate all your plots and squish them in the other dimension. (Though I don't know whether you consider that a good outcome ...) I take it you mean to switch the layout so that the conditioned bwplots are side by side, narrow but tall, with horizontal=TRUE, and then incorporate into the paper by first rotating 90 degrees. But is there a way to rotate the axis labels then? Having the z-label written sideways is probably OK, but having the x- and y-axis labels also sideways is just too much. -- Maciej Kalisiak [EMAIL PROTECTED] http://www.dgp.toronto.edu/~mac __ R-help@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
[R] Block-diagonal matrix
Dear R-users, Does anybody know how to construct a block-diagonal matrix (with the blocks being different matrixs, concerning the dimension and the values), without use loops ? Thanks all, Caio - [[alternative HTML version deleted]] __ R-help@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
Re: [R] label *on the side* in conditional lattice plots?
On 8/31/05, Maciej Kalisiak [EMAIL PROTECTED] wrote: I take it you mean to switch the layout so that the conditioned bwplots are side by side, narrow but tall, with horizontal=TRUE, and Oops, I obviously meant horizontal=FALSE... -- Maciej Kalisiak [EMAIL PROTECTED] http://www.dgp.toronto.edu/~mac __ R-help@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
Re: [R] R environment
Jean Eid wrote: This is probably a weird question but I need to know if there is a way... I run an R batch job without saving the variables at each step to the disk. Is there a way to invoke another session of R and link it to the same environment for read only. The problem is that I am running optim with every step getting the parameters into the global env using - However, I forgot to issue a save(list=ls(),...) right after so I can load and see how the parameters are changing. It's been couple of days and it is still running so I am hoping that I can invoke another session of R and link it to the environment of the batch session. Does this sound totally ridiculous ? it is a debian machine with R 2.1.1 If you happened to have compiled R with debug information, you might be able to use gdb or another debugger to examine variables in the running process, but you probably didn't, and it's probably easier to kill the job, fix it, and start it again, than it would be to learn how to see the active variables using gdb. Duncan Murdoch __ R-help@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
[R] Question
Dear Sir/Madam I would be pleased if anybody can help me. I'm using linear mixed model (lme) function.I'm doing some simulation in my research and need to be assigned variance components values during of my program. Specifically, when I use lme function, I can get some information by use summary() and I can assign some valuse like variance of fixed parameters and variance of random error term by using for example varFix and sigma.But I don't know how I can assign for variance of random effect. I know in SPLUS we have command var.ran, how about R ? Thanks alot. M.Torabi __ R-help@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
[R] Linux Standalone Server Suggestions for R
Hi All, My group is looking for any suggestions on what to purchase to achieve the most powerful number crunching system that $50k can buy. The main application that will be used is R so input on what hardware benefits R most will be appreciated. The requirements are that it be a single standalone server (i.e. not a cluster solution), and it that must be able to run unix/linux. If anyone has any experience/ suggestions regarding the following questions that would also be greatly appreciated. AMD vs Intel chips, especially 64-bit versions of the two? Using Itanium/Opterons and if so how much of a performance boost did you achieve vs other 64-bit chip sets? Also, does anyone know if there is an upper thresh hold on much memory R can use? Thanks in advance for any help and suggestions, Jia-Shing So Programmer Analyst Biostatistics and Bioinformatics Lab University of California, San Diego __ R-help@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
[R] Data Mining Conference Program Announced
DATA MINING 2006 CONFERENCE sponsored by Salford Systems San Diego, California: March 29 - March 31, 2006 The Conference will offer Real-World Case Study Presentations including Cutting Edge Topics: Crime Prevention * Anti-Terrorism * Gambling * Sports * Video Games * Food Water Science * Diet Research * Standardized Testing There will be special courses available for attendees who are new to Data Mining covering CART(R) Decision Trees MARS(R) Modern regression analysis TreeNet(tm) Jerome Friedman's Multiple Additive Trees Random Forests(tm) Leo Breiman's Tree Ensembles See how Data Mining is Used for Business, Biomedial, and Environmental applications. Find out why previous attendees rate our conferences the most informative in the industry. If you would like more information, please click here: http://www.salforddatamining.com/program-sd.htm To be placed on the conference mailing list, please click here: http://www.salforddatamining.com/2006InfoRequest.php Best regards, Lisa Solomon Ph: (619)543-8880 __ R-help@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
Re: [R] Linux Standalone Server Suggestions for R
you can test out a live PPC 64 bit system here: http://www.openpowerproject.org/us/signup.php I have successfully built R in my home dir and compiled a few packages for it. Here are the machines available: Universität AugsburgPeking University Server OpenPower 720 OpenPower 720 Equipment 4-Way POWER54-Way POWER5 Memory 8GB 16GB InstallationDebian SUSE Enterprise 9 I think the 16GB solution is approaching or beyond your budget. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jia-Shing So Sent: Wednesday, August 31, 2005 10:03 PM To: r-help@stat.math.ethz.ch Cc: Phuoc Hong Subject: [R] Linux Standalone Server Suggestions for R Hi All, My group is looking for any suggestions on what to purchase to achieve the most powerful number crunching system that $50k can buy. The main application that will be used is R so input on what hardware benefits R most will be appreciated. The requirements are that it be a single standalone server (i.e. not a cluster solution), and it that must be able to run unix/linux. If anyone has any experience/ suggestions regarding the following questions that would also be greatly appreciated. AMD vs Intel chips, especially 64-bit versions of the two? Using Itanium/Opterons and if so how much of a performance boost did you achieve vs other 64-bit chip sets? Also, does anyone know if there is an upper thresh hold on much memory R can use? Thanks in advance for any help and suggestions, Jia-Shing So Programmer Analyst Biostatistics and Bioinformatics Lab University of California, San Diego __ R-help@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 __ R-help@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
Re: [R] basic anova and t-test question
Does the following answer your question: set.seed(1) z0 - rnorm(100) p.z - 2*pnorm(-abs(z0)) sum(p.z0.05) [1] 5 pchisq(sum(z0^2), 100, lower=FALSE) [1] 0.917285 Some of the 100 (in this case) normal random deviates seem statistically significant, even though the ensemble is not. spencer graves [EMAIL PROTECTED] wrote: Hello, I'm posting this to receive some comments/hints about a rather statistical than R-technical question ... . In an anova of a lme factor SSPos11 shows up non-significant, but in the t-test of the summay 2 of the 4 levels (one for constrast) are significant. See below for some truncated output. I realize that the two test are different (F-test/t-test), but I'm looking for for a meaning. Maye you have a schenario that explains how these differences can be created and how you'd go ahead and analyse it further. When I use SSPos11 as te only fixed effect, it does it is not significant in either anova nor t-test, and a boxplot of the factor shows that the levels are all quite similar (similar variance and mean). Might the effect I observe be linked to an unbalance design in the multifactorial model? thanks a lot for your help, +kind regards, Arne anova(fit) numDF denDF F-value p-value (Intercept) 1 540 323.4442 .0001 SSPos1 3 540 15.1206 .0001 ... SSPos11 3 540 1.1902 0.3128 ... summary(fit) Linear mixed-effects model fit by REML Data: d.orig AIC BIClogLik 1007.066 1153.168 -469.5329 Random effects: Formula: ~1 | Method (Intercept) Residual StdDev: 0.4000478 0.4943817 Fixed effects: log(value + 7.5) ~ SSPos1 + SSPos2 + SSPos6 + SSPos7 + SSPos10 + SSPos11 + SSPos13 + SSPos14 + SSPos18 + SSPos19 + Value Std.Error DF t-value p-value (Intercept) 2.8621811 0.23125065 540 12.376964 0. SSPos1C -0.1647937 0.06293993 540 -2.618269 0.0091 SSPos1G -0.3448095 0.05922479 540 -5.822047 0. SSPos1T 0.1083988 0.06087095 540 1.780797 0.0755 ... SSPos11C -0.1540292 0.06171635 540 -2.495761 0.0129 SSPos11G -0.1428980 0.05993122 540 -2.384368 0.0175 SSPos11T -0.0039434 0.06133920 540 -0.064289 0.9488 ... [[alternative HTML version deleted]] __ R-help@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 -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@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
[R] Dataset size in R
Dear listers, I would like to know whether a maximum size is set for data sets in R. I'm planning on analysing data sets which have 33 points for a sample. The response is from GCxGC output. Also, with data analysis, is there a time-cost saving by performing the analysis in Linux as against doing it in Windows XP? Many thanks, Peter [[alternative HTML version deleted]] __ R-help@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
