Re: [R] gfortran command not found?
Hi Alon, It works for me. According to YAST I got libgfortran4.3, gcc-43fortran and gcc-fortran installed Kees Marc Schwartz wrote: On Jun 11, 2009, at 12:34 PM, Alon Ben-Ari wrote: Hello, I have openSUSE 11.1 Trying to install randomForest as SU after invoking R install.packages(randomForest) and I get this * Installing *source* package ‘randomForest’ ... ** libs gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -fpic -O2 -c classTree.c -o classTree.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -fpic -O2 -c regTree.c -o regTree.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -fpic -O2 -c regrf.c -o regrf.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include -fpic -O2 -c rf.c -o rf.o gfortran -fpic -O2 -c rfsub.f -o rfsub.o make: gfortran: Command not found make: *** [rfsub.o] Error 127 ERROR: compilation failed for package ‘randomForest’ * Removing ‘/usr/lib/R/library/randomForest’ The downloaded packages are in ‘/tmp/RtmpLEyfgR/downloaded_packages’ Updating HTML index of packages in '.Library' Warning message: In install.packages(randomForest) : installation of package 'randomForest' had non-zero exit status I checked that I have th fortran library S | Name | Summary | Type --+---+--+ i | libgfortran41 | The GNU Fortran Compiler Runtime Library | package i | libgfortran43 | The GNU Fortran Compiler Runtime Library | package Any ideas how to solve this impass? I have not worked on SUSE, but check to see where gfortran is located: $ which gfortran and be sure that it returns the path to the executable and that the path to it is in your $PATH. You might also want to review: http://cran.r-project.org/doc/manuals/R-admin.html#Using-FORTRAN HTH, Marc Schwartz __ 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. __ 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] R on netbooks et al?
Johannes Huesing wrote: chaogai chao...@xs4all.nl [Thu, Mar 05, 2009 at 07:04:19PM CET]: I'm having similar experiences on my Acer Aspire One. Everything will work good. Only thing that takes a lot of time is compiling R if you are in the habit of doing so. On the Fedora version that came with my Acer Aspire One, I am even thinking of compiling R itself as the current R version is 2.6.0 ... Otherwise, everything seems fine and the keyboard is indeed the greatest letdown so far (the tiny left mouse button a close second). I did do that. Most practical is to get the R-devel from the repositories. It is the wrong version, will bring what you need to build regarding other dependencies. Then remove R-devel and you can get your 2.8.1 sources from CRAN. Not sure about the exact names of the things. Now happy on Suse 11.1 after a brief fling with the Fedora 10. __ 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] Interaction term not significant when using glm???
I think the interaction is not so strong anymore if you do what glm does: use a logit transformation. testdata - matrix(c(rep(0:1,times=4),rep(c(FLC,FLC,free,free),times=2), rep(c(no,yes),each =4),3,42,1,44,27,20,3,42),ncol=4) colnames(testdata) -c(spot,constr,vernalized,Freq) testdata - as.data.frame(testdata) testdata$Freq - as.numeric(as.character(testdata$Freq)) testdata$spot - as.numeric(as.character(testdata$spot)) T2 - reshape(testdata,v.names='Freq',timevar='spot',idvar=names(testdata)[c(2,3)],direction='wide') T2$Prop - T2$Freq.0/(T2$Freq.0+T2$Freq.1) plot(log(T2$Prop/(1-T2$Prop)),x=interaction(T2$constr,T2$vernalized)) Kees joris meys wrote: Dear all, I have a dataset where the interaction is more than obvious, but I was asked to give a p-value, so I ran a logistic regression using glm. Very funny, in the outcome the interaction term is NOT significant, although that's completely counterintuitive. There are 3 variables : spot (binary response), constr (gene construct) and vernalized (growth conditions). Only for the FLC construct after vernalization, the chance on spots should be lower. So in the model one would suspect the interaction term to be significant. Yet, only the two main terms are significant here. Can it be my data is too sparse to use these models? Am I using the wrong method? # data generation testdata - matrix(c(rep(0:1,times=4),rep(c(FLC,FLC,free,free),times=2), rep(c(no,yes),each =4),3,42,1,44,27,20,3,42),ncol=4) colnames(testdata) -c(spot,constr,vernalized,Freq) testdata - as.data.frame(testdata) # model T0fit - glm(spot~constr*vernalized, weights=Freq, data=testdata, family=binomial) anova(T0fit) Kind regards Joris [[alternative HTML version deleted]] __ 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. __ 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] R on netbooks et al?
I'm having similar experiences on my Acer Aspire One. Everything will work good. Only thing that takes a lot of time is compiling R if you are in the habit of doing so. herrdittm...@yahoo.co.uk wrote: Dear useRs, With the rise of netbooks and 'lifestyle laptops I am tempted to get one of these to mainly run R on it. Processor power and hard disk space seem to be ok. What I wonder is the handling and feel with respect to R. Has anyone here installed or is running R on one of these, and if so, what is your experience? Would it be more of a nice looking gadget than a feasable platform to do some stats on? Many thanks, Bernd __ 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. __ 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] rgl persp3d bounding box color problem.
rgl_0.83-3 did not help Duncan Murdoch wrote: On 3/2/2009 2:48 PM, chaogai wrote: Oops, sorry R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rgl_0.81svGUI_0.9-44svSocket_0.9-43 svMisc_0.9-46 0.81 isn't the current version of rgl on CRAN. Please try that one, or even better, the development version on R-forge. Duncan Murdoch Duncan Murdoch wrote: On 3/2/2009 2:00 PM, chaogai wrote: Whatever it is, it is also happening on my Acer, Suse 11.1, 32 bits, self build R. Versions of R and rgl? Duncan Murdoch Kees Bo Zhou wrote: Thanks Duncan. I haven't got a chance to try it in windows yet. But I won't be surprised if it's my driver's fault. I had OpenGL problems on this dell laptop before. Date: Sun, 1 Mar 2009 18:29:20 -0500 From: murd...@stats.uwo.ca To: bozhou1...@hotmail.com CC: remkoduur...@gmail.com; r-help@r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 01/03/2009 5:54 PM, Bo Zhou wrote: site down.. here is the code library(rgl) plot1: persp3d(x=1:11,y=1:210,z=matrix(rep(1,11*210),11,210),col=matrix(rep(#FF,11*210),11,210)) plot2: persp3d(x=1:11,y=1:10,z=matrix(rep(1,11*10),11,10),col=matrix(rep(#FF,11*10),11,10)) Works fine on Mac OS 10.5 too. Looks like a bug in your OpenGL driver... Duncan Murdoch Thanks! Bo Date: Mon, 2 Mar 2009 09:28:31 +1100 Subject: Re: [R] rgl persp3d bounding box color problem. From: remkoduur...@gmail.com To: bozhou1...@hotmail.com I would not mind trying, but the link no longer works... Remko - Remko Duursma Post-Doctoral Fellow Centre for Plant and Food Science University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia Mobile: +61 (0)422 096908 On Mon, Mar 2, 2009 at 8:16 AM, Bo Zhou bozhou1...@hotmail.com wrote: Thanks, Duncan. What's your platform? Could this be an issues related to my platform? I'm on Ubuntu 8.10 64bit using cran's R package. I built rgl package on my machine using install.packages(). I'm going to give it a try in windows. I would be very grateful if anyone using similar setup could give it a try. Thanks, Bo Date: Sun, 1 Mar 2009 07:03:10 -0500 From: murd...@stats.uwo.ca To: bozhou1...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 28/02/2009 4:20 PM, Bo Zhou wrote: Hi guys, I hit on a problem when I use rgl. Could you try to run the code here in this link and see why the first persp3d gives a red bounding box and the second shows black? They both show as black on my system. Duncan Murdoch http://rafb.net/p/g1i7ur33.html (sorry for not pasting the code here directly but my previous email got filtered by this list so I suspect my code looks like spam to the spam filter) I'm expecting black color to be the right result but the code is virtually same except different data size. Looks like a mem bug to me? BTW you will need to install the rgl package Thanks, Bo _ [[alternative HTML version deleted]] __ 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. _ [[alternative HTML version deleted]] __ 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. _ [[alternative HTML version deleted]] __ 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. _ Hotmail® is up to 70% faster. Now good news travels really fast. [[alternative HTML version deleted
Re: [R] rgl persp3d bounding box color problem.
Whatever it is, it is also happening on my Acer, Suse 11.1, 32 bits, self build R. Kees Bo Zhou wrote: Thanks Duncan. I haven't got a chance to try it in windows yet. But I won't be surprised if it's my driver's fault. I had OpenGL problems on this dell laptop before. Date: Sun, 1 Mar 2009 18:29:20 -0500 From: murd...@stats.uwo.ca To: bozhou1...@hotmail.com CC: remkoduur...@gmail.com; r-help@r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 01/03/2009 5:54 PM, Bo Zhou wrote: site down.. here is the code library(rgl) plot1: persp3d(x=1:11,y=1:210,z=matrix(rep(1,11*210),11,210),col=matrix(rep(#FF,11*210),11,210)) plot2: persp3d(x=1:11,y=1:10,z=matrix(rep(1,11*10),11,10),col=matrix(rep(#FF,11*10),11,10)) Works fine on Mac OS 10.5 too. Looks like a bug in your OpenGL driver... Duncan Murdoch Thanks! Bo Date: Mon, 2 Mar 2009 09:28:31 +1100 Subject: Re: [R] rgl persp3d bounding box color problem. From: remkoduur...@gmail.com To: bozhou1...@hotmail.com I would not mind trying, but the link no longer works... Remko - Remko Duursma Post-Doctoral Fellow Centre for Plant and Food Science University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia Mobile: +61 (0)422 096908 On Mon, Mar 2, 2009 at 8:16 AM, Bo Zhou bozhou1...@hotmail.com wrote: Thanks, Duncan. What's your platform? Could this be an issues related to my platform? I'm on Ubuntu 8.10 64bit using cran's R package. I built rgl package on my machine using install.packages(). I'm going to give it a try in windows. I would be very grateful if anyone using similar setup could give it a try. Thanks, Bo Date: Sun, 1 Mar 2009 07:03:10 -0500 From: murd...@stats.uwo.ca To: bozhou1...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 28/02/2009 4:20 PM, Bo Zhou wrote: Hi guys, I hit on a problem when I use rgl. Could you try to run the code here in this link and see why the first persp3d gives a red bounding box and the second shows black? They both show as black on my system. Duncan Murdoch http://rafb.net/p/g1i7ur33.html (sorry for not pasting the code here directly but my previous email got filtered by this list so I suspect my code looks like spam to the spam filter) I'm expecting black color to be the right result but the code is virtually same except different data size. Looks like a mem bug to me? BTW you will need to install the rgl package Thanks, Bo _ [[alternative HTML version deleted]] __ 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. _ [[alternative HTML version deleted]] __ 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. _ [[alternative HTML version deleted]] __ 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. _ Hotmail® is up to 70% faster. Now good news travels really fast. [[alternative HTML version deleted]] __ 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. __ 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] rgl persp3d bounding box color problem.
Oops, sorry R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] rgl_0.81svGUI_0.9-44svSocket_0.9-43 svMisc_0.9-46 Duncan Murdoch wrote: On 3/2/2009 2:00 PM, chaogai wrote: Whatever it is, it is also happening on my Acer, Suse 11.1, 32 bits, self build R. Versions of R and rgl? Duncan Murdoch Kees Bo Zhou wrote: Thanks Duncan. I haven't got a chance to try it in windows yet. But I won't be surprised if it's my driver's fault. I had OpenGL problems on this dell laptop before. Date: Sun, 1 Mar 2009 18:29:20 -0500 From: murd...@stats.uwo.ca To: bozhou1...@hotmail.com CC: remkoduur...@gmail.com; r-help@r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 01/03/2009 5:54 PM, Bo Zhou wrote: site down.. here is the code library(rgl) plot1: persp3d(x=1:11,y=1:210,z=matrix(rep(1,11*210),11,210),col=matrix(rep(#FF,11*210),11,210)) plot2: persp3d(x=1:11,y=1:10,z=matrix(rep(1,11*10),11,10),col=matrix(rep(#FF,11*10),11,10)) Works fine on Mac OS 10.5 too. Looks like a bug in your OpenGL driver... Duncan Murdoch Thanks! Bo Date: Mon, 2 Mar 2009 09:28:31 +1100 Subject: Re: [R] rgl persp3d bounding box color problem. From: remkoduur...@gmail.com To: bozhou1...@hotmail.com I would not mind trying, but the link no longer works... Remko - Remko Duursma Post-Doctoral Fellow Centre for Plant and Food Science University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia Mobile: +61 (0)422 096908 On Mon, Mar 2, 2009 at 8:16 AM, Bo Zhou bozhou1...@hotmail.com wrote: Thanks, Duncan. What's your platform? Could this be an issues related to my platform? I'm on Ubuntu 8.10 64bit using cran's R package. I built rgl package on my machine using install.packages(). I'm going to give it a try in windows. I would be very grateful if anyone using similar setup could give it a try. Thanks, Bo Date: Sun, 1 Mar 2009 07:03:10 -0500 From: murd...@stats.uwo.ca To: bozhou1...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] rgl persp3d bounding box color problem. On 28/02/2009 4:20 PM, Bo Zhou wrote: Hi guys, I hit on a problem when I use rgl. Could you try to run the code here in this link and see why the first persp3d gives a red bounding box and the second shows black? They both show as black on my system. Duncan Murdoch http://rafb.net/p/g1i7ur33.html (sorry for not pasting the code here directly but my previous email got filtered by this list so I suspect my code looks like spam to the spam filter) I'm expecting black color to be the right result but the code is virtually same except different data size. Looks like a mem bug to me? BTW you will need to install the rgl package Thanks, Bo _ [[alternative HTML version deleted]] __ 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. _ [[alternative HTML version deleted]] __ 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. _ [[alternative HTML version deleted]] __ 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. _ Hotmail® is up to 70% faster. Now good news travels really fast. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R
Re: [R] How to connect R and WinBUGS/OpenBUGS/LinBUGS in Linux in Feb. 2009
I do not know about the ubuntu instructions, they would not help me on
Suse. The wine version is 1.1.9.
I thought that was the latest,but when I checked latest is 1.1.15, which
does indeed throw the blackbox error.
So, now it does not work for me either
Sorry I gave bad advise
kees
On Thu, 19 Feb 2009 01:38:15 +0100, Paul Heinrich Dietrich
paul.heinrich.dietr...@gmail.com wrote:
I went to this webpage (http://ubuntuforums.org/showthread.php?t=624644)
and
followed the instructions to the letter on getting the latest Wine. I
installed WinBUGS again, but this time I cannot open it in Wine. It says
Black Box, Trap #101, and some text I can't copy/paste here. Is this the
latest Wine that you have, or something different? Thanks.
chaogai-2 wrote:
Hi,
For me running winbugs through wine just works. Even when I do not
specify
any directories.
The example they give in the bugs helpfile was my starting point.
Setup is suse 11.1, latest Wine, R, R2WinBUGS winbugs.
I assume you first tried without specifying directories?
The directories you use do not work for me, with WINEPATH the culprit.
If you do not have the latest wine I advise to upgrade not specify
directories.
Good luck,
Kees
On Wed, 18 Feb 2009 01:27:18 +0100, Paul Heinrich Dietrich
paul.heinrich.dietr...@gmail.com wrote:
Hi Uwe,
Thank you for your guidance. I have installed R2WinBUGS and WinBUGS14
under
wine. Using ?bugs for help, it tells me:
useWINE: logical; attempt to use the Wine emulator to run 'WinBUGS',
defaults to 'FALSE' on Windows, and 'TRUE' otherwise. Not available in
S-PLUS.
WINE: character, path to 'wine' binary file, it is tried hard (by a
guess
and the utilities 'which' and 'locate') to get the information
automatically if not given.
newWINE: Use new versions of Wine that have 'winepath' utility
WINEPATH: character, path to 'winepath' binary file, it is tried hard
(by a
guess and the utilities 'which' and 'locate') to get the information
automatically if not given.
..and the following code is a simple Bayesian version of a t-test...
Directory Paths
MyModelPath - /home/me/Compound/R/WinBUGS/
MyBUGSPath - /home/me/.wine/drive_c/Program Files/WinBUGS14/
MyModelFile - paste(MyModelPath, model.bug, sep=)
WINEPATH - /usr/bin/wine
Create Data Set
# Here is some fake data
n_draws - 50
x - round(runif(n_draws, 1, 2))
y - ifelse(x == 1, rnorm(n_draws, 1, 1), rnorm(n_draws, 1.2, 0.8))
MyData - as.data.frame(cbind(y, x))
y.n - NROW(MyData$y)
x.j - length(unique(x))
summary(MyData)
## Format Data for WinBUGS
##
MyBUGSData - list(y=MyData$y, x=MyData$x, n=y.n, x.j=x.j)
MyBUGSData
## WinBUGS Model File
###
library(R2WinBUGS)
cat(model
{
for (i in 1:n)
{
y[i] ~ dnorm(mu[i], tau)
mu[i] - alpha + beta[x[i]]
}
### STZ (Sum-To-Zero) Constraints
beta[1] - -sum(beta[2:x.j])
### Priors
alpha ~ dnorm(0.0, 1.0E-4)
for (i in 2:x.j)
{
beta[i] ~ dnorm(0.0, 1.0E-4)
}
tau ~ dgamma(0.01, 0.01)
precision - sqrt(1/tau)
},
file=MyModelFile)
file.show(MyModelFile)
# WinBUGS Model
#
MyModel - bugs(MyBUGSData, inits=NULL,
model.file=MyModelFile,
parameters.to.save=c(alpha, beta, precision),
n.chains=3, n.iter=2000, n.burnin=1000, n.thin=1, codaPkg=TRUE,
bugs.directory = MyBUGSPath, working.directory=MyModelPath,
useWINE=TRUE, WINEPATH=WINEPATH, debug=TRUE)
The output says:
ERROR:
cannot open the connection
I'm wondering if I've misinterpreted how to set my paths with wine,
because
I can go to the following path, double-click on WinBUGS14.exe, and open
it
just fine: /home/me/.wine/drive_c/Program Files/WinBUGS14/
I can also go to Applications Wine Browse C:\ Drive and navigate to
WinBUGS.
Please help if I've done something wrong. Thanks.
--
__
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.
--
__
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] How to connect R and WinBUGS/OpenBUGS/LinBUGS in Linux in Feb. 2009
Hi,
For me running winbugs through wine just works. Even when I do not specify
any directories.
The example they give in the bugs helpfile was my starting point.
Setup is suse 11.1, latest Wine, R, R2WinBUGS winbugs.
I assume you first tried without specifying directories?
The directories you use do not work for me, with WINEPATH the culprit.
If you do not have the latest wine I advise to upgrade not specify
directories.
Good luck,
Kees
On Wed, 18 Feb 2009 01:27:18 +0100, Paul Heinrich Dietrich
paul.heinrich.dietr...@gmail.com wrote:
Hi Uwe,
Thank you for your guidance. I have installed R2WinBUGS and WinBUGS14
under
wine. Using ?bugs for help, it tells me:
useWINE: logical; attempt to use the Wine emulator to run 'WinBUGS',
defaults to 'FALSE' on Windows, and 'TRUE' otherwise. Not available in
S-PLUS.
WINE: character, path to 'wine' binary file, it is tried hard (by a guess
and the utilities 'which' and 'locate') to get the information
automatically if not given.
newWINE: Use new versions of Wine that have 'winepath' utility
WINEPATH: character, path to 'winepath' binary file, it is tried hard
(by a
guess and the utilities 'which' and 'locate') to get the information
automatically if not given.
..and the following code is a simple Bayesian version of a t-test...
Directory Paths
MyModelPath - /home/me/Compound/R/WinBUGS/
MyBUGSPath - /home/me/.wine/drive_c/Program Files/WinBUGS14/
MyModelFile - paste(MyModelPath, model.bug, sep=)
WINEPATH - /usr/bin/wine
Create Data Set
# Here is some fake data
n_draws - 50
x - round(runif(n_draws, 1, 2))
y - ifelse(x == 1, rnorm(n_draws, 1, 1), rnorm(n_draws, 1.2, 0.8))
MyData - as.data.frame(cbind(y, x))
y.n - NROW(MyData$y)
x.j - length(unique(x))
summary(MyData)
## Format Data for WinBUGS
##
MyBUGSData - list(y=MyData$y, x=MyData$x, n=y.n, x.j=x.j)
MyBUGSData
## WinBUGS Model File
###
library(R2WinBUGS)
cat(model
{
for (i in 1:n)
{
y[i] ~ dnorm(mu[i], tau)
mu[i] - alpha + beta[x[i]]
}
### STZ (Sum-To-Zero) Constraints
beta[1] - -sum(beta[2:x.j])
### Priors
alpha ~ dnorm(0.0, 1.0E-4)
for (i in 2:x.j)
{
beta[i] ~ dnorm(0.0, 1.0E-4)
}
tau ~ dgamma(0.01, 0.01)
precision - sqrt(1/tau)
},
file=MyModelFile)
file.show(MyModelFile)
# WinBUGS Model
#
MyModel - bugs(MyBUGSData, inits=NULL,
model.file=MyModelFile,
parameters.to.save=c(alpha, beta, precision),
n.chains=3, n.iter=2000, n.burnin=1000, n.thin=1, codaPkg=TRUE,
bugs.directory = MyBUGSPath, working.directory=MyModelPath,
useWINE=TRUE, WINEPATH=WINEPATH, debug=TRUE)
The output says:
ERROR:
cannot open the connection
I'm wondering if I've misinterpreted how to set my paths with wine,
because
I can go to the following path, double-click on WinBUGS14.exe, and open
it
just fine: /home/me/.wine/drive_c/Program Files/WinBUGS14/
I can also go to Applications Wine Browse C:\ Drive and navigate to
WinBUGS.
Please help if I've done something wrong. Thanks.
--
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] surprising predicting capabilities
Hi,
I noticed the following fortune in R 2.7 and 2.6.2:
fortune('Spreads')
If anything, there should be a Law: Thou Shalt Not Even Think Of Producing A
Graph That Looks Like Anything From A Spreadsheet.
-- Ted Harding (in a discussion about producing graphics)
R-help (August 2008)
Just wondering, what function and library gave this detailed prediction?
Cheers
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Windows Vista 64-bit support
The standard windows build works in Vista 64. A 64 bits build depends on tools outside the realm of the R-core team; a 64 bits compiler On Monday 17 March 2008 06:17:31 pm Daniel Gatti wrote: Where does the R build for Vista X64 stand? The last update message is from July last year (see [R] Improved Windows Vista compatibility from Prof Brian Ripley on 2007-07-11). Is it likely to happen in 2008? I suspect that more people will start using it as Vista is adopted more widely. And I'd certainly use it for large genomics data sets. Thanks, Dan Gatti UNC-CH __ 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. __ 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] best text editor for Linux?
After to much windows contamination, my brain does not do the cryptic part of Emacs+ESS C-x M-c M-headache. Eclipse is is currently my choice. (But the installation instructions could be better) Kees On Saturday 02 February 2008 05:49:10 am 宋时歌 wrote: On Linux platform, nothing beats Emacs + ESS. Shige On Feb 2, 2008 11:06 AM, Wade Wall [EMAIL PROTECTED] wrote: Hi all, I know this question has been asked in the past, but I am wondering if anyone running R on Linux has any guidance as to a text editor that works well with R. At the present time I am running R on Windows and using TINN-R. For a number of reasons I want to switch to Linux, but can't find much in the way of a text editor in sync with R. Any experiences, recommendations would be appreciated. Wade Wall [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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. __ 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.
