Re: [R] can't get text to appear over individual panels in multi-panel plot
On 18 Jun 2004, at 8:26, Deepayan Sarkar wrote: On Thursday 17 June 2004 22:57, Patrick Bennett wrote: yes, i can reproduce that same graph when i print to the pdf-device. but the panel titles do not appear when I print to the Quartz-device. Hmm. I won't be able to help you then, let's hope someone else can. I think this is a problem with the quartz device. I have often see that margin texts are plotted even in ordinary plot() if quartz thinks there is no space for them. They do still appear if you copy the screen graphics as a pdf file. In Linux (my principal platform) I typically reduce the white margins, but if I use the same mar pars in MacOS X I won't get axis labels. Quartz is the culprit I suppose. Actually, in your example I couldn't get the texts when I saved the plot as a pdf (menu entry). However, when I opened an X11 device, the text was reproduced OK. So it looks like a quartz problem. For X11 in MacOS X: It may not be in the default installation, but it is in the installation CD/DVD of MacOS X. Then you got to start it explicitly before launching x11() within R shell. In general, I wouldn't recommend using x11() in Mac, since quartz() looks so much better: x11 looks just as clumsy as x11 in Linux or the ordinary Windows plotting device in some other OS. -- And beware: I have a suspicion that if you stop your X11 in MacOS X, your mouse will die at logout and you got to boot (or restart the mouse demon if you know who he is). cheers, jari oksanen -- Jari Oksanen, Oulu, Finland __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Compiling R with Intel compilers - recommended options?
Hi, I'm a sysadmin who's been tasked with installing R on our 1000-node compute cluster. I have licences for the Intel C and FORTRAN compilers, so I'm using the following to compile: CFLAGS=-O2 -axWK FFLAGS=$CFLAGS CXXFLAGS=$CFLAGS CC=icc F77=ifort CXX=icc FPICFLAGS=-fpic ./configure --without-x --without-tcltk The compilation seems to go OK, with a few warnings. What concerns me is when I run the make check - how long should this take? I've had one running for over 12 hours now, and it's still on: running code in 'base-Ex.R' ... and hasn't produced any output since; it just sits there burning CPU. I guess my question is: I'm sure someone has successfully compiled R on X86 Linux using the Intel compilers before - what options did you use to make it work? And how long should this check phase take? Many thanks... Tim -- Dr Tim Cutts Informatics Systems Group Wellcome Trust Sanger Institute Hinxton, Cambridge, CB10 1SA, UK __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Compiling R with Intel compilers - recommended options?
What OS and hardware is this? Eventually you mention `X86 Linux' but are you using x86 Linux and if so how fast processors? On a 3GHz machine make check takes a couple of minutes using gcc (and in our experience Portland Group is faster than gcc -- we have not tried Intel as local advice suggests it is slower than PG). Which version of R? R 1.9.0 does this with gcc 3.4.0 on Linux ix86, at the first use of LAPACK. So if you are not trying 1.9.1beta (to be released on Monday), please do so. After that, make check does give output so where exactly does it hang, and if you interrupt that check, how far has it got in the output file? On Fri, 18 Jun 2004, Tim Cutts wrote: Hi, I'm a sysadmin who's been tasked with installing R on our 1000-node compute cluster. I have licences for the Intel C and FORTRAN compilers, so I'm using the following to compile: CFLAGS=-O2 -axWK FFLAGS=$CFLAGS CXXFLAGS=$CFLAGS CC=icc F77=ifort CXX=icc FPICFLAGS=-fpic ./configure --without-x --without-tcltk The compilation seems to go OK, with a few warnings. What concerns me is when I run the make check - how long should this take? I've had one running for over 12 hours now, and it's still on: running code in 'base-Ex.R' ... and hasn't produced any output since; it just sits there burning CPU. I guess my question is: I'm sure someone has successfully compiled R on X86 Linux using the Intel compilers before - what options did you use to make it work? Did you search the archives? I found a lot of hits, none recent for ix86 Linux. And how long should this check phase take? -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Is there an easy way to generate linearly independent ve
On 18-Jun-04 Fred wrote: I want to get linearly independent vectors, not orthogonal ones. The functions eigen, svd, I think it may provide orthogonal vectors which are not what I expect. It depends what sort of characteristics you want your non-orthogonal linearly independent vectors to have. It's very easy to produce examples of such vectors: simple and easy examples are like (e.g. for n=4) 1 0 0 0 1 1 0 0 1 1 1 0 1 1 1 1 or 1 0 0 0 1 1 0 0 0 1 1 0 0 0 1 1 and similar (all of which can be extended downwards arbitrarily if you want n linearly independent vectors in k n dimensions). If these are too simplistic for you, please indicate how interesting you want them to be. The suggestions about using random numbers should work: it's not likely that an NxN matrix of random numbers will be near singular, so a test of the matrix to reject any which are too close is going to be fairly efiicient. E.g. you might consider a simple test like accepting the matrix M if max(abs(eigen(M)$values)))/min(abs(eigen(M)$values))) 10 (the 10 is arbitrary, for illustration). Hope this helps, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 167 1972 Date: 18-Jun-04 Time: 09:15:38 -- XFMail -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] multiple plots for data sets of inconsistent size
I am wanting to plot pca loadings onto sites superimposed on a contour
map. There are a maximum of 20 sites at which loadings might appear -
however due to the nature of my data, missing data has meant that some
stations have not been included in some of the pca.
For example, I am performing pca for 5 different variables at 20 different
sites for a number of different time intervals and want to perform a cross
comparison to see where key trends lie. Where data is not available for
any particular station at any given time interval I am still keen to
analyse the principal components on the others.
I have been using the following code to produce the plots I want:
for (i in 1:4) {
image(east.grid,north.grid,t(map.matrix),col=my.colors,
axes=TRUE,xlab=,ylab=)
text(stations$x.axis,stations$y.axis,labels=as.character(stations$station))
title(paste(Component,i))
pc - p6.5am.pca$rotation[,i]
pc.pos - (pc 0)
if (any(pc.pos)) {
symbols(stations$x.axis[pc.pos],stations$y.axis[pc.pos],
circles=scale*pc[pc.pos],lwd=2,fg=red,inches=FALSE,add=TRUE)
}
if (any(!pc.pos)) {
symbols(stations$x.axis[!pc.pos],stations$y.axis[!pc.pos],
circles=-scale*pc[!pc.pos],lwd=2,lty=2,fg=blue,inches=FALSE,
add=TRUE)
}
box()
}
My problem is this - due to the large number of plots required I would
like to be able to batch process the results, but in the case of applying
the above code when one (or more) station(s) is missing from the pca I get
an error message as the x and y lengths differ. Is there a way I can get the code
to simply return a zero loading at a site if it hasn't been included in
the calculation of the pca? (or is there another better way around this
problem?)
I hope that this question makes some sense.
Any ideas?
Thanks,
laura
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[R] OT: virus affecting a list subscriber
I presume I am not alone in receiving return-to-sender mailings provoked by a well known virus eg [EMAIL PROTECTED] (reason: 550 [EMAIL PROTECTED]... User unknown) [EMAIL PROTECTED] (reason: 550 [EMAIL PROTECTED]... User unknown) [EMAIL PROTECTED] (reason: 550 [EMAIL PROTECTED]... User unknown) [EMAIL PROTECTED] (reason: 550 [EMAIL PROTECTED]... User unknown) [EMAIL PROTECTED] (reason: 550 [EMAIL PROTECTED]... User unknown) [EMAIL PROTECTED] (reason: 550 [EMAIL PROTECTED]... User unknown) [EMAIL PROTECTED] (reason: 550 [EMAIL PROTECTED]... User unknown) If one has not recently virus-checked one's computer recently, it might be a good idea. I *of course* run linux, so it can't be me ;) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] [Q] Newbie (continued.. at least I got R running allready :-)
Hi all a week ago, I posted a newbie question in data smoothing maximum-extraction with R. I got quite a lot of response, but I'm still kinda stuck with it... I'll restate the problem : i got a datafile with 2400 measuerements (every 250msec) of a CO2 measurement device, capturing the breath of a subject. I uploaded such a sample here : http://www.psy.kuleuven.ac.be/leerpsy/data.csv now I wish to figure out where each breath expiration ceiling takes place , as shown on this graph : http://www.psy.kuleuven.ac.be/leerpsy/graph.bmp I'm kinda stuck on how to get this running in R. I really hope someone can help me out. If you guys can get me running, I promise to promote R as often as I can here on our faculty (which still uses Statistica for almost everything) thanks a million in advance ! __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] non-linear binning? power-law in R
On Thu, 17 Jun 2004, Dr. Herwig Meschke wrote: Why not try to avoid binning (and density plot) at all? An alternative could be a qqplot (as a log-log-plot), e.g. plot(ppoints(length(x4)), x4[order(x4)], log=xy) abline(lm(log(x4[order(x4)])~log(ppoints(length(x4, col=red) If the assumptions of uniform distribution and power transformation y=a*x**b are true, the coefficient of lm estimates the exponent b. Thanks, this looks very cool (although I am going to have to learn what it all means ;) However, playing with the above with the following for example... x4 - runif(100)**4 plot(ppoints(length(x4)), x4[order(x4)], log=xy) abline(lm(log(x4[order(x4)])~log(ppoints(length(x4, col=red) Shows (perhaps after a few repeats) that the fitted curve is dominated by the rare events, and the rare events have the highest variance, leading to potential big errors. By uniformly binning the log transformed data you group the rarest values in the bigest bin, and can therefore get better estimates of the true slope of the curve. My problem is now a technical one of working out how to do this, so isn't too fundamental. I can post up the differences in the values (and error) of the estimated curves when I get round to doing this. Thanks again for the help, Dan. Herwig __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Compiling R with Intel compilers - recommended options?
Dear Cutts and Prof. Ripley, On Fri, Jun 18, 2004 at 09:11:42AM +0100, Prof Brian Ripley wrote: Some benchmarks show icc is faster than gcc and pgcc. Even fortran compiler ifort is also faster than pgf77 (See the result on www.polyhedron.com). But I still recommend gcc and g77 as c and fortran compilers if you are on X86 Linux platforms. I once compiled R 1.9.0 by icc and ifort. It failed some of the checks. I also found that the difference between the speed of gcc+g77 and icc+ifort was not significant when I 'make test-Gct'. My platform Gentoo Linux pentium4 1.5GHz, 256M RAM and kernel 2.4.26. gcc version 3.3 icc and ifort version 8.0 non-commercial version. BTW, can you tell me the flags you used to compile R by pgcc and pgf77. Thank you. Jin What OS and hardware is this? Eventually you mention `X86 Linux' but are you using x86 Linux and if so how fast processors? On a 3GHz machine make check takes a couple of minutes using gcc (and in our experience Portland Group is faster than gcc -- we have not tried Intel as local advice suggests it is slower than PG). Which version of R? R 1.9.0 does this with gcc 3.4.0 on Linux ix86, at the first use of LAPACK. So if you are not trying 1.9.1beta (to be released on Monday), please do so. After that, make check does give output so where exactly does it hang, and if you interrupt that check, how far has it got in the output file? On Fri, 18 Jun 2004, Tim Cutts wrote: Hi, I'm a sysadmin who's been tasked with installing R on our 1000-node compute cluster. I have licences for the Intel C and FORTRAN compilers, so I'm using the following to compile: CFLAGS=-O2 -axWK FFLAGS=$CFLAGS CXXFLAGS=$CFLAGS CC=icc F77=ifort CXX=icc FPICFLAGS=-fpic ./configure --without-x --without-tcltk The compilation seems to go OK, with a few warnings. What concerns me is when I run the make check - how long should this take? I've had one running for over 12 hours now, and it's still on: running code in 'base-Ex.R' ... and hasn't produced any output since; it just sits there burning CPU. I guess my question is: I'm sure someone has successfully compiled R on X86 Linux using the Intel compilers before - what options did you use to make it work? Did you search the archives? I found a lot of hits, none recent for ix86 Linux. And how long should this check phase take? -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Compiling R with Intel compilers - recommended options?
Sorry, I was a bit sparing with details. Early in the morning, and all that. Many thanks for the swift reply! On 18 Jun 2004, at 9:11 am, Prof Brian Ripley wrote: What OS and hardware is this? Hardware: 700+ machines are 800 MHz Pentium III, 1 GB RAM, Red Hat 7.2 168 machines are dual 2.8 GHz Xeon, 4 GB RAM, Red Hat 8.0 I'm compiling on the older machines to make sure there won't be library problems. The compiler versions are: Intel(R) C++ Compiler for 32-bit applications, Version 8.0 Build 20031016Z Package ID: l_cc_p_8.0.055 Intel(R) Fortran Compiler for 32-bit applications, Version 8.0 Build 20040412Z Package ID: l_fc_pc_8. Eventually you mention `X86 Linux' but are you using x86 Linux and if so how fast processors? On a 3GHz machine make check takes a couple of minutes using gcc (and in our experience Portland Group is faster than gcc -- we have not tried Intel as local advice suggests it is slower than PG). So 12 hours is bit excessive. :-) At least now I know. Thanks! Which version of R? R 1.9.0 does this with gcc 3.4.0 on Linux ix86, at the first use of LAPACK. Ah. This is indeed 1.9.0, since that is what was asked for. So if you are not trying 1.9.1beta (to be released on Monday), please do so. After that, make check does give output so where exactly does it hang, and if you interrupt that check, how far has it got in the output file? With 1.9.0, I never get an output file. On interrupting the make check, it says: make[4]: *** Deleting file `base-Ex.Rout' and hangs again. I have to background it and kill it. The same thing happens with 1.9.1. I think I'll use gcc/g77 as suggested by others to get a working install for now, and then I will look into a better optimised version at a more leisurely pace. Regards, Tim -- Dr Tim Cutts Informatics Systems Group Wellcome Trust Sanger Institute Hinxton, Cambridge, CB10 1SA, UK __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Compiling R with Intel compilers - recommended options?
On Fri, 18 Jun 2004, Tim Cutts wrote: Sorry, I was a bit sparing with details. Early in the morning, and all that. Many thanks for the swift reply! On 18 Jun 2004, at 9:11 am, Prof Brian Ripley wrote: What OS and hardware is this? Hardware: 700+ machines are 800 MHz Pentium III, 1 GB RAM, Red Hat 7.2 168 machines are dual 2.8 GHz Xeon, 4 GB RAM, Red Hat 8.0 I'm compiling on the older machines to make sure there won't be library problems. The compiler versions are: Intel(R) C++ Compiler for 32-bit applications, Version 8.0 Build 20031016Z Package ID: l_cc_p_8.0.055 Intel(R) Fortran Compiler for 32-bit applications, Version 8.0 Build 20040412Z Package ID: l_fc_pc_8. Eventually you mention `X86 Linux' but are you using x86 Linux and if so how fast processors? On a 3GHz machine make check takes a couple of minutes using gcc (and in our experience Portland Group is faster than gcc -- we have not tried Intel as local advice suggests it is slower than PG). So 12 hours is bit excessive. :-) At least now I know. Thanks! Which version of R? R 1.9.0 does this with gcc 3.4.0 on Linux ix86, at the first use of LAPACK. Ah. This is indeed 1.9.0, since that is what was asked for. So if you are not trying 1.9.1beta (to be released on Monday), please do so. After that, make check does give output so where exactly does it hang, and if you interrupt that check, how far has it got in the output file? With 1.9.0, I never get an output file. On interrupting the make check, it says: make[4]: *** Deleting file `base-Ex.Rout' and hangs again. I have to background it and kill it. Looks like the same issue as gcc 3.4.0. The same thing happens with 1.9.1. I think I'll use gcc/g77 as suggested by others to get a working install for now, and then I will look into a better optimised version at a more leisurely pace. Fine. The issue on gcc 3.4.0 is that if you compile src/modules/lapack/dlamc.f without -ffloat-store it loops forever. I suspect you need to compile it without optimization or with the equivalent of -ffloat-store. It's a separate file in 1.9.1 to make this easier/less penalty and configure sets -ffloat-store if g77 is detected. LAPACK calls Fortran functions to try to force stores, and that worked on versions of gcc = 3.3.3 (and of course only machines with extended registers like ix86 need the subterfuge). -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Compiling R with Intel compilers - recommended options?
On 18 Jun 2004, at 11:58 am, Prof Brian Ripley wrote: Fine. The issue on gcc 3.4.0 is that if you compile src/modules/lapack/dlamc.f without -ffloat-store it loops forever. I suspect you need to compile it without optimization or with the equivalent of -ffloat-store. It's a separate file in 1.9.1 to make this easier/less penalty and configure sets -ffloat-store if g77 is detected. LAPACK calls Fortran functions to try to force stores, and that worked on versions of gcc = 3.3.3 (and of course only machines with extended registers like ix86 need the subterfuge). From my reading of the Intel compiler documentation, the equivalent option for icc and ifort is -mp, so I'll have a go at that. Tim -- Dr Tim Cutts Informatics Systems Group Wellcome Trust Sanger Institute Hinxton, Cambridge, CB10 1SA, UK __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] set working directory
I have just upgraded from rw1081 to rw1090 (using Windows 2000).
Now when I type the command:
setwd('d:/folder_name)
I get the following error message:
Error in setwd(dir) : cannot change working directory
If I use the change dir tab in the file menu i can sucessfully change
working directories, but this is not so convenient as i have my whole model
stored as a text file that I prefer to copy into R.
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RE: [R] set working directory
Try adding a missing singe quote (') at the end of your working directory.
setwd('d:/folder_name')
S.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Louize Hill
Sent: Friday, June 18, 2004 13:38
To: [EMAIL PROTECTED]
Subject: [R] set working directory
I have just upgraded from rw1081 to rw1090 (using Windows 2000).
Now when I type the command:
setwd('d:/folder_name)
I get the following error message:
Error in setwd(dir) : cannot change working directory
If I use the change dir tab in the file menu i can sucessfully change
working directories, but this is not so convenient as i have my whole model
stored as a text file that I prefer to copy into R.
__
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-
Legal Notice: This electronic mail and its attachments are i...{{dropped}}
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Re: [R] set working directory
Bashir Saghir (Aztek Global) wrote:
Try adding a missing singe quote (') at the end of your working directory.
setwd('d:/folder_name')
Well, that was a mispelling in the mail, but not in the real example,
since not specifying the quote causes a syntax error.
I'm quite sure the folder-name was misspelled in the real example.
Uwe Ligges
S.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Louize Hill
Sent: Friday, June 18, 2004 13:38
To: [EMAIL PROTECTED]
Subject: [R] set working directory
I have just upgraded from rw1081 to rw1090 (using Windows 2000).
Now when I type the command:
setwd('d:/folder_name)
I get the following error message:
Error in setwd(dir) : cannot change working directory
If I use the change dir tab in the file menu i can sucessfully change
working directories, but this is not so convenient as i have my whole model
stored as a text file that I prefer to copy into R.
__
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Legal Notice: This electronic mail and its attachments are i...{{dropped}}
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Re: [R] R help in Firefox on Windows XP
Thank you Brian, Installing 0.8 first and then upgrading solved the problem. I noticed that installing 0.9 from scratch creates a registry key [HKEY_LOCAL_MACHINE\SOFTWARE\mozilla.org\Mozilla] CurrentVersion=1.7 Installing 0.8 creates [HKEY_LOCAL_MACHINE\SOFTWARE\mozilla.org\Mozilla] CurrentVersion=1.6 and upgrading to 0.9 afterwards does not change this entry. This might be the reason. Prof Brian Ripley wrote: Works for me. Did it work with Firefox 0.8? (I upgraded from 0.8.) I would try 0.8 and then upgrade. On Thu, 17 Jun 2004, Erich Neuwirth wrote: I had to reinstall my machine, so I installed Firefox 0.9 as browser I am using WinXP and R 1.9.1 beta. Now search in R html help does not work. I checked that the Java VM is working correctlt, Sun's test site says my installation is OK. Firefoxalso tells me that Applet Searchengine loaded Applet Searchengine started it just does not find anything. Does anybody know how to solve this? Prof Brian Ripley wrote: Works for me. Did it work with Firefox 0.8? (I upgraded from 0.8.) I would try 0.8 and then upgrade. On Thu, 17 Jun 2004, Erich Neuwirth wrote: I had to reinstall my machine, so I installed Firefox 0.9 as browser I am using WinXP and R 1.9.1 beta. Now search in R html help does not work. I checked that the Java VM is working correctlt, Sun's test site says my installation is OK. Firefoxalso tells me that Applet Searchengine loaded Applet Searchengine started it just does not find anything. Does anybody know how to solve this? __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] non-linear binning? power-law in R
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[R] R as controller
Hi all, this may be a 'stupid' question, but it would be great if it exists. What's it about? For the control of experiments, special (and expensive) software is often necessary. The main 'difficulty' I have is to read data from different (measurement) devices and send them to some actuators (reading from a serial device and the protocols). Is there a package in R for reading and writing to a serial port, including the protocols for ADAM modules etc? Or is there anyone having plans to program such a package? If it would exist, R could be as a controller, which would make life much easier, at least my life :). tnx, Kurt __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] can't get text to appear over individual panels in multi-panel plot
On Fri, 2004-06-18 at 09:28, Jari Oksanen wrote: On 18 Jun 2004, at 8:26, Deepayan Sarkar wrote: On Thursday 17 June 2004 22:57, Patrick Bennett wrote: yes, i can reproduce that same graph when i print to the pdf-device. but the panel titles do not appear when I print to the Quartz-device. Hmm. I won't be able to help you then, let's hope someone else can. I had a closer look at this, and it indeed looks like quartz() is anally checking that there is enough space for text or it refuses to print it at all. Like I wrote, the command worked with x11() device in MacOS X, but failed with default quartz(). I checked again (in another machine), and it seems that you may get text if you expand the par.strip: try adding par.strip.text=list(lines=2) in your Lattice plotting command (lines=1.8 was the smallest that worked in my case). This is a fault (``undesirable feature'') in quartz. This doesn't concern Lattice only, but all graphics commands: quartz() refuses to show axis labels or titles in too narrow margins, or to write text too close to axes (if xpd is not set) in quite ordinary plot(). cheers, jari oksanen -- Jari Oksanen -- Dept Biology, Univ Oulu, 90014 Oulu, Finland email [EMAIL PROTECTED], homepage http://cc.oulu.fi/~jarioksa/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R as controller
What OS is this? How do you access a serial port? On most modern OSes user processes such as R have no direct access to serial ports. If access is via a Unix device, binary connections will probably work. In my limited experience that expensive software runs under a low-level OS, MS-DOS or a real-time OS. On Fri, 18 Jun 2004, groensels wrote: this may be a 'stupid' question, but it would be great if it exists. What's it about? For the control of experiments, special (and expensive) software is often necessary. The main 'difficulty' I have is to read data from different (measurement) devices and send them to some actuators (reading from a serial device and the protocols). Is there a package in R for reading and writing to a serial port, including the protocols for ADAM modules etc? Or is there anyone having plans to program such a package? If it would exist, R could be as a controller, which would make life much easier, at least my life :). -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] msm
russell alexander wrote: Hello, I'm writing about msm. It may be that consistent users of Markov models have a good idea as to what constitutes workable data for a model. I think of general rules, in basic statistical studies where n is limited to exclude fairly precise figures in the lower range. On the other hand Markov models don't seem to be often enough used for parameters to be as well laid out. I also get the feeling that msm is organized to work optimally with certain sizes and shapes of data. Is there a source that anyone is aware of on this? (I have the Nelder text on optimization, and also have a feeling that what's possible is pretty closely connected with optimization questions) It's very difficult to give general guidelines for how much data is sufficient to estimate a continuous-time Markov model. There are two distinct forms of data which these models are used for. The simplest case is when you have observed the entire trajectory of the process. In this case, complex transition matrices can sometimes be estimated with relatively small datasets.However, if you only have observations at arbitrary times, then certain models will result in very flat likelihoods. In particular, for models with reversible transitions (recurrent states) there can be an infinite number of possible paths followed in between two arbitrary times. Then you will need substantially more data. Models with non-recurrent states are generally easier to estimate. I'd just suggest that you try out the models you are interested in on your data. Choosing a suitable optimization technique can often help, but sometimes models are simply over-parameterised. I don't mind discussing Markov models on r-help, but if you have a question about msm it's probably safer to mail me directly as the author, as it is an obscure contributed package which, as far as I am aware, very few people use! Chris -- Christopher Jackson [EMAIL PROTECTED], Research Associate, Department of Epidemiology and Public Health, Imperial College School of Medicine, Norfolk Place, London W2 1PG, tel. 020 759 43371 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] S+ArrayAnalyzer and BioConductor Announcement
Greetings to all and apologies for any cross-postings. If you know of anyone else who could benefit from this announcement please forward to them. Best regards and good luck to everyone, Michael O'Connell. BioConductor Project and Insightful Corp. Collaboration Announcement This week, Insightful Corporation announced the availability of S+ArrayAnalyzer version 2.0, an updated module for S-PLUS based on collaboration with the BioConductor Project - a widely-used open source and open development software project for the analysis and comprehension of genomic data. The software will be described in a free 1 hour public web seminar on Tuesday, June 22nd, 2004 at 11:30 AM EST / 8:30 AM PST entitled: Using S+ArrayAnalyzer 2.0 to Improve Gene Expression Analysis and Deploy Best Practices You can register for this event at http://www.insightful.com/news_events/webcasts/pharm04/arrayanalyzer.asp The collaboration between Insightful and BioConductor delivers benefits to commercial and academic researchers analyzing high-throughput assay data and microarray experiments: - S+ArrayAnalyzer S+AA embraces and extends the Bioconductor 1.4 object model so that both offerings share a common framework. This allows researchers in the field to create new software methods and algorithms for two widely-used software platforms using a single underlying object model and to use the same syntax for future collaborative research. - S+ArrayAnalyzer adds many features that can improve productivity for users, such as installers, more data access options, a guided-workflow interface, interactive graphics with hyperlinked annotation and Web deployment of applications. - S+ArrayAnalyzer is a commercially supported product from Insightful, a long-established vendor with fully staffed tech support, training, and consulting. This collaboration between Insightful and the BioConductor Group has brought the expertise of the open-source and research communities and the rigorous development environment of the commercial software world together. Through programs such as sponsorship of a graduate student in the BioConductor project, and feedback from its professional Quality Assurance testing team, Insightful's participation in this collaboration has served to improve the availability and reliability of microarray analysis software for both the academic research and commercial user. In addition, through its relationships with customers in commercial drug discovery and awareness of their unique needs, Insightful has helped drive continued advancements and innovation in both the open source and commercial offerings: for example, a new differential expression library (lpe), written by Insightful and the University of Virginia, has been ported to R and included in both S+ArrayAnalyzer and Bioconductor v1.4. The BioConductor-Insightful collaboration helps ensure the distribution and high-level end-user support of key bioinformatics tools to the broadest possible population of researchers, said spokespeople for The BioConductor Project. BioConductor is an academic project focused on creation and distribution of high-quality open source statistical and computational methods and software for bioinformatics, while Insightful has over a decade of experience in user interface design, documentation, and user support for statistical computing. The results of this collaboration should benefit researchers in both commercial and non-profit organizations. Our collaboration with BioConductor is a blueprint for how Insightful can work with the open source community to bring highly innovative and productive data analysis applications to the widest possible user base, said Jeff Coombs, CEO of Insightful. This cooperation improves the analytic solutions available to our common base of S programmers and the non-statisticians who benefit from using applications developed with S-PLUS and R. S+ArrayAnalyzer is available now with pricing for commercial and academic organizations available by calling (800)569-0123 x479, or via email at [EMAIL PROTECTED] ABOUT BIOCONDUCTOR BioConductor is an academic project focused on creation and distribution of high-quality open source statistical and computational methods and software for bioinformatics. It includes contributions to the management and analysis of cDNA and oligonucleotide microarray and SAGE platforms, to the structure and flexible manipulation of genomic annotation data, and to the computational infrastructure required for effective bioinformatics, including GUI component libraries, novel structures and algorithms for networks and graphical systems, and improvements to the R language, especially in the domain of programmatic verification, documentation and distribution of software packages. BioConductor is widely used by investigators on many different platforms and is a basis for training in statistical genomics and bioinformatics in a number of prominent universities on four continents. Spokespeople for the
[R] Barplots and error indicators: Some R-Code
I' ve seen that several people are looking for a function that creates a
barplot with an error indicators (I was one of them myself). Maybe you will
find the following code helpful (There are some examples how to use it at
the end):
# Creates a barplot.
#bar.plot() needs a datavector for the height of bars and a error
#indicator for the interval
#many of the usual R parameters can be set: e.g. ylim, main, col, etc.
#The direction of the error indicator can be specified as bo for both,
lo lower, up #upper
#The width of the indicator hat is set as a percentage of the x-width of the
plot:e.g. *hat=0.05
bar.plot-function(data, err.ind, ind.side=NA, hat=NA, ylim=c(0,
max(data+err.ind, na.rm=TRUE)*1.2), col=NA, xlab=your x-lab, ylab=your
y-lab, main=your main, names.arg=NA, space=0.2){
if (is.na(ind.side)){
ind.side-up} #only upper error indicator (default), else: lo or bo
if (is.na(hat)){
hat-0.01} #fraction of the x axis that defines the size of the error
indicator hat
if (is.na(col)){col-white} #the default color is white
x.cor-barplot(data, ylim=ylim, xlab=xlab, ylab=ylab, main=main,
names.arg=names.arg, col=col, space=space)
smidge-diff(par(usr)[1:2])*hat
up.ind-data+err.ind
lo.ind-data-err.ind
segments(0,0,x.cor,0) # draws X-Axis
if (ind.side==up){
segments(x.cor, data, x.cor, up.ind)
segments(x.cor, up.ind, x.cor+smidge, up.ind)
segments(x.cor, up.ind, x.cor-smidge, up.ind)
}else{
if (ind.side==bo){
segments(x.cor, data, x.cor, up.ind)
segments(x.cor, up.ind, x.cor+smidge, up.ind)
segments(x.cor, up.ind, x.cor-smidge, up.ind)
segments(x.cor, data, x.cor, lo.ind)
segments(x.cor, lo.ind, x.cor+smidge, lo.ind)
segments(x.cor, lo.ind, x.cor-smidge, lo.ind)
}else{
segments(x.cor, data, x.cor, lo.ind)
segments(x.cor, lo.ind, x.cor+smidge, lo.ind)
segments(x.cor, lo.ind, x.cor-smidge, lo.ind)
}
}
}
#Examples
par(mfrow=c(2,2))
data-c(3.2, 3.3, 3.6, 4, 3.1, 3.3, 3.1, 4.5, 3.2, 3.3, 3.1, 3.4)
se-sqrt(data)
bar.plot(data, se) #easy example
data-c(3.2, 3.3, 3.6, 4, 3.1, 3.3, 3.1, 4.5, 3.2, 3.3, 3.1, 3.4)
se-c(sqrt(data))
bar.plot(data, se,ind.side=lo, ylim=c(0, 10), col=lavender, space=0.25,
hat=0)
data-c(15, 15, 19, 22)
se-c(3, 5, 6, 4.5)
nam-c(L.c,O.v,C.i,L.u)
bar.plot(data, se, col=orange, ind.side=bo, hat=0.05, main=,
xlab=species, ylab=CT conc.)
data-c(4,5,1,1.3,6,7.1,5,2.6)
se-c(sqrt(data))
nam-rep(c(C,T),4)
spa-rep(c(1.5, 0.2),4)
col-rep(c(green,red),4)
bar.plot(data, se, col=col, ind.side=up, main=Trees !, ylab=CT conc.,
space=spa, names.arg=nam)
***
Dieter Häring
Eidg. Forschungsanstalt für Agraroekologie und Landbau (FAL)
Reckenholzstrasse 191
8046 Zürich
Tel. 01 / 377 71 62
FAX 01 / 377 72 01
mailto:[EMAIL PROTECTED]
www.reckenholz.ch
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] can't get text to appear over individual panels in multi-panel plot
On Fri, 18 Jun 2004, Jari Oksanen wrote: On 18 Jun 2004, at 8:26, Deepayan Sarkar wrote: On Thursday 17 June 2004 22:57, Patrick Bennett wrote: yes, i can reproduce that same graph when i print to the pdf-device. but the panel titles do not appear when I print to the Quartz-device. Hmm. I won't be able to help you then, let's hope someone else can. I think this is a problem with the quartz device. I have often see that margin texts are plotted even in ordinary plot() if quartz thinks there is no space for them. They do still appear if you copy the screen graphics as a pdf file. In Linux (my principal platform) I typically reduce the white margins, but if I use the same mar pars in MacOS X I won't get axis labels. Quartz is the culprit I suppose. It would be useful to send bug reports for this sort of thing... Actually, in your example I couldn't get the texts when I saved the plot as a pdf (menu entry). However, when I opened an X11 device, the text was reproduced OK. So it looks like a quartz problem. I get the right output on both quartz() and x11(). Windows plotting device in some other OS. -- And beware: I have a suspicion that if you stop your X11 in MacOS X, your mouse will die at logout and you got to boot (or restart the mouse demon if you know who he is). I have never seen this problem. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Initializing SparseM matrix matrix.csc
Hi! Would like to initialize a huge matrix.csc (Pacakge SparseM) with all elements 0 and afterwards set a few alements nonzero. The matrix which I like to allocate is so huge that I can not use A - matrix(a,n1,p) before: A.csr - as.matrix.csc(A) because I can not allocate such a huge matrix A. But I believe that the much more memmory efficient model in case of csc matrix should do it for a sparse matrix. How to do this. Sincerely Eryk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Initializing SparseM matrix matrix.csc
A - as.matrix.csr(0,5,4) A An object of class matrix.csr Slot ra: [1] 0 Slot ja: [1] 1 Slot ia: [1] 1 2 2 2 2 2 Slot dimension: [1] 5 4 A[3,4] - 3 A An object of class matrix.csr Slot ra: [1] 0 3 Slot ja: [1] 1 4 Slot ia: [1] 1 2 2 3 3 3 Slot dimension: [1] 5 4 as.matrix(A) [,1] [,2] [,3] [,4] [1,]0000 [2,]0000 [3,]0003 [4,]0000 [5,]0000 url:www.econ.uiuc.edu/~rogerRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 On Jun 18, 2004, at 9:20 AM, Wolski wrote: Hi! Would like to initialize a huge matrix.csc (Pacakge SparseM) with all elements 0 and afterwards set a few alements nonzero. The matrix which I like to allocate is so huge that I can not use A - matrix(a,n1,p) before: A.csr - as.matrix.csc(A) because I can not allocate such a huge matrix A. But I believe that the much more memmory efficient model in case of csc matrix should do it for a sparse matrix. How to do this. Sincerely Eryk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Barplots and error indicators: Some R-Code
[EMAIL PROTECTED] wrote:
I' ve seen that several people are looking for a function that creates a
barplot with an error indicators (I was one of them myself). Maybe you will
find the following code helpful (There are some examples how to use it at
the end):
# Creates a barplot.
#bar.plot() needs a datavector for the height of bars and a error
#indicator for the interval
#many of the usual R parameters can be set: e.g. ylim, main, col, etc.
#The direction of the error indicator can be specified as bo for both,
lo lower, up #upper
#The width of the indicator hat is set as a percentage of the x-width of the
plot:e.g. *hat=0.05
bar.plot-function(data, err.ind, ind.side=NA, hat=NA, ylim=c(0,
max(data+err.ind, na.rm=TRUE)*1.2), col=NA, xlab=your x-lab, ylab=your
y-lab, main=your main, names.arg=NA, space=0.2){
if (is.na(ind.side)){
ind.side-up}#only upper error indicator (default), else: lo or bo
if (is.na(hat)){
hat-0.01} #fraction of the x axis that defines the size of the error
indicator hat
if (is.na(col)){col-white} #the default color is white
x.cor-barplot(data, ylim=ylim, xlab=xlab, ylab=ylab, main=main,
names.arg=names.arg, col=col, space=space)
smidge-diff(par(usr)[1:2])*hat
up.ind-data+err.ind
lo.ind-data-err.ind
segments(0,0,x.cor,0) # draws X-Axis
if (ind.side==up){
segments(x.cor, data, x.cor, up.ind)
segments(x.cor, up.ind, x.cor+smidge, up.ind)
segments(x.cor, up.ind, x.cor-smidge, up.ind)
}else{
if (ind.side==bo){
segments(x.cor, data, x.cor, up.ind)
segments(x.cor, up.ind, x.cor+smidge, up.ind)
segments(x.cor, up.ind, x.cor-smidge, up.ind)
segments(x.cor, data, x.cor, lo.ind)
segments(x.cor, lo.ind, x.cor+smidge, lo.ind)
segments(x.cor, lo.ind, x.cor-smidge, lo.ind)
}else{
segments(x.cor, data, x.cor, lo.ind)
segments(x.cor, lo.ind, x.cor+smidge, lo.ind)
segments(x.cor, lo.ind, x.cor-smidge, lo.ind)
}
}
}
#Examples
par(mfrow=c(2,2))
data-c(3.2, 3.3, 3.6, 4, 3.1, 3.3, 3.1, 4.5, 3.2, 3.3, 3.1, 3.4)
se-sqrt(data)
bar.plot(data, se) #easy example
data-c(3.2, 3.3, 3.6, 4, 3.1, 3.3, 3.1, 4.5, 3.2, 3.3, 3.1, 3.4)
se-c(sqrt(data))
bar.plot(data, se,ind.side=lo, ylim=c(0, 10), col=lavender, space=0.25,
hat=0)
data-c(15, 15, 19, 22)
se-c(3, 5, 6, 4.5)
nam-c(L.c,O.v,C.i,L.u)
bar.plot(data, se, col=orange, ind.side=bo, hat=0.05, main=,
xlab=species, ylab=CT conc.)
data-c(4,5,1,1.3,6,7.1,5,2.6)
se-c(sqrt(data))
nam-rep(c(C,T),4)
spa-rep(c(1.5, 0.2),4)
col-rep(c(green,red),4)
bar.plot(data, se, col=col, ind.side=up, main=Trees !, ylab=CT conc.,
space=spa, names.arg=nam)
***
Dieter Häring
Eidg. Forschungsanstalt für Agraroekologie und Landbau (FAL)
Reckenholzstrasse 191
8046 Zürich
Tel. 01 / 377 71 62
FAX 01 / 377 72 01
mailto:[EMAIL PROTECTED]
www.reckenholz.ch
Bar charts have many problems as pointed out in Bill Cleveland's book
Elements of Graphing Data. Bar charts with error bars have even more
problems. I prefer dot plots with error bars. The Dotplot function in
the Hmisc package will make such graphs. Hmisc's xYplot will do
likewise for line graphs, including an option for error bands and shaded
error bands.
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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[R] Problems running RSPerl w. SuSe 9.0 / Perl 5.8.1
Hi, installation of RSPerl works fine without errors. Running RSPerl does not work at all. If I start R, and then enter this command: library(RSPerl) this error appears: - library(RSPerl) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library /usr/local/lib/R/library/RSPerl/libs/RSPerl.so: /usr/lib/perl5/vendor_perl/5.8.1/i586-linux-thread-multi/auto/Apache/Languag e/Language.so: undefined symbol: perl_cmd_perl_TAKE1 Error in library(RSPerl) : .First.lib failed -- Does anyone know why this happens? I have perl 5.8.1 from the SuSe 9.0 distribution. I used the R pecompiled rpm package R-base-1.9.0-1.i586.rpm for Suse. First I thought it is a problem of the perl module mentioned above, but after removing Language.so from my perl installation, the problem re-appeared with a different perl module. I also tried to compile R from scratch ( gcc 3.3.1), reinstalled RSPerl, but the problem remains. We have no Idea how to get RSPerl to work but we need it very urgently. Do you have any Ideas how to resolve this? Thank you very much in advance. Kind Regards Michael = More detailed information: I searched through all of my shared librarys and found the missing Symbol 'perl_cmd_perl_TAKE1' in the library /usr/lib/apache/libproxy.so. But somehow Language.so does not find this symbol. Is there something wrong with the library search path? ( LD_LIBRARY_PATH is not defined on my system ) [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Resolution of plots
On Thu, 17 Jun 2004, Thomas Lumley wrote: On Wed, 16 Jun 2004, Prof Brian Ripley wrote: You will have to tell us more. Exporting how: to what format using what device and what exact command on what operating system? The only device I know of that even knows about dpi is bitmap() and that has no such limit unless imposed by your implementation of ghostscript. There is an issue with PNG. libpng provides png_set_pHYs to set resolution (in pixels/metre) but provides a default if it is not set. We don't set it, and so get the default resolution. That seems not to be quite correct. First, the pHYs chunk is optional in PNG files. If present, what is recorded in the file is the units, PNG_RESOLUTION_UNKNOWN (dpi) or PNG_RESOLUTION_METER (pixels/metre) plus two numbers (x and y res). Reading applications are allowed to treat missing pHYs data or numbers 0 as they like, and for example PhotoShop and GIMP display both as 72 dpi. So I think what we are doing is entirely within the spec. I am in the process of adding an arg to allow this to be set (with square pixels, all R supports). -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Barplots and error indicators: Some R-Code
Dear all,
-Original Message-
From: Frank E Harrell Jr [SMTP:[EMAIL PROTECTED]
Sent: Friday, June 18, 2004 4:48 PM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Barplots and error indicators: Some R-Code
Bar charts have many problems as pointed out in Bill Cleveland's book
Elements of Graphing Data. Bar charts with error bars have even more
problems. I prefer dot plots with error bars. The Dotplot function in
it might be a bit off-topic but can anyone suggest some online
material concerning good graph / bad graph examples?
I imagine something like:
a) These are the data and this is the main feature of the data which
should be represented.
b) This is a bad idea how to represent a)
c) This is a good idea how to represent a)
I know there are excellent books by Cleveland and also by Tufte
(The Elements of Graphing Data, The Visual Display of Quantitative
Information, The cognitive style of PowerPoint, ...) but it would be
sometimes just more convenient to refer to some online material.
Maybe even some online material about the problems of barplots with
error bars?
Thank you very much,
Roland
+
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
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Re: [R] Problems running RSPerl w. SuSe 9.0 / Perl 5.8.1
Exactly the same question was asked here by From: Emmanuel Engelhart [EMAIL PROTECTED] Date: Fri, 11 Jun 2004 13:31:17 +0100 so please talk to your colleagues (and note what PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html says about doing your homework). Note also that RSPerl is part of the Omegahat project which has its own mailing lists (which may currently be down) and R-help is not the appropriate place for question about third-party addons to R. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] set working directory
I agree with Uwe: I just tried setwd missing a quote in R
1.9.1 alpha and got syntax error. When I had quotes paired but the
name was not a valid directory, I got the error Louize reported: Error
in setwd(dir) : cannot change working directory. When I gave a valid
directory, the command worked.
To make sure I don't make spelling errors in a directory under
Windows 2000, I copy the address from the Windows Explorer into
something like MS Word first, replace \ with / and then copy the
result into R.
hope this helps. spencer graves
Uwe Ligges wrote:
Bashir Saghir (Aztek Global) wrote:
Try adding a missing singe quote (') at the end of your working
directory.
setwd('d:/folder_name')
Well, that was a mispelling in the mail, but not in the real example,
since not specifying the quote causes a syntax error.
I'm quite sure the folder-name was misspelled in the real example.
Uwe Ligges
S.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Louize Hill
Sent: Friday, June 18, 2004 13:38
To: [EMAIL PROTECTED]
Subject: [R] set working directory
I have just upgraded from rw1081 to rw1090 (using Windows 2000).
Now when I type the command:
setwd('d:/folder_name)
I get the following error message:
Error in setwd(dir) : cannot change working directory
If I use the change dir tab in the file menu i can sucessfully change
working directories, but this is not so convenient as i have my whole
model
stored as a text file that I prefer to copy into R.
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- Legal
Notice: This electronic mail and its attachments are i...{{dropped}}
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Re: [R] Barplots and error indicators: Some R-Code
Rau, Roland wrote: Dear all, -Original Message- From: Frank E Harrell Jr [SMTP:[EMAIL PROTECTED] Sent: Friday, June 18, 2004 4:48 PM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Subject:Re: [R] Barplots and error indicators: Some R-Code Bar charts have many problems as pointed out in Bill Cleveland's book Elements of Graphing Data. Bar charts with error bars have even more problems. I prefer dot plots with error bars. The Dotplot function in it might be a bit off-topic but can anyone suggest some online material concerning good graph / bad graph examples? I imagine something like: a) These are the data and this is the main feature of the data which should be represented. b) This is a bad idea how to represent a) c) This is a good idea how to represent a) I know there are excellent books by Cleveland and also by Tufte (The Elements of Graphing Data, The Visual Display of Quantitative Information, The cognitive style of PowerPoint, ...) but it would be sometimes just more convenient to refer to some online material. Maybe even some online material about the problems of barplots with error bars? Thank you very much, Roland This doesn't cover everything you want but look at http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/StatGraphCourse -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to store estimates results as scalars of a matrix?
Dear R users,
I've written a loop to generate Moran's test (spdep package) on serval
subsamples of a large dataset. See below a short example.
My loop is working fine, however I would like to be able to store the test
results as lines of a matrix, that I would latter be able to export as a
dataset. My problem is that I'm not sure how I could do this using R.
Any help will be much appreciated.
All the very best,
JP
coords2 - as.matrix(jcdist.data[1:87, 6:7])
col.tri.nb-tri2nb(coords2)
for(n in c(1,88,175,262,349)) {
f- n+86
work - jcdist.data[n:f, 10:12]
res -moran.test(spNamedVec(res1, work), nb2listw(col.tri.nb,
style=W))
moran-res$estimate[1]
upper-res$estimate[1] + (qnorm(0.025, lower.tail=FALSE)
*sqrt(res$estimate[3]))
lower-res$estimate[1] - (qnorm(0.025, lower.tail=FALSE)
*sqrt(res$estimate[3]))
print(moran)
print(upper)
print(lower)
}
+
+ }
Moran I statistic
0.659114
Moran I statistic
0.7802115
Moran I statistic
0.5380164
Moran I statistic
0.650799
Moran I statistic
0.771808
Moran I statistic
0.5297899
Moran I statistic
0.6513354
Moran I statistic
0.7723458
Moran I statistic
0.5303249
Moran I statistic
0.6614869
Moran I statistic
0.7825066
Moran I statistic
0.5404672
Moran I statistic
0.6429097
Moran I statistic
0.7638195
Moran I statistic
0.5219998
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[R] cross table
Hi, I have a dataframe with 3 columns: month (1 to 12), length and length class. I'm trying to make a cross table with the counts of lengths per length class and month. I don´t have all classes per month. | 1 2 3 ... - 120 | 0 1 0 150 | 5 6 0 170 | 3 0 7 ... I have already tryed many commands, without success - unfortunately. May someone help me? Thanks in advance! Antonio Olinto - WebMail Bignet - O seu provedor do litoral www.bignet.com.br __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Another NEWBIE
Hi, I'm a very fresh newbie to R. My first main question is, what the limitations of R are, what methods can R NOT do, esp. compared to (a) SPSS and (b) SAS? The second question is, how do you handle the data entry, data management and data manipulation in R, to me it seems to be really complicated and confusing?! Are there a kind of helping tools? The third question: are there differences in linux and windows versions of R? At the monemt I'm running R on a WinXP System. Is this ok or would a Linux solutuon be the better way (for using R)? I hope my questions are not to lame ... Cheers, Frank -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Html help does not work in Mac OSX 10.3.4
I recently upgraded from R 1.8 to 1.9. I removed 1.8 following the instructions. Html help has not worked since. When htmlhelp=TRUE the help.start() command results in the patience message and nothing else happens. I am using mac osx 10.3.4. Help worked fine when I was using R 1.8. I need help help ;-] Thanks! -- Emilio A. Laca One Shields Avenue, 2306 PES Building Agronomy and Range Science[EMAIL PROTECTED] University of California fax: (530) 752-4361 Davis, California 95616(530) 754-4083 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Double centering matrix construction
Dear All do you know how to transform a matrix to a so-called double centering matrix such that sum(col) and sum(row) of the transformed matrix are all 0 vector. thanks regards yong wang __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re: problem in long select from RODBC
On Wednesday 16 of June 2004 14:42, Wolski wrote:
sqlQuery(channel, select dir, c \
from firsthit3 \
where dir LIKE \%SCHULEN%\)
Another option is paste(). This works for me (selectedCities is a constant
set outside of this function):
getData - function(var,condition,whatTotal=sum(vctcnt)) {
temp - sqlQuery(pg,paste(
select year, month, ori, , whatTotal, as total,
from victims where ori in ,selectedCities,
condition,
group by year,month,ori,
order by year,ori))
...
}
and it is run like:
data.youth- getData(murdyouth, and offage = 24 ,
whatTotal=sum(vctcnt*wtus))
Have a nice day,
Matej
--
Matej Cepl, http://www.ceplovi.cz/matej
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138 Highland Ave. #10, Somerville, Ma 02143, (617) 623-1488
The state is the great fictitious entity by which everyone seeks
to live at the expense of everyone else.
-- Frederick Bastiat
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Re: [R] printing R generated postcript files
On Wednesday 16 of June 2004 21:23, Dirk Eddelbuettel wrote:
That may be related. I only recently set R_PAPERSIZE to be driven from
Debian's global paperconf setting which is supposed result in
/etc/R/Renviron having
## edd Apr 2004: use Debian's paperconf settings, with thanks to Matej
Cepl
R_PAPERSIZE=${R_PAPERSIZE-$(cat /etc/papersize)}
yet I just noticed that my own installation doesn't have that. And yes,
looks like a build-time patch failed. bNeed to check that ...
This probably means that you should install libpaper-utils (especially
papersize(5) may be helpful).
Matej
--
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A modest little person, with much to be modest about.
-- Winston Churchill
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RE: [R] Double centering matrix construction
?sweep Date: Fri, 18 Jun 2004 16:32:58 -0500 (CDT) From: Yong Wang [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: [R] Double centering matrix construction Dear All do you know how to transform a matrix to a so-called double centering matrix such that sum(col) and sum(row) of the transformed matrix are all 0 vector. thanks regards yong wang __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] cross table
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
What have you tried? In particular, have you tried table? Dates and times may present difficulties, but help.search('table') in R 1.9.1 alpha under Windows 2000 just produced a number of options.
hope this helps. spencer graves
Antonio Olin wrote:
Hi,
I have a dataframe with 3 columns: month (1 to 12), length and length class.
I'm trying to make a cross table with the counts of lengths per length class
and month. I don´t have all classes per month.
| 1 2 3 ...
-
120 | 0 1 0
150 | 5 6 0
170 | 3 0 7
...
I have already tryed many commands, without success - unfortunately.
May someone help me? Thanks in advance!
Antonio Olin
-
WebMail Bignet - O seu provedor do litoral
www.bignet.com.br
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Re: [R] Another NEWBIE
SPSS and SAS are data analysis packages with some scripting capabilities. The S language is an object oriented programming language for statistics. If you want to analyze data using traditional techniques, use SPSS or SAS or Statistica or Excel or you-name-it. If you need to invent new statistical techniques tailored to some particular application, then you need S, and its most popular current dialect seems to me to be R. There are doubtless things that SPSS, SAS, etc., can do that cannot be accomplished in R with 2 or 10 fairly obvious commands. However, I believe that if R had been available 35 years ago, SAS, SPSS, etc., would have been written in R (or in some other dialect of S not subject to the GNU license, which attorneys consider controversial and dangerous). Beyond these generalities, I believe you can find answers to many of your questions with the posting guide! http://www.R-project.org/posting-guide.html;. hope this helps. spencer graves F.Kalder wrote: Hi, I'm a very fresh newbie to R. My first main question is, what the limitations of R are, what methods can R NOT do, esp. compared to (a) SPSS and (b) SAS? The second question is, how do you handle the data entry, data management and data manipulation in R, to me it seems to be really complicated and confusing?! Are there a kind of helping tools? The third question: are there differences in linux and windows versions of R? At the monemt I'm running R on a WinXP System. Is this ok or would a Linux solutuon be the better way (for using R)? I hope my questions are not to lame ... Cheers, Frank -- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] printing R generated postcript files
On Fri, Jun 18, 2004 at 05:26:26PM +0200, Matej Cepl wrote:
On Wednesday 16 of June 2004 21:23, Dirk Eddelbuettel wrote:
That may be related. I only recently set R_PAPERSIZE to be driven from
Debian's global paperconf setting which is supposed result in
/etc/R/Renviron having
## edd Apr 2004: use Debian's paperconf settings, with thanks to Matej
Cepl
R_PAPERSIZE=${R_PAPERSIZE-$(cat /etc/papersize)}
yet I just noticed that my own installation doesn't have that. And yes,
looks like a build-time patch failed. bNeed to check that ...
This probably means that you should install libpaper-utils (especially
papersize(5) may be helpful).
Hm, when I tested this the shell expansion failed even though I have
libpaper-utils installed:
[EMAIL PROTECTED]:~ dpkg -l | grep libpaper
ii libpaper-dev 1.1.14 Library for handling paper characteristics (
ii libpaper-utils 1.1.14 Library for handling paper characteristics (
ii libpaper1 1.1.14 Library for handling paper characteristics
ii libpaperg 1.1.14 Library for handling paper characteristics (
ii libpaperg-dev 1.1.14 Library for handling paper characteristics (
[EMAIL PROTECTED]:~ cat /etc/papersize
letter
[EMAIL PROTECTED]:~ grep ^R_PAPERSIZE /etc/R/Re
Renviron Renviron.dpkg-old Renviron~
[EMAIL PROTECTED]:~ echo 'postscript(/tmp/foo.ps); plot(rnorm(100)); dev.off()'
| R --vanilla --silent
postscript(/tmp/foo.ps); plot(rnorm(100)); dev.off()
Error in postscript(/tmp/foo.ps) : invalid page type $(cat
/etc/papersize)' (postscript)
Execution halted
[EMAIL PROTECTED]:~
I tried all quote tick variants around $(cat /etc/papersize) as well
without any luck.
In case you have that working, could you wave the cluebat at me? I somehow
suspect that this cannot work but I may miss some magic shell pixie dust ...
Dirk
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[R] setGeneric / standardGeneric when args are not literals
Hi,
This works
setGeneric(clear, function(obj) standardGeneric(clear))
[1] clear
but this doesn't. Why?
funName - clear
setGeneric(funName, function(obj) standardGeneric(funName))
Error in .recursiveCallTest(body, fname) :
(converted from warning) The body of the generic function for clear
calls standardGeneric to dispatch on a different name (funName)!
This is R-1.8.1 on RH-7.3
I came across it while trying to write a helper function that would
safely create generics when a function with such a name already
exists. Here is what I adapted from S4Objects but it doesn't work
becuase of the above-mentioned problem. Any suggestion how to make it
work, please?
setMakeGenericMethod - function(methodName, className, fun) {
# sets a method and creates the generics if neccessary
if (!isGeneric(methodName)) {
if (is.function(methodName)) {
fun.default - get(methodName)
}
else {
fun.default - function(object) standardGeneric(methodName)
}
}
setGeneric(methodName, fun.default)
setMethod(methodName, className, fun)
}
Thanks,
Vadim
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[R] setGeneric / standardGeneric when args are not literals - corrected
This is a correction to my previous message, I forgot to swap two lines
in the body of setMakeGenericMethod. Sorry about that. The correct (full
message) reads like this:
Hi,
This works
setGeneric(clear, function(obj) standardGeneric(clear))
[1] clear
but this doesn't. Why?
funName - clear
setGeneric(funName, function(obj) standardGeneric(funName))
Error in .recursiveCallTest(body, fname) :
(converted from warning) The body of the generic function for clear
calls standardGeneric to dispatch on a different name (funName)!
This is R-1.8.1 on RH-7.3
I came across it while trying to write a helper function that would
safely create generics when a function with such a name already
exists. Here is what I adapted from S4Objects but it doesn't work
because of the above-mentioned problem. Any suggestion how to make it
work, please?
setMakeGenericMethod - function(methodName, className, fun) {
# sets a method and creates the generics if necessary
if (!isGeneric(methodName)) {
if (is.function(methodName)) {
fun.default - get(methodName)
}
else {
assign(methodName, methodName)
browser()
fun.default - function(object) standardGeneric(methodName)
}
setGeneric(methodName, fun.default)
}
setMethod(methodName, className, fun)
}
Thanks,
Vadim
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Re: [R] Another NEWBIE
On Fri, 18 Jun 2004, F.Kalder wrote: I'm a very fresh newbie to R. First piece of advice: read the posting guide before posting, and in particular use a meaningful subject line. My first main question is, what the limitations of R are, what methods can R NOT do, esp. compared to (a) SPSS and (b) SAS? R is a full-featured programming language, with no such limitations. The second question is, how do you handle the data entry, data management and data manipulation in R, to me it seems to be really complicated and confusing?! Are there a kind of helping tools? There is documentation. For example, chapter 2 of MASS (see the FAQ or the posting guide) is devoted to this, and R ships with a `Data Import/Manual'. We don't know your background or skill level, but the FAQ points you to lots of documentation. The third question: are there differences in linux and windows versions of R? At the monemt I'm running R on a WinXP System. Is this ok or would a Linux solutuon be the better way (for using R)? That's in the README of the Windows version. BTW, perhaps you should ask in a suitable forum what the limitations of Windows are relative to Linux since like any application R is limited by the OS it runs on. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
