Re: [R] R on a flash drive
John Kane jrkrideau at yahoo.ca writes: I usually have R, Tinn-R and portable versions of OpenOoffice.org, and Firefox installed on the USB. Tinn-R works well as a portable editor on a USB flash drive. Likewise, by following the instructions here: http://at-aka.blogspot.com/2006/06/portable- emacs-22050-on-usb.html you can run emacs for windows from your USB flash drive. Michael __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Responding to a posting in the digest
Moshe Olshansky m_olshansky at yahoo.com writes: Is there a convenient way to respond to a particular posting which is a part of the digest? I mean something that will automatically quote the original message, subject, etc. Thank you! Moshe Olshansky m_olshansky at yahoo.com __ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. A simple solution is to respond via the Gmane (web) list. There is a link to the Gmane R lists from the 'search' page of any CRAN mirror. Hope this helps, Michael Bibo [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mandriva Spring 2007 and R
Roland Rau roland.rproject at gmail.com writes: Hi Jonathan, Jonathan Morse wrote: I am new to Linux (not to R) and recently installed Mandriva Spring 2007 on my partitioned hard drive. My next objective is to install R in the Linux environment, unfortunately Mandriva is not one of the Linux distributions available for download... Could someone please let me know which distribution I should use? One possibility is, of course, that you compile it yourself for your computer. Compiling R was my first shot at compiling programs when I was new to Linux, and it was not very difficult. It is described nicely in the R Installation Administration Manual. http://cran.r-project.org/doc/manuals/R-admin.html Basically, you only need to take care of the following steps to get you started: - did you download and unpack the source distribution (see section 1.1 of the manual)? - do you have the required tools installed (see section A.1 of the manual)? (C compiler, Fortran compiler, libreadline, libjpeg, libpng, tex/latex, Perl5, xorg-x11-dev) - compilation (see section 2.1 in the manual) I hope this helps? Best, Roland __ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Just to add to Roland's comments - remember to install the -dev packages for all of the tools he mentions. I learned this from the R installation manual, and it has been valuable in installing other software from source. The output from ./configure will usually tell you if something is missing. Personally, I no longer use Mandriva, but comments I made re v10.1 may or may not be relevant: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/54320.html. Hope this helps, Michael __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 2.3.1 and SPSS 14.0
David Kaplan dkaplan at education.wisc.edu writes: Hi, Are there any incompatibilities with R 2.3.1 and SPSS 14.0 with regard to the read.spss command? Thanks in advance. David David, Version 14 of SPSS doesn't seem to have made any changes to the .sav file format. Therefore read.spss should work as it has. I haven't had any problems importing data files created in SPSS 14.0. Problems can arise when importing data files created by the SPSS Data Entry product (currently at version 4.0), and this is covered in the R Data Import/Export manual. Michael __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] read.spss 'error reading system-file header'
Finn Sandø fs at fs-analyse.dk writes: When I try to import an spss sav file with read.spss() I am getting the following error 'Error in read.spss(X:\\.sav) : error reading system-file header' and the import process is aborted. I have tried in v. 2.3.0 and 2.3.1 The sav-file loads without problems in spss v14 I have tried saving in older spss v7 but are getting the same result. The read.spss() has other errors (the 'Unrecognized record type 7, subtype 7 encountered in system file') but it does not seem to have any impact. These are also the error messages you get when the .sav file in question was created with the SPSS Data Entry product. If that is the case, then it is covered by section 3.1 of the R Data Import/Export document. Michael __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Easy, Robust and Stable GUI???
pat_primate (sent by Nabble.com lists at nabble.com writes: I know that this isn't really a R help question, but I am a psychology student at TRU (tru.ca) and my psych department is going to be switching statistical software in the near future. I thought this might be a good oppertunity to advocate for open source if an acceptable option is available. I have looked around a bit and R seems to be the most stable and mature (not to mention powerful) open source statistical program going. The only downfall is that the school has been using spss for years and would demand a similarly user friendly GUI based statistical program to replace it. I have looked at a few of the R guis and most of them look like they are just command line interfaces in pretty desktop windows and not really a gui like spss. If anyone knows of any stable, userfriendly and robust guis for R that would be similar to using spss please let me know, as I would love for my scho ol to start embracing open source software. I too am trying to move my organisation from SPSS to R. While it is well worth considering the various command line vs GUI arguments, I appreciate that an easy to use GUI is important when weaning oneself and others from a system such as SPSS. I would suggest you have a look at R-Commander. It is available simply as an R package from CRAN (Rcmdr). It has a familiar, menu-driven interface for a good range of data manipulation and analysis tasks, but without losing the power of the command line option. It is actively developed, and John Fox is very approachable. Perhaps most importantly, it is extensible, so you can tailor it to suit, and add functions to the menu system. Michael Bibo Queensland Health [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R and filemaker pro DB
I have been looking for a database application to use in conjunction with R (on a Windows network). When I approached my organization's IT department to ask about using MySQL, they made a counter-offer of Filemaker Pro (v8). It is not specifically mentioned in 'R Data Import/Export', nor do searches of the archives turn up much information. Does anyone have any experience using Filemaker Pro with R? Should package RODBC work with Filemaker, as it is odbc-compliant? (I will be doing some trials anyway). Any other relevant advice welcome. Michael Bibo Queensland Health [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re: Installing R on Mandrake 10.1
Christian christianmacaro at gmail.com writes: Dear all. First of all, thanks to Jon, Martin, Bogdan and Roland since they tried to help me. In order I tried to 1) install the libf2c0-3.4.1-4mdk.i586.rpm. 2) install R 2.0.1 from the source. 1) Didn't work, since the info is still not satisfied 2) I wasn't able to configure it. I mean: a) as root I uzipped the archive in the home/krisse directory b) ./configure in the home/krisse/R-2.0.1 directory the resulting message was that neither a fortran compiler nor f2c was found. Then I looked for a fortran compiler What I have understood is that a fortran compiler is already included in the gcc3.4.1-4mdk (already installed). Is that correct? In the /usr/bin directory there are g++ an similar things but none of the g77, f77, xlf, frt, pgf77, fl32, af77, fort77, f90, xlf90, pgf90, epcf90, f95, fort, xlf95, lf95, g95, and fc. snip Christian, I have been using R with Mandrake since about mdk 9.2. Like you, I really don't consider myself any sort of Linux expert - I rely more on the gui-based tools. At first I used the R rpm's from CRAN (thanks to those who provided them). In more recent times I have installed from source in order to remain up to date with both Mandrake and R, and to benefit from a slight performance improvement. I am currently running R 2.0.1 patched under Mandrake 10.1 Official. All of the dependencies were available on my Mandrake 10.1 Official DVD, and installed using urpmi, via the 'software management' gui in the Mandrake Control Centre. This gui enables you to browse all the software packages available on the installation CDs/DVD - by category or through searching for keywords in the package descriptions. You can also browse available packages on other online repositories if you choose to set those up - see http://easyurpmi.zarb.org/. Urpmi, through the gui, does a reasonable job of finding dependencies of dependencies, although I admit it is certainly not perfect. The suggestion has already been made to install Latex related packages. One way to do this is to choose Lyx for installation, and all the dependencies should be taken care of. At least it works for me. When I browse my installed software for 'fortran' in package descriptions, I get the following list of installed packages: gcc-3.4.1-4mdk gcc-g77-3.4.1-4mdk gdb-6.2-2mdk libf2c0-3.4.1-4mdk liblapack3-3.0-11mdk These should all be available from your installation media (assuming a DVD or a complete set of CDs (4, I think)). When installing R from source, however, I did have a couple of issues, which were solved through searching the archives. But to possibly save you the time: make sure both 'libreadline' and 'libreadline-devel' are installed (again, simply search for 'libreadline in the package descriptions) - this is so that your keyboard arrow keys work to access previous commands. make sure both 'xorg-x11-100dpi-' and 'xorg-x11-75dpi-fonts' are installed (search:fonts) - this enables all fonts to display properly, eg when using Rcmdr (which, by the way is a great learning tool). My belated thanks to those who originally posted these hints. Hope this helps, Michael Bibo Queensland Health [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Rcmdr X11 protocol error message
John Fox wrote: Dear Michael and Peter, I've made the following changes to the current development version of the Rcmdr package (on my web site, at http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr/index.html, but not posted to CRAN): (1) The default for the Rcmdr grab.focus option is now set to FALSE for non-Windows systems. (2) There's a new report.X11.warnings option, which is set to FALSE by default; this suppresses these warnings so that they don't appear in Rcmdr warning dialogs. This just papers over the problem without really solving it. I'm not happy with these solutions, but perhaps they'll help until we discover the source of the problems. (I tested on my Quantian system.) Thanks for your help. John Thanks, John. The commitment of contributors to R and to this list never ceases to amaze me! The temporary solutions will help. As I have indicated, I am not a programmer, so I can't offer much in terms of the underlying Tcl/Tk issues, but I am happy to test anything out for you on my system (if you can explain it simply enough for me). I have another reliable observation with the new version of Rcmdr, which I offer only because it might provide a clue as to what's going on: If you generate a scatterplot for two numerical variables grouped by a factor, the plot is drawn, but the dialogue box remains on screen, and is unresponsive. When the graphics device is closed, you get an error message: 'Error: No graphics device active'. If you then try to generate the same scatterplot ungrouped (which previously worked fine) you receive a message; 'Warning: display list redraw incomplete'. This only occurs the first time you try to draw the ungrouped scatterplot. Hope it helps. Peter, Any hints as to how to generate that trace of the execution you mentioned? Michael [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Rcmdr X11 protocol error message
John Fox wrote: Dear Peter and Michael, I installed Quantian on a spare machine that I have and observed the same warning messages that Michael has been reporting. These (and the problem with help files but not with viewing data sets that Peter reported) occurred with version 0.9-11 of Rcmdr but not with an earlier version. Since the code for the Rcmdr package was substantially reworked this summer, that seems to me a good candidate for the source of these problems, though I don't see why the changes should be problematic. I'm afraid that I'm insufficiently familiar with the inner workings of X11 and Tcl/Tk to be much help in figuring out what's wrong. Everything seems to work fine under Windows, as far as I can tell. It occurs to me that if the warning messages are benign, one approach would be to suppress them. I already intercept warnings and present them in dialog boxes; I could grep for X11 protocol error and simply ignore these. That doesn't seem to me a good solution, however. It would be better to understand what's happening. I'm copying this message to Dirk since he's mentioned that he plans to put the newer Rcmdr in Quantian. Dirk: Have you tested with Rcmdr 0.9-11? Thank you. John John, Peter and Dirk, I'm glad I'm not the only one with a handle on it now. I've already exceeded my level of knowledge and skill in both Linux and R. But I'm happy to help track it down, if I can be of assistance. As I have said to John, the major value of Rcmdr to me is to help 'sell' R to others in my organisation currently using SPSS, and for this purpose, the Windows version at work is working fine. It is more of an annoyance at home, as it doesn't seem to stop anything working. Peter asked: BTW, sometimes Tk errors allow you to see a trace of the execution. Would this happen to be one of those situations? The short answer is I don't know (see my first line :-)). There is no button on the dialogue box saying 'more details...' or anything that obvious. Is there a log file somewhere on the system or some other way to generate such a trace? I have been experimenting, and the following seem reliable (at least on my system): Error messages don't seem to happen for the first graph generated. The second graph drawn also generates an error dialogue box with the error message repeated about 11 times. The third and subsequent times exactly the same graph is generated leads to an error message repeated about 21 times. (I don't know if the number of repetitions is meaningful). Note that the graphs are generated and visible when the error messages appear. Running any analysis that only writes output to the output window (such as fitting a regression model) generates the error messages before the output is written to the output window. The output appears when the error dialogue box is OK'd. I guess it's more likely to be responding to exiting the dialogue box than writing the output. But this only happens when such error messages have been generated previously in that session by creating a (second) graph. If the diagnostic panel plots for a regression model are called, the error messages appear, but this time the plots themselves are not visible in the graphics device (it is blank). When the error messages are OK'd, the plots appear in the device. When exiting Rcmdr, then, and OK'ing the Exit? dialogue box, the final error messages appear, but again only if they have already been generated by a graph call. I don't know if this will be helpful, but I thought reliable observations might give some clues. Regards, Michael [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Rcmdr X11 protocol error message
John Fox jfox at mcmaster.ca writes: Dear Michael, A question: Do you observe these problems with tcltk in general or just with the Rcmdr package? Is it possible for you to test a Tcl/Tk program outside of R? And Peter asked which version of Tcl/Tk. Apparently my system has version 8.4 installed, specifically: Tcl-8.4.5-3-mdk (tclsh8.4) and Tk-8.4.5-3-mdk (libtk8.4.so). As I understand it, these are installed from RPMs on the installation DVD, and I note that they are mandrake specific. John - I wasn't sure if I had any other Tcl/Tk applications installed (it's not always obvious when installing from RPM's). I have certainly not encountered these error messages with any other application. I quickly downloaded WISH Supernotepad 1.2.3. This application requires Tcl/Tk 8.4 or greater. There are no graphics window in this application, but plenty of dialogue boxes. It gave no errors. Is this an appropriate test? If this is a mandrake-configuration-specific problem, it may not be worth spending too much time investigating, as R Commandr still works. I can always try re-installing Tcl/Tk from source when/if I have time. Regards, Michael __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Rcmdr X11 protocol error message
John Fox jfox at mcmaster.ca writes: Dear Peter and Michael, Peter: Thank you for fielding this question. Michael initially contacted me directly, and I suggested that he write to the list since I didn't know the possible source of the problem, had never seen it (either under Windows or Linux), and never had a report of it before. Michael: Does this problem occur only with certain Rcmdr dialogs or generally? I'd also be curious to learn whether anyone else has experienced this problem, and whether anyone has run the Rcmdr package under Mandrake Linux without a problem. Regards, John Might the following offer a clue? Extract from FAQ for SJava (http://www.omegahat.org/RSJava/FAQ.html) Event Loops # When I run the X11() graphics device and a Java GUI, sometimes I get errors like the following Xlib: unexpected async reply (sequence 0x1356)! 1: X11 protocol error: BadDrawable (invalid Pixmap or Window parameter) 2: X11 protocol error: BadDrawable (invalid Pixmap or Window parameter) What's happening? Both Java and R are reading events from the X11 event loop ``at the same time''. As a result, R is reading events meant for Java and vice-versa and bad things happen! There are two solutions: * use the Java graphics device which uses the Java graphics facilities to do the rendering; * don't run the GUI and the X11 device at the same time. The second solution is clearly not ideal. What we can do is to compile the X11 device code to be thread-safe. However, the same effect will be seen if we load another X11 event handler (e.g. the Tcl/Tk library). Michael [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Rcmdr X11 protocol error message
I am using R 1.9.1 with R Commander GUI under Windows at work, and under Linux
Mandrake 10 OR at home. I am having no problems running R Commander under windows.
Under Linux, though, the opening and sometimes closing of windows from R Commander
produces identical and repetitive error messages (in dialogue boxes and mirrored in
the console):
Warning: X11 protocol error: BadWindow (invalid Window parameter) X 10-20.
These error messages occur most frequently when graphics windows are opening, but can
also occur when dialogue boxes pop up, and sometimes even when results are written to
the output window. However, when the error message is OK'd, the plot, or whatever,
is displayed as it should be. It is not entirely consistent, and will sometimes stop
happening for parts of a session. Exactly the same commands run directly from the R
console do not produce the same problem. I searched the mailing list archives, and
found the following exact description of what I have been experiencing, from November
2003:
Message-id: [EMAIL PROTECTED]
Hi all,
I've got this using Rcmdr package only.
R-cmdr scatterplot.matrix(~PC1+PC2+PC3+PC4 | Species,
reg.line=FALSE, smooth=FALSE, span=0.5, diagonal= 'density',
by.groups=TRUE, data=iris)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
Warning: X11 protocol error: BadWindow (invalid Window parameter)
What's this? The plot is shown.
This is exactly the error message I get, with similar 10-20 line repetition. And the
plots are generated anyway. Unfortunately, I could not find any reply to this email.
My system is running R 1.9.1 on Linux Mandrake 10 OR (installed from source, not RPM),
with XFree86 4.3, P4 2.4GH, 1GB Ram. The problem occurs in several different window
managers/desktop environments. I'm wondering if it is something to do with the
interaction of tcl/tk with the particular X11 config, but I've reached the limit of my
skills in diagnosing. If anyone can suggest anything, I would appreciate it.
Regards,
Michael Bibo
Research Officer,
Community Health Services,
West Moreton Health Service District,
Queensland Health.
[EMAIL PROTECTED]
***
This email, including any attachments sent with it, is confi...{{dropped}}
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re:Importing SPSS Data Entry data files
On 16 Apr, Unung Istopo Hartanto asked about using R library 'foreign' to import SPSS Data Entry data files. SPSS Data Entry is an application that allows for the creation of formatted data entry forms (as does EpiInfo, Epidata and CSPro (all free downloads)). As such it creates the usual SPSS data files, but adds forms information, which the 'foreign' package does not know how to handle. The solution is relatively simple: SPSS Data Entry Builder itself allows for the exporting of the data file without the forms information (File - Export - Data). This gives you a 'standard' SPSS data file, which you can import into R using the 'foreign' library, or through R Commander. Michael Bibo Research Officer Alcohol, Tobacco and Other Drugs Service Resource Unit West Moreton Community Health Services West Moreton Health Service District Queensland Health [EMAIL PROTECTED] Ph. +61 7 3817 2474 P.O. Box 878 Ipswich, 4305 Australia *** This email, including any attachments sent with it, is confidential and for the sole use of the intended recipient(s). This confidentiality is not waived or lost, if you receive it and you are not the intended recipient(s), or if it is transmitted/received in error. Any unauthorised use, alteration, disclosure, distribution or review of this email is prohibited. It may be subject to a statutory duty of confidentiality if it relates to health service matters. If you are not the intended recipient(s), or if you have received this email in error, you are asked to immediately notify the sender by telephone or by return email. You should also delete this email and destroy any hard copies produced. __ [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] Barplot and R 1.9.0
I would like to preface this by saying that I have not been using R for long, and consider myself a beginner. But the more I use and learn R, the more impressed I am with both the 'product' itself, and the efforts of those developing it. It has been noted (eg Duncan Murdoch, 15 April), that the barplot function in R 1.9.0, when used on a tabulated single factor, produces a plot only one bar wide, and seems to superimpose the other bars. It may be useful for users to note that the barplot2 function from the 'gregmisc' package still works as barplot did in R 1.8.1. Consider: library(gregmisc) x-rep(1:3,20) barplot(table(x)) barplot2(table(x)) for an example. Michael Bibo Queensland Health [EMAIL PROTECTED] *** This email, including any attachments sent with it, is confidential and for the sole use of the intended recipient(s). This confidentiality is not waived or lost, if you receive it and you are not the intended recipient(s), or if it is transmitted/received in error. Any unauthorised use, alteration, disclosure, distribution or review of this email is prohibited. It may be subject to a statutory duty of confidentiality if it relates to health service matters. If you are not the intended recipient(s), or if you have received this email in error, you are asked to immediately notify the sender by telephone or by return email. You should also delete this email and destroy any hard copies produced. __ [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
