Re: [R] Problems with graphics
Thank you for your response, which is a partial solution to my problem. Actually, I would like to do the following plot. I have a data frame that includes the following variables: time, y=a response variable experimentally determined, ystd=its standard deviation, m=the modeled/simulated values for y, and F a classification/grouping variable. I would like to have a treillis plot, each panel corresponding to a level of F and includes y plotted against time with dots as symbol and with bars for standard deviation using ystd and m superimposed , plotted as a line. Thanks for your help, Chris Petr Pikal wrote: Hi Well, you did not specified what you have tried to do and how did you fail but On 2 Oct 2006 at 16:41, Christophe Nguyen wrote: Date sent:Mon, 02 Oct 2006 16:41:29 +0200 From: Christophe Nguyen [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject: [R] Problems with graphics Dear all, I am a SAS user, who's trying R. I am a little bit lost for graphics. What is the simplest way for plotting y as a function of x with one symbol (line or dot) for each level of a class variable z (for SAS If z is factor plot(x,y pch=as.numeric(z), ...) otherwise you need to change it to one. BTW, you can use the similar approach with lines and points - col, lwd, cex,... and othe parameters. langage= plot x*y=z). Can I add vertical bars for standard deviation there are various options, one is to use arrows with angle=90. arrows(x,y,x, y+ystd, angle=90) stored in a separate variable (say ystd). Finally, is it possible to do all this with xyplot function arranging plots according to A and B factor: xyplot(y~x|A*B) with as many plots and symbol as there is that is completely different story and you probably need to elaborate your own panel.function. HTH Petr levels in the z variable for each panel? Thanks for the help. Chris -- ___ Christophe NGUYEN UMR 1220 INRA-ENITAB Transfert sol-plante et cycle des éléments minéraux dans les écosystčmes cultivés Centre INRA de Bordeaux-Aquitaine 71, avenue Edouard Bourlaux, BP 81 33883 Villenave d'Ornon, FRANCE Tel : 00 33 (0)5 57 12 25 07 Fax : 00 33 (0)5 57 12 25 15 email : [EMAIL PROTECTED] page infoservice: http://www.bordeaux.inra.fr/tcem __m°O°m __ 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. Petr Pikal [EMAIL PROTECTED] -- ___ Christophe NGUYEN UMR 1220 INRA-ENITAB Transfert sol-plante et cycle des éléments minéraux dans les écosystèmes cultivés Centre INRA de Bordeaux-Aquitaine 71, avenue Edouard Bourlaux, BP 81 33883 Villenave d'Ornon, FRANCE Tel : 00 33 (0)5 57 12 25 07 Fax : 00 33 (0)5 57 12 25 15 email : [EMAIL PROTECTED] page infoservice: http://www.bordeaux.inra.fr/tcem __m°O°m __ 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] Problems with graphics
On 10/3/06, Christophe Nguyen [EMAIL PROTECTED] wrote: Thank you for your response, which is a partial solution to my problem. Actually, I would like to do the following plot. I have a data frame that includes the following variables: time, y=a response variable experimentally determined, ystd=its standard deviation, m=the modeled/simulated values for y, and F a classification/grouping variable. I would like to have a treillis plot, each panel corresponding to a level of F and includes y plotted against time with dots as symbol and with bars for standard deviation using ystd and m superimposed , plotted as a line. See demo(intervals) (code viewable using file.show(system.file(demo/intervals.R, package = lattice)) ) for some ideas. The Hmisc package also has some extensions supporting confidence intervals. If you want more specific help, give a reproducible example. Deepayan __ 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.
[R] Some questions about plotting with R
Greetings list, I'm currently in the process of migrating some Matlab code to R. It's going well, but I'm running into trouble with plotting. There are a few questions I have. 1) Is there any way to do a 3D line plot in R? This would be what the Matlab function plot3 does. 2) I would like to create 3 separate plots. With Matlab, this is done by doing ... figure; plot... figure; plot... figure; plot... In R, I've found the function frame(), which I thought would do something similar. However, calling frame() seems to have no effect, as only 1 frame is created, and all three graphs are drawn to it, resulting in only the final graph being displayed. Help! 3) Is there a good site/book that lists the similarities/differences in plotting with R? I've found http://www.mathepi.com/methods/ matlabtor.html which is good for general Matlab to R concepts, but it's missing information on plotting. Cheers, Wee-Jin __ 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] Some questions about plotting with R
On 4 Oct 2006, at 09:03, Robin Hankin wrote: Hi Wee-Jin check out R-and-octave.txt, on the contributed docs section of CRAN. HTH Robin -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 Thanks for the response Robin, but that document doesn't help me with either my quest for plot3, or multiple figures (i.e. the 'figure' command in Octave/Matlab). cheers, Wee-Jin __ 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] Linear model with hidden variables
Richard, I'm not sure I fully understand your question but the flexmix package does mixtures of linear models which may be what you want. Hth, Ingmar From: Richard A. O'Keefe [EMAIL PROTECTED] Date: Wed, 4 Oct 2006 18:36:55 +1300 (NZDT) To: r-help@stat.math.ethz.ch Subject: [R] Linear model with hidden variables I have some data on a moving vehicle where, amongst other things, it looks as though it would be informative to fit a model with the following structure: Z = B.Y + errorz Y = C.X + errorz The X variables are observed predictor variables; 6 of the variables look promising (on the basis of what they mean). The Z variables are observed response variables; there are 4 of them. There is a priori reason to believe, and scatterplots to suggest, that the Z variables are really essentially two-dimensional, so the Y variables are hidden intermediate variables. There should be 2 of them. There are actually two physical candidates for what they might be, but they happen not to have been measured. There are 800 cases. (More precisely, there are 14 periods, each with about 800 samples, and I am interested in fitting a separate model in each period.) A simple least squares fit for this model would minimise the sum of error squares for the Zs. Oh, I do mean there to be constant terms. I suppose I could go back to first principles and work it all out, but has anyone ever done something like this in R? There seems to be every imaginable variation on lm and some that I find unimaginable, so presumably a means to do this is already around somewhere. __ 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. __ 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] Some questions about plotting with R
On Wed, Oct 04, 2006 at 09:10:23AM +0100, Wee-Jin Goh wrote: On 4 Oct 2006, at 09:03, Robin Hankin wrote: Hi Wee-Jin check out R-and-octave.txt, on the contributed docs section of CRAN. HTH Robin -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 Thanks for the response Robin, but that document doesn't help me with either my quest for plot3, or multiple figures (i.e. the 'figure' command in Octave/Matlab). For 3d figures you can check the persp command, and for multiple figures, just use x11(): x11() plot() x11() plot() ... You might want to check ?Devices to see how R handles graphics devices. Gabor cheers, Wee-Jin __ 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. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ 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] Some questions about plotting with R
On Wed, 2006-10-04 at 09:10 +0100, Wee-Jin Goh wrote: On 4 Oct 2006, at 09:03, Robin Hankin wrote: Hi Wee-Jin check out R-and-octave.txt, on the contributed docs section of CRAN. HTH Robin -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 Thanks for the response Robin, but that document doesn't help me with either my quest for plot3, or multiple figures (i.e. the 'figure' command in Octave/Matlab). cheers, Wee-Jin If you want three separate graphics windows (Devices) then, X11() # not really needed as plot() will produce a new device if none is # open plot(1:10) X11() plot(1:10) X11() plot(1:10) ... Will create a new device. see ?Devices for a list of devices you can open on your system or ?capabilities . It is so long since I used a Windows version of R, that I forget if X11() opens a Windows graphics device there as well. As for 3D stuff, you might take a look at persp() (in base R) and the scatterplot3D package. If you want to see what R's Graphics can do, then the book R Graphics by Paul Murrell [1] will tell you all you need to know, and the excellent, online R graphics gallery [2] has lots of examples. HTH G [1] http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html [2] http://addictedtor.free.fr/graphiques/ -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% *Note new Address and Fax and Telephone numbers from 10th April 2006* %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC [f] +44 (0)20 7679 0565 UCL Department of Geography Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street London, UK[w] http://www.ucl.ac.uk/~ucfagls/cv/ WC1E 6BT [w] http://www.ucl.ac.uk/~ucfagls/ %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] Some questions about plotting with R
Hi Thanks for the response Robin, but that document doesn't help me with either my quest for plot3, or multiple figures (i.e. the 'figure' command in Octave/Matlab). cheers, Wee-Jin If you want three separate graphics windows (Devices) then, X11() # not really needed as plot() will produce a new device if none is # open plot(1:10) X11() plot(1:10) X11() plot(1:10) This isn't in R-and-octave.txt: I'll add it when I get a minute. And come to think of it, R-and-octave.txt doesn't mention plot3, probably because it's not implemented in octave AFAIR. I'll add a section of 3D graphics, When I Get A Minute (tm). You also have p3d() of the onion package for 3D plotting, which you might find closer in spirit to the matlab functionality. best wishes rksh ... Will create a new device. see ?Devices for a list of devices you can open on your system or ?capabilities . It is so long since I used a Windows version of R, that I forget if X11() opens a Windows graphics device there as well. As for 3D stuff, you might take a look at persp() (in base R) and the scatterplot3D package. If you want to see what R's Graphics can do, then the book R Graphics by Paul Murrell [1] will tell you all you need to know, and the excellent, online R graphics gallery [2] has lots of examples. -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ 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] Some questions about plotting with R
This isn't in R-and-octave.txt: I'll add it when I get a minute. And come to think of it, R-and-octave.txt doesn't mention plot3, probably because it's not implemented in octave AFAIR. I'll add a section of 3D graphics, When I Get A Minute (tm). You also have p3d() of the onion package for 3D plotting, which you might find closer in spirit to the matlab functionality. Thanks for all the information given so far! It's been absolutely terrific! Currently, I'm creating new devices using quartz() since I'm on the Mac. On my Linux box, I'd use X11() as suggested. This works beautifully. For 3D plots, p3d from the onion package works pretty much exactly as plot3 does on Octave and Matlab. Thanks a lot for the help. You guys are great. Wee-Jin __ 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] nested design; intercept
Dear R-help, I am sorry if this is more of a stats question than an R-question, but I have found it difficult to get a clear answer by other means. Q. Would it be wrong to specify a nested model and retain a common intercept, e.g. lm(NH4 ~ Site/TideCode + 1) I am aware (?) that my Site-coefficients are now calculated relative to my reference Site (treatment.contrasts), *but* that my TideCode levels now relate to their reference level within Site. Is that correct? Thank you in advance for help. Regards, Mark Difford. Mark Difford Ph.D. candidate, Botany Department, Nelson Mandela Metropolitan University, Port Elizabeth, SA. __ 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] FW: new to R: don't understand errors
Hello Jerad, It was suggested I contact you for possible help with this issue. Well, as you can see for the emails below, that is what I was told at R-help. Any insight to my lsa problems (also listed below) would be of great help. from what I see, the problem probably indeed lies within the textfiles: for performance reasons, it was not possible to include any check routines that exclude a file if it contains no words (or words below a docFrequency) and thus produces an empty column-vector. I am pretty sure that you do not want to use docFrequency with a value like 50 (it would mean that a term in a document is only included if it appears more than 50 times in *that* document). I will send you the alpha-release of the updated lsa package in a separate message which also includes a parameter called minGlobFreq which is filtering out terms that appear less than x times in the whole document collection. I guess that is what you were looking for. Considering the sanitizing: if you set minDocFreq to 1 and set minWordLength to 1, you should not get an error with your document collection as you then are basically taking everything (even a single character appearing only once). It probably is not so problematic as the LSA step will anyway group this low-frequency terms in a lower order factor. Of course you will still get an error if you use documents that are completely empty, so delete all 0 bytes documents beforehands. I am thinking about what to do with this sanitizing part. It is not a good idea to integrate that into the textmatrix method -- it would slow things down tremendously. So what about this idea: does it make sense to provide a sanitizing collection of methods that help to select the files you want to work with (copy them to a different directory or just return a list with the filenames of the ones that are good)? What should we do with other sanitizing options (deleting urls from texts, deleting short words, etc.)? Hope, I could be of help, Best, Fridolin -- Fridolin Wild, Institute for Information Systems and New Media, Vienna University of Economics and Business Administration (WUW), Augasse 2-6, A-1090 Wien, Austria fon +43-1-31336-4488, fax +43-1-31336-746 __ 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] Possible bug?
Yes, the installer missed some file(s) in RHOME/bin. When I choose Message translations, the /bin directory contains the following files. R.dll R.exe RSetReg.exe Rblas.dll Rcmd.exe Rgui.exe Rlapack.dll Rproxy.dll Rterm.exe Stangle.sh Sweave.sh helpPRINT.bat md5check.exe When I install without choosing Message translations, the /bin directory contains the following files. INSTALL R.dll R.exe REMOVE RSetReg.exe Rblas.dll Rcmd.exe Rd2dvi.sh Rd2txt Rdconv Rdiff.sh Rgui.exe Rlapack.dll Rprof Rproxy.dll Rterm.exe SHLIB Sd2Rd Stangle.sh Sweave.sh build check helpPRINT.bat massage-Examples md5check.exe On 10/4/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 10/4/2006 12:02 AM, Ray Brownrigg wrote: On Wednesday 04 October 2006 14:17, Duncan Murdoch wrote: On 10/3/2006 9:00 PM, ronggui wrote: This morning I downloaded R-2.4.0 and install in under Windows. I customized the installation and choose Message translations,but I could not launch Rgui.exe successfully( Rterm.exe worked fine). If I did't choose Message translations, Rgui.exe worked fine. Message translations is Simplified Chinese. Did you test any of the betas or release candidates? I run an English language version of Windows, and I don't even get offered the chance to install in Simplified Chinese, so I certainly didn't test this. Duncan Murdoch 7*runif(1) [1] 2.897160 Well, I have a (self compiled) R-2.4.0 beta (2006-09-24 r39497) which doesn't exhibit the behaviour in the same environment (Windows XP Professional English version but with Simplified Chinese set as the locale) that the released R-2.4.0-win32.exe does. [Perhaps my version didn't set up the equivalent of Message translations so this may be a red herring, but it does output the startup message in Chinese, and error messages are also output in Chinese.] What happens with the release version is an error message: R for Windows GUI front-end has encountered a problem and needs to close. We are sorry for the inconvenience. Then it offers to Please tell Microsoft about the problem, and if you click here the error signature has: AppName: rgui.exe AppVer: 2.40.39566.0ModName: r.dll ModVer: 2.40.39566.0 Offset: 000f22b3 There is a lot more information as well, but I don't know how much is relevant. By Simplified Chinese set as the locale I mean 'Control Panel/Regional and Language Options' with Chinese (PRC) set in 'Regional Options/Standards and Formats' and 'Advanced/Language for non-Unicode Programs'. [I don't rely on the Chinese environment, so this doesn't materially affect me, but I may be able to help with diagnosis.] Could you take a look in RHOME/modules at the file iconv.dll? We upgraded it to version 1.11.0.0 relatively late in the cycle; it's possible that your successful install uses a different version. (The version should be available in the popup if you hover the mouse over it, or in the properties if you right click it.) If that's not it, then I'd guess the problem is that the installer missed some file(s); could you compare the installed file lists from the beta and the release, and send me a list of files that occur only in the beta? It's normal for that list to be fairly long, because when you build yourself a lot of unnecessary files are left behind. Duncan Murdoch -- »ÆÈÙ¹ó Department of Sociology Fudan University [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Possible bug?
On 10/4/2006 7:14 AM, ronggui wrote: Yes, the installer missed some file(s) in RHOME/bin. When I choose Message translations, the /bin directory contains the following files. R.dll R.exe RSetReg.exe Rblas.dll Rcmd.exe Rgui.exe Rlapack.dll Rproxy.dll Rterm.exe Stangle.sh Sweave.sh helpPRINT.bat md5check.exe When I install without choosing Message translations, the /bin directory contains the following files. INSTALL R.dll R.exe REMOVE RSetReg.exe Rblas.dll Rcmd.exe Rd2dvi.sh Rd2txt Rdconv Rdiff.sh Rgui.exe Rlapack.dll Rprof Rproxy.dll Rterm.exe SHLIB Sd2Rd Stangle.sh Sweave.sh build check helpPRINT.bat massage-Examples md5check.exe That makes it look as though the installer aborted partway through. Could you try to re-install, but run with the command line option /LOG? This will create a log file in your TEMP directory (pointed to by your TEMP environment variable, or perhaps in Local Settings/Temp in your Windows home directory), named something like Setup Log 2006-10-04 #001.txt It might give some hint as to what went wrong, e.g. some file was in use and couldn't be replaced, etc. Duncan Murdoch On 10/4/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 10/4/2006 12:02 AM, Ray Brownrigg wrote: On Wednesday 04 October 2006 14:17, Duncan Murdoch wrote: On 10/3/2006 9:00 PM, ronggui wrote: This morning I downloaded R-2.4.0 and install in under Windows. I customized the installation and choose Message translations,but I could not launch Rgui.exe successfully( Rterm.exe worked fine). If I did't choose Message translations, Rgui.exe worked fine. Message translations is Simplified Chinese. Did you test any of the betas or release candidates? I run an English language version of Windows, and I don't even get offered the chance to install in Simplified Chinese, so I certainly didn't test this. Duncan Murdoch 7*runif(1) [1] 2.897160 Well, I have a (self compiled) R-2.4.0 beta (2006-09-24 r39497) which doesn't exhibit the behaviour in the same environment (Windows XP Professional English version but with Simplified Chinese set as the locale) that the released R-2.4.0-win32.exe does. [Perhaps my version didn't set up the equivalent of Message translations so this may be a red herring, but it does output the startup message in Chinese, and error messages are also output in Chinese.] What happens with the release version is an error message: R for Windows GUI front-end has encountered a problem and needs to close. We are sorry for the inconvenience. Then it offers to Please tell Microsoft about the problem, and if you click here the error signature has: AppName: rgui.exe AppVer: 2.40.39566.0ModName: r.dll ModVer: 2.40.39566.0 Offset: 000f22b3 There is a lot more information as well, but I don't know how much is relevant. By Simplified Chinese set as the locale I mean 'Control Panel/Regional and Language Options' with Chinese (PRC) set in 'Regional Options/Standards and Formats' and 'Advanced/Language for non-Unicode Programs'. [I don't rely on the Chinese environment, so this doesn't materially affect me, but I may be able to help with diagnosis.] Could you take a look in RHOME/modules at the file iconv.dll? We upgraded it to version 1.11.0.0 relatively late in the cycle; it's possible that your successful install uses a different version. (The version should be available in the popup if you hover the mouse over it, or in the properties if you right click it.) If that's not it, then I'd guess the problem is that the installer missed some file(s); could you compare the installed file lists from the beta and the release, and send me a list of files that occur only in the beta? It's normal for that list to be fairly long, because when you build yourself a lot of unnecessary files are left behind. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] integers to POSIXct
What is the recommended way to convert/coerce and integer to a POSIXct please? d - as.POSIXct(Sys.Date()) i - as.integer(d) as.POSIXct(i) Error in as.POSIXct.default(i) : do not know how to convert 'i' to class POSIXlt This appears to be the behaviour in 2.3.1 and 2.4.0 on windows XP. I have tried searching on this and found as.Date.integer in package zoo which performs a similar function but wondered if there was something basic I was missing in the base distribution? cheers __ 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] Linear model with hidden variables
Dear Richard, This looks like a latent-variable structural-equation model of the kind that one can fit with the sem package. If, however, both of the Y's affect all of the Z's, then the model isn't identified. (You also don't say what you assume about the errors from different equations -- are they correlated?) I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Richard A. O'Keefe Sent: Wednesday, October 04, 2006 12:37 AM To: r-help@stat.math.ethz.ch Subject: [R] Linear model with hidden variables I have some data on a moving vehicle where, amongst other things, it looks as though it would be informative to fit a model with the following structure: Z = B.Y + errorz Y = C.X + errorz The X variables are observed predictor variables; 6 of the variables look promising (on the basis of what they mean). The Z variables are observed response variables; there are 4 of them. There is a priori reason to believe, and scatterplots to suggest, that the Z variables are really essentially two-dimensional, so the Y variables are hidden intermediate variables. There should be 2 of them. There are actually two physical candidates for what they might be, but they happen not to have been measured. There are 800 cases. (More precisely, there are 14 periods, each with about 800 samples, and I am interested in fitting a separate model in each period.) A simple least squares fit for this model would minimise the sum of error squares for the Zs. Oh, I do mean there to be constant terms. I suppose I could go back to first principles and work it all out, but has anyone ever done something like this in R? There seems to be every imaginable variation on lm and some that I find unimaginable, so presumably a means to do this is already around somewhere. __ 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. __ 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.
[R] rendering date/times from 64bit julian format?
Hellos, I have date/times in 64-bit Julian format, that is the number of milliseconds since 1 jan 1970 (or something like that).E.g., 1159884877406 For the life of me I can't figure out how to render these in a more readable format, e.g., 2006-10-04 23:12:93.191 (and I have tried to do my best searching the archives and help etc ...) Thank you most sincerely, Derek Eder -- Derek N. Eder Gothenburg University VINKLA - Vigilance and Neurocognition laboratory __ 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.
[R] [OT] Survival and Function as co-primary endpoints in clinical trials. How to simulate in R ?
Dear R-Helpers, Apologies in advance as this is partly (widely ?) OT. Not sure where to ask, R is my favorite computer tool (no kidding) and there are plenty of knowledgable and helpful people on the list. Background: There are discussions among experts and regulatory authorities (cf guideline http://www.emea.europa.eu/pdfs/human/ewp/056598en.pdf) that, in for example Amyotrophic Lateral Sclerosis, a functional endpoint (respiratory function, muscular testing, rating scale) should be associated (co-primary, 2 primaries etc..) to survival in drug trials. My problem: I wish to illustrate that from my point of view and when you have a drug that improves survival this is not what you should do for the following reasons: - Death leads to missing data on function (sic) - This does not occur at random if the drug impacts survival - The assessment of function is biased in defavor of the drug improving survival (keeping alive patients with poor function) and in favor of the placebo group (those who survive have better function) The questions: 1-Would some one please suggest litterature where this is discussed or examples of similar situations 2- I would like to simulate the process in R ie generate survival (exponential for a start although Weibull may be be more appropriate) data with several drug effects on survival (I can do this), and also simulate various effects on function (for example vital capacity) which would be correlated to the effect on survival (not sure I know what Ineed to do and how to do it...). I realize this is not clear language and a clear question but to help formulate the question better I would appreciate pointers to relevant litterature/scripts on simulation of clinical trials in general or more specific to my problem in R. Please answer to me directly to avoid OT inconvenience to the list and so that I am not black listed...I'll be happy to summarize if relevant to the list. Best regards, Jean-Louis Jean-Louis Abitbol, MD Chief Medical Officer Trophos SA, Parc scientifique de Luminy, Case 931 Luminy Biotech Entreprises 13288 Marseille Cedex 9 France Email: [EMAIL PROTECTED] Backup Email: [EMAIL PROTECTED] Cellular: (33) (0)6 24 47 59 34 Direct Line: (33) (0)4 91 82 82 73-Switchboard: (33) (0)4 91 82 82 82 Fax: (33) (0)4 91 82 82 89 __ 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.
[R] Optim: Function definition
Hi all,
I apply optim to the function obj, which minimizes the goodness of
fit statistic and obtains Pearson minimum chi-squared estimate for x[1],
x[2] and x[3]. The vector fr contains the four observed frequencies.
Since fr[i] appears in the denominator, I would like to substitute 0
in the sum if fr[i]=0.
I tried an ifelse condition which works, but in some cases the
solution seems rather odd. Is there anything wrong with the way second
objective function is coded?
obj-function(x){
(fr[1]-x[1]*x[2]-x[3]*sqrt(x[1]*(1-x[1])*x[2]*(1-x[2])))^2/fr[1]+
(fr[2]-(1-x[1])*x[2]+x[3]*sqrt(x[1]*(1-x[1])*x[2]*(1-x[2])))^2/fr[2]+
(fr[3]-x[1]*(1-x[2])+x[3]*sqrt(x[1]*(1-x[1])*x[2]*(1-x[2])))^2/fr[3]+
(fr[4]-(1-x[1])*(1-x[2])-x[3]*sqrt(x[1]*(1-x[1])*x[2]*(1-x[2])))^2/fr[4]
}
obj-function(x){
ifelse(fr[1]==0,0,(fr[1]-x[1]*x[2]-x[3]*sqrt(x[1]*(1-x[1])*x[2]*(1-x[2])))^2/fr[1])+
ifelse(fr[2]==0,0,(fr[2]-(1-x[1])*x[2]+x[3]*sqrt(x[1]*(1-x[1])*x[2]*(1-x[2])))^2/fr[2])+
ifelse(fr[3]==0,0,(fr[3]-x[1]*(1-x[2])+x[3]*sqrt(x[1]*(1-x[1])*x[2]*(1-x[2])))^2/fr[3])+
ifelse(fr[4]==0,0,(fr[4]-(1-x[1])*(1-x[2])-x[3]*sqrt(x[1]*(1-x[1])*x[2]*(1-x[2])))^2/fr[4])
}
sval=rep(0.1,3)
fr-c(0,0.1,0.2,0.3)
optim(sval,obj, method=BFGS)$par
Thank you,
Serguei
--
___
Austrian Institute of Economic Research (WIFO)
Name: Serguei Kaniovski P.O.Box 91
Tel.: +43-1-7982601-231 Arsenal Objekt 20
Fax: +43-1-7989386 1103 Vienna, Austria
Mail: [EMAIL PROTECTED]
http://www.wifo.ac.at/Serguei.Kaniovski
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[R] how to generate matrices based on an indicator variable
Hi, I am trying to create matrices X's based on one indicator variable, r. Given a 4 x4 matrix X= [ 0,0,0,0 0,0,0,0 0,0,0,0 0,0,0,1] r= c(0, 0, 0, 1) I'd like to create separate matrices where when i = 1, X= [1,0,0,0 0,0,0,0 0,0,0,0 0,0,0,1] when i =2 , X= [0,0,0,0 0,1,0,0 0,0,0,0 0,0,0,1] when i = 3, X= [0,0,0,0 0,0,0,0 0,0,1,0 0,0,0,1] when i = 4, X= [0,0,0,0 0,0,0,0 0,0,0,0 0,0,0,1] Any suggestions would be very appreciated. Thanks [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rendering date/times from 64bit julian format?
Derek Eder [EMAIL PROTECTED] writes: Hellos, I have date/times in 64-bit Julian format, that is the number of milliseconds since 1 jan 1970 (or something like that).E.g., 1159884877406 For the life of me I can't figure out how to render these in a more readable format, e.g., 2006-10-04 23:12:93.191 (and I have tried to do my best searching the archives and help etc ...) This should be close: format(ISOdatetime(1970,1,1,0,0,0)+1159884877406/1000,%Y-%m-%d %H:%M:%OS3) [1] 2006-10-03 15:14:37.406 Beware the timezone issues though. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rendering date/times from 64bit julian format?
On 4 October 2006 at 14:50, Derek Eder wrote: | I have date/times in 64-bit Julian format, that is the number of | milliseconds since 1 jan 1970 (or something like that).E.g., | 1159884877406 | | For the life of me I can't figure out how to render these in a more | readable format, e.g., 2006-10-04 23:12:93.191 (and I have tried to | do my best searching the archives and help etc ...) To paraphrase an old saying about Unix, you could say that R's very powerful Date/Time operations are indeed very user-friendly -- but unfortunately also picky in selecting their friends. To key to this conversion is to use implicit casting. Witness now - Sys.time() class(now) [1] POSIXt POSIXct format(as.numeric(now), digits=16) [1] 1159968337.833141 so we *do* have the current time in a POSIXct as such a number. So for your purposes, create an 'offset', maybe via offset - ISOdatetime(1970,1,1,0,0,0,tz=GMT) class(offset) [1] POSIXt POSIXct as.numeric(offset) [1] 0 which gives you half the solution -- a POSIXct to start from, conveniently placed at the 'epoch.. Pick whichever timezone works for you. Then simply add your milliseconds -- but converted to seconds as that is how the internal representation is scaled: offset + 1159884877406/1000 [1] 2006-10-03 14:14:37.406 GMT class(offset + 1159884877406/1000) [1] POSIXt POSIXct Now your returned object is still POSIXct so you get to do all sort of fany conversions for free. The really nice thing is that thanks for a number of post-R 2.3.1 enhancements by Brian Ripley, we do have reall milisecond granularity in R. Hope this helps, Dirk PS Kurt, would this be worthy of a new FAQ entry? -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ 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] how to generate matrices based on an indicator variable
This produces a list whose ith element is matrix Xi : X4 - replace(matrix(0, 4, 4), cbind(4, 4), 1) lapply(1:4, function(i) replace(X4, cbind(i,i), 1)) On 10/4/06, Ya-Hsiu Chuang [EMAIL PROTECTED] wrote: Hi, I am trying to create matrices X's based on one indicator variable, r. Given a 4 x4 matrix X= [ 0,0,0,0 0,0,0,0 0,0,0,0 0,0,0,1] r= c(0, 0, 0, 1) I'd like to create separate matrices where when i = 1, X= [1,0,0,0 0,0,0,0 0,0,0,0 0,0,0,1] when i =2 , X= [0,0,0,0 0,1,0,0 0,0,0,0 0,0,0,1] when i = 3, X= [0,0,0,0 0,0,0,0 0,0,1,0 0,0,0,1] when i = 4, X= [0,0,0,0 0,0,0,0 0,0,0,0 0,0,0,1] Any suggestions would be very appreciated. Thanks \ __ 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] integers to POSIXct
Here are a few ways: now - Sys.time() Epoch - now - as.numeric(now) i + Epoch structure(i, class = c(POSIXt, POSIXct)) class(i) - c(POSIXt, POSIXct) On 10/4/06, paul sorenson [EMAIL PROTECTED] wrote: What is the recommended way to convert/coerce and integer to a POSIXct please? d - as.POSIXct(Sys.Date()) i - as.integer(d) as.POSIXct(i) Error in as.POSIXct.default(i) : do not know how to convert 'i' to class POSIXlt This appears to be the behaviour in 2.3.1 and 2.4.0 on windows XP. I have tried searching on this and found as.Date.integer in package zoo which performs a similar function but wondered if there was something basic I was missing in the base distribution? cheers __ 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. __ 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.
[R] One-arm survival sample estimates
A few months ago, I posted a query regarding code for a sample size
estimate for a one arm survival trial. Below is some code I created to
calculate such an estimate - perhaps it may be of some use.
#cox.pow computes sample size for a one arm survival trial. med.0 is
the null median
#survival, med.a is the alternative median survival, a.time is the
accrual time, and
#f.time is the follow up (assumes constant accrual and two sided test).
Approach taken
#from Lawless 1982, p. 108
cox.pow-function(med.0,med.a,a.time,f.time,alpha,beta) {
#initialize number of events to 0
r-0
#find necessary number of events
while (qchisq((1-alpha/2),(2*r+1))*(med.0/med.a) =
qchisq(beta,(2*r+1)) ) {r-r+1}
#find proportion of patients that will experience event for given
median survivals,
#accrual and follow up times (formula from Cox 1983)
p - 1 - (exp(-0.69*f.time/med.a)*(1 -
exp(-0.69*a.time/med.a))/(0.69*a.time/med.a))
#sample size is r/p
n-round(r/p,0)
return(n)
}
#compute necessary sample size for alternative median 9.3 vs. null
median 6.3 with 20
#months accrual and 4 months follow up
cox.pow(6.3,9.3,20,4,.05,.2)
Regards,
-Cody
Cody Hamilton, Ph.D
Institute for Health Care Research and Improvement
Baylor Health Care System
This e-mail, facsimile, or letter and any files or attachmen...{{dropped}}
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[R] (not so real) function (more like #include)
Hello R users,
I have a very long function with parts of that looking like a list of
jobs. The first part of the function defines a lot of local
variables, which are used by the jobs. Now I extracted the job part
und putted them into an external file, used by source(, local=T),
which is more comfortable to me. Apart from that it gives me the
opportunity that more users can work on the project. Is it possible
to define a function for that code and passing to it the environment
of f() without save(list=ls()) and load() ?
Thanks in advance
Meinhard Ploner
longfun - f() {
## lot of local variables:
a - ...
b - ...
d - ...
...
out - ...
source(job1.txt, local=TRUE) #changes out, uses a, b, d, ...
source(job2.txt, local=TRUE) # changes out, uses a, b, d, ...
...
}
version
_
platform i386-apple-darwin8.6.1
arch i386
os darwin8.6.1
system i386, darwin8.6.1
status
major 2
minor 3.1
year 2006
month 06
day01
svn rev38247
language R
version.string Version 2.3.1 (2006-06-01)
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[R] ciclo for in matrix construction ( matlab - R )
hi, i'm new to R i have a little script in matlab now i'm porting it to R but i've some problem. how can i write in R language this matlab/octave code: LX = L ; L is a matrix ss = size(LX,1); E_N_2 = zeros(ss,2); for i = 1:ss E_2 = E_0 + LX(i,1)*C(3)+LX(i,2)*C(4); E_0 , C(3), c(4) are costant N_2 = N_0 + LX(i,2)*C(3)-LX(i,1)*C(4); r=[ E_2,N_2]; E_N_2(i,:)=r; end E_N_2 i'm try so : library(matlab) LX - L ss - dim(LX) ss - ss[1] E_N_2 - zeros(ss,2) for(i in 1:ss) . .? thanks for any help :-) Massimo my mayor problem is to know how the cicle for works [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error in names-.default
Hi All, Can some one explain me the following error- Error in names-.default 'names' attribute [1199] must be the same length as the vector [17]. Thanks, Pratap - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ciclo for in matrix construction ( matlab - R )
hi, i'm new to R i have a little script in matlab now i'm porting it to R but i've some problem. how can i write in R language this matlab/octave code: LX = L ; L is a matrix ss = size(LX,1); E_N_2 = zeros(ss,2); for i = 1:ss E_2 = E_0 + LX(i,1)*C(3)+LX(i,2)*C(4); E_0 , C(3), c(4) are costant N_2 = N_0 + LX(i,2)*C(3)-LX(i,1)*C(4); r=[ E_2,N_2]; E_N_2(i,:)=r; end E_N_2 i'm try so : library(matlab) LX - L ss - dim(LX) ss - ss[1] E_N_2 - zeros(ss,2) for(i in 1:ss) . .? thanks for any help :-) Massimo my mayor problem is to know how the cicle for works [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linking R with Fortran 90: make: m2c: Command not found
many Thanks to Mike Prager and José Fernández Menéndez for your help. I tried what Mike suggested in various ways but the problem is still there. Jose's solution worked beautifully in producing a dll. After dyn.load() the dll, however, is.loaded() gives me a false answer. I still need to investigate this later part. Progress has been made, nevertheless. Jason from http://gcc.gnu.org/wiki/GfortranFAQ: Gfortran creates a file namemod= for each module name. This confuses the gnu make, which thinks that .mod files are Modula2 source code files. You must override this built-in rule by adding the following line somewhere in your Makefile. %.o : %.mod hope this helps!!! Jason Liao, http://www.geocities.com/jg_liaoAssociate Professor of Biostatistics Drexel University School of Public Health 245 N. 15th Street, Mail Stop 660 Philadelphia, PA 19102-1192 phone 215-762-3934 __ 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. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (not so real) function (more like #include)
longfun could just pass a, b and d to each of the individual
functions and each of the individual functions could pass
out back as a return value.
f1 - f2 - function(a, b, d) a+b+d
longfun1 - function() {
a - b - d - 1
out - f1(a, b, d)
out - f2(a, b, d) + out
out
}
longfun1() # 6
If the problem is that a, b and d actually represent 100 variables, say,
and its a nuisance to pass them all explicitly you could do this:
f1 - f2 - function() with(parent.frame(), a + b + d)
longfun2 - function() {
a - b - d - 1
out - f1()
out - f2() + out
out
}
longfun2() # 6
or you could do it this way if you would prefer to have longfun
control the scoping rather than having it done within each
individual function:
f1 - f2 - function() a+b+d
longfun3 - function() {
a - b - d - 1
environment(f1) - environment(f2) - environment()
out - f1()
f2() + out
}
longfun3() # 6
On 10/4/06, Meinhard Ploner [EMAIL PROTECTED] wrote:
Hello R users,
I have a very long function with parts of that looking like a list of
jobs. The first part of the function defines a lot of local
variables, which are used by the jobs. Now I extracted the job part
und putted them into an external file, used by source(, local=T),
which is more comfortable to me. Apart from that it gives me the
opportunity that more users can work on the project. Is it possible
to define a function for that code and passing to it the environment
of f() without save(list=ls()) and load() ?
Thanks in advance
Meinhard Ploner
longfun - f() {
## lot of local variables:
a - ...
b - ...
d - ...
...
out - ...
source(job1.txt, local=TRUE) #changes out, uses a, b, d, ...
source(job2.txt, local=TRUE) # changes out, uses a, b, d, ...
...
}
version
_
platform i386-apple-darwin8.6.1
arch i386
os darwin8.6.1
system i386, darwin8.6.1
status
major 2
minor 3.1
year 2006
month 06
day01
svn rev38247
language R
version.string Version 2.3.1 (2006-06-01)
__
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Re: [R] strip function
On 10/4/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote:
Hi,
I would like to asign titles into strip of a panel of curves designed
thanks to a xyplot function (lattice package)
I ve tried the strip function, ...
here is my code
I would like to write in the strip of each panel conditionning varialbe
(here, it is data[,1])
xyplot (data[,3] ~ data[,2] | data[,1] , strip.default (which.given=1,
which.panel = c(1:15), var.name= c
(26,28,15,2,31,10,16,21,21.5,5,17,14,7,8,30),
factor.levels=c(26,28,15,2,31,10,16,21,21.5,5,17,14,7,8,30),strip.names=c(1,0),strip.levels=c(0,0)),panel=function(x,y)
{
panel.xyplot(x,y,pch=4,col=3)
type = c(p, r)
COEFF-coef(lm(log(y)~x))
panel.curve(exp(COEFF[1]+COEFF[2]*x),col=4)
a-round(COEFF[1],digit=2)
b-round(COEFF[2],digit=2)
formula-as.name(paste(y=exp(,a,b,x),sep=))
panel.text(10,700,formula)
})
I cannot get anny result exept one page with a big strip on which is
written 26 and then the curve without specified strip
CAn anyone give me some advices ?
Yes;
(1) acquire some rudimentary R programming skills, which you currently
do not seem to have. See the links under Documentation in
http://www.r-project.org for some possible starting points.
(2) read the posting guide at
http://www.R-project.org/posting-guide.html, and follow its
suggestions. In particular, give a _reproducible example_ and describe
what you _want to do_, not some badly written code which fails to do
it (in fact I'm surprised that your code does anything at all).
Deepayan
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[R] Bivariate Weibull distribution -- Copula
Hi All, I am struggling in a bivariate Weibull distribution although I searched R-Site-Help and found suggestion with Copula. Seems the maximum likelihood estimate is beyond what I can understand. My case is: given two known marginal distribution (both are Weibull), and the correlation between them. How can I get the bivariate distribution based on these two? I wish if there is anybody has the experience in bivariate distribution could give me the hints. Thanks! Jen. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to convert all columns of a data frame into factors
Try this: replace(BOD, TRUE, lapply(BOD, factor)) On 10/4/06, Weiwei Shi [EMAIL PROTECTED] wrote: Hi, I use apply apply(x, 2, factor) but it does not work. please help. thanks. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ 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. __ 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] how to convert all columns of a data frame into factors
Alternatively:
x[] - lapply(x, factor)
Recall that a data frame is a list, so lapply() is a natural choice.
Andy
From: Gabor Grothendieck
Try this:
replace(BOD, TRUE, lapply(BOD, factor))
On 10/4/06, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I use apply
apply(x, 2, factor)
but it does not work. please help. thanks.
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
Did you always know?
No, I did not. But I believed...
---Matrix III
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Re: [R] how to convert all columns of a data frame into factors
On Wed, 2006-10-04 at 11:33 -0400, Weiwei Shi wrote: Hi, I use apply apply(x, 2, factor) but it does not work. please help. thanks. In what sense does it not work? And how can you possibly expect anyone on this list to help you as you neither supply the error message you received nor provide us with x or a reproducible example, nor tell us what you want to achieve. E.g. dat - sample(LETTERS, 100, replace = TRUE) dat - matrix(dat, ncol = 10) dat apply(dat, 2, factor) which appears to be converting a character vector into a factor, which is then coerced to a numeric vector (as there are only numeric and character matrices in R) - but I may be wrong: as.numeric(factor(dat[,1])) [1] 7 7 2 5 8 1 4 7 3 6 which is the first column of the object returned by apply(dat, 2, factor). Is this not what you wanted? So perhaps you could provide the list with some further information as you are asked to in the posting guide! HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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.
[R] Tabulation and missing values
I think this is one for Gabor. I don't seem to be able to find my way to an answer despite numerous rereadings of factor and table. Here is a toy example: ### Some data EthnicCode - c(European/Other, NA, European/Other, European/Other, Pacific, European/Other, European/Other, European/Other, Maori, Maori, European/Other, European/Other, Asian, Pacific) ### I don't want the categories in the default order ### I also want to be able to include or exclude NA ### argument exclude controls inclusion of NA table(EthnicCode) table(EthnicCode,exclude=NULL) ### Creating a factor allows reordering EthnicFactor - factor(EthnicCode, exclude=) levels(EthnicFactor) - list(Maori=Maori,Pacific=Pacific, Asian=Asian, Europ/Other=European/Other, is.na=NA) ### I can tabulate with categories in the desired order table(EthnicFactor[,drop=TRUE]) ### But I can't seem to include the missing observations table(EthnicFactor,exclude=NULL) David Scott _ David Scott Visiting (Until January 07) Department of Probability and Statistics The University of Sheffield The Hicks Building Hounsfield Road Sheffield S3 7RH United Kingdom Phone: +44 114 222 3908 Email: [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] Tabulation and missing values
Is the idea here to have the NA entries be a factor level? Try this: table(format(EthnicCode)) with appropriate mods if you want to rearrange the levels. On 10/4/06, David Scott [EMAIL PROTECTED] wrote: I think this is one for Gabor. I don't seem to be able to find my way to an answer despite numerous rereadings of factor and table. Here is a toy example: ### Some data EthnicCode - c(European/Other, NA, European/Other, European/Other, Pacific, European/Other, European/Other, European/Other, Maori, Maori, European/Other, European/Other, Asian, Pacific) ### I don't want the categories in the default order ### I also want to be able to include or exclude NA ### argument exclude controls inclusion of NA table(EthnicCode) table(EthnicCode,exclude=NULL) ### Creating a factor allows reordering EthnicFactor - factor(EthnicCode, exclude=) levels(EthnicFactor) - list(Maori=Maori,Pacific=Pacific, Asian=Asian, Europ/Other=European/Other, is.na=NA) ### I can tabulate with categories in the desired order table(EthnicFactor[,drop=TRUE]) ### But I can't seem to include the missing observations table(EthnicFactor,exclude=NULL) David Scott _ David Scott Visiting (Until January 07) Department of Probability and Statistics The University of Sheffield The Hicks Building Hounsfield Road Sheffield S3 7RH United Kingdom Phone: +44 114 222 3908 Email: [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. __ 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] how to convert all columns of a data frame into factors
On Wed, 2006-10-04 at 17:04 +0100, Gavin Simpson wrote: On Wed, 2006-10-04 at 11:33 -0400, Weiwei Shi wrote: Hi, I use apply apply(x, 2, factor) but it does not work. please help. thanks. Ah, lesson one: read the email clearly before replying - just like my old Geography teacher used to tell me! This works dat - sample(LETTERS, 100, replace = TRUE) # use a data. frame not a matrix dat - data.frame(matrix(dat, ncol = 10)) dat lapply(dat, factor) # as a list # or, as a data.frame data.frame(lapply(dat, factor)) G In what sense does it not work? And how can you possibly expect anyone on this list to help you as you neither supply the error message you received nor provide us with x or a reproducible example, nor tell us what you want to achieve. E.g. dat - sample(LETTERS, 100, replace = TRUE) dat - matrix(dat, ncol = 10) dat apply(dat, 2, factor) which appears to be converting a character vector into a factor, which is then coerced to a numeric vector (as there are only numeric and character matrices in R) - but I may be wrong: as.numeric(factor(dat[,1])) [1] 7 7 2 5 8 1 4 7 3 6 which is the first column of the object returned by apply(dat, 2, factor). Is this not what you wanted? So perhaps you could provide the list with some further information as you are asked to in the posting guide! HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] Error in names-.default
On Wed, 2006-10-04 at 16:07 +0100, nalluri pratap wrote: Hi All, Can some one explain me the following error- Error in names-.default 'names' attribute [1199] must be the same length as the vector [17]. Thanks, Pratap You haven't shown us what you did, but it looks like you tried to replace the names of an object with a vector (of length 1199) when a vector of length 17 was required. See this example: dat - as.data.frame(matrix(rnorm(100), ncol = 10)) names(dat) - LETTERS[1:10] names(dat) [1] A B C D E F G H I J names(dat) - LETTERS Error in `names-.default`(`*tmp*`, value = c(A, B, C, D, E, : 'names' attribute [26] must be the same length as the vector [10] Where I have tried to replace names(dat) (which should be of length 10) with a vector of length 26 (all the letters A-Z). The error message above is not the same as the one you show though, so this might not be the problem. As the posting guide asks, please give a reproducible example or provide enough information for us to help you. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] how to convert all columns of a data frame into factors
Just one small point on this. This may not matter to you but just in case it does, if L - lapply(BOD, factor) then replace(BOD, TRUE, L) data.frame(L) are not exactly the same in the case that BOD has additional attributes (which in this case it does). The first one will preserve the attributes and the second one does not. attributes(BOD) # note reference attribute attributes(replace(BOD, TRUE, L) # reference preserved attributes(data.frame(L)) # no reference On 10/4/06, Gavin Simpson [EMAIL PROTECTED] wrote: On Wed, 2006-10-04 at 17:04 +0100, Gavin Simpson wrote: On Wed, 2006-10-04 at 11:33 -0400, Weiwei Shi wrote: Hi, I use apply apply(x, 2, factor) but it does not work. please help. thanks. Ah, lesson one: read the email clearly before replying - just like my old Geography teacher used to tell me! This works dat - sample(LETTERS, 100, replace = TRUE) # use a data. frame not a matrix dat - data.frame(matrix(dat, ncol = 10)) dat lapply(dat, factor) # as a list # or, as a data.frame data.frame(lapply(dat, factor)) G In what sense does it not work? And how can you possibly expect anyone on this list to help you as you neither supply the error message you received nor provide us with x or a reproducible example, nor tell us what you want to achieve. E.g. dat - sample(LETTERS, 100, replace = TRUE) dat - matrix(dat, ncol = 10) dat apply(dat, 2, factor) which appears to be converting a character vector into a factor, which is then coerced to a numeric vector (as there are only numeric and character matrices in R) - but I may be wrong: as.numeric(factor(dat[,1])) [1] 7 7 2 5 8 1 4 7 3 6 which is the first column of the object returned by apply(dat, 2, factor). Is this not what you wanted? So perhaps you could provide the list with some further information as you are asked to in the posting guide! HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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. __ 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] Tabulation and missing values
On Thu, 2006-10-05 at 05:10 +1300, David Scott wrote: I think this is one for Gabor. I don't seem to be able to find my way to an answer despite numerous rereadings of factor and table. Here is a toy example: ### Some data EthnicCode - c(European/Other, NA, European/Other, European/Other, Pacific, European/Other, European/Other, European/Other, Maori, Maori, European/Other, European/Other, Asian, Pacific) ### I don't want the categories in the default order ### I also want to be able to include or exclude NA ### argument exclude controls inclusion of NA table(EthnicCode) table(EthnicCode,exclude=NULL) ### Creating a factor allows reordering EthnicFactor - factor(EthnicCode, exclude=) levels(EthnicFactor) - list(Maori=Maori,Pacific=Pacific, Asian=Asian, Europ/Other=European/Other, is.na=NA) ^^^ Are you sure you want that last entry. You are basically creating a level is.na, for those entries that have character NA (not same as NA). When you use table(EthnicFactor[,drop=TRUE]) you are dropping empty levels, not dropping NAs which is why your self-inflicted is.na disappears, but not when you use exclude=NULL, which I don't get either, as ?table has exclude = c(NA, NaN) not NULL. Just do: table(factor(EthnicCode)) but that loses the NAs in the factor created (see ?factor and argument exclude). Compare: dat - factor(EthnicCode) dat # preserves NAs as a level dat2 - factor(EthnicCode, exclude = ) dat2 table(dat) table(dat2) # NAs as a level displayed table(dat2, exclude = NA) # no NAs Is that what you were looking for? HTH G ### I can tabulate with categories in the desired order table(EthnicFactor[,drop=TRUE]) ### But I can't seem to include the missing observations table(EthnicFactor,exclude=NULL) David Scott -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] how to convert all columns of a data frame into factors
thanks, Andy and Jacques.
I forgot to convert the result from lapply to data.frame when I tried
lapply last time, :)
I should have done this
data.frame(lapply(x, factor))
On 10/4/06, Liaw, Andy [EMAIL PROTECTED] wrote:
Alternatively:
x[] - lapply(x, factor)
Recall that a data frame is a list, so lapply() is a natural choice.
Andy
From: Gabor Grothendieck
Try this:
replace(BOD, TRUE, lapply(BOD, factor))
On 10/4/06, Weiwei Shi [EMAIL PROTECTED] wrote:
Hi,
I use apply
apply(x, 2, factor)
but it does not work. please help. thanks.
--
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.
Did you always know?
No, I did not. But I believed...
---Matrix III
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[R] R Graphics: Saving PDF and other formats from Windows Graphic Device for LaTeX
Hello, I can't seem to save (or find the default location) when I use the Window Graphic Device's pull down menu. It does not seem to save to the directory I have set using setwd(...). How do I make the pull down menu's work? What is the best format to save R graphics for inclusion into a LaTeX documents? I will use PdfTex, or LaTeX - PS - PsToPdf to generate the final PDF file. Which is likely to give the best graphics quality in the final PDF document? The final graphs will be about 3x3 inch (fit in a column in two-column format). I will be grateful if someone can share their experience. Anupam. __ 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.
[R] extracting nested variances from lme4 model
I have a model: mod1-lmer( x ~ (1|rtr)+ trth/(1|cs) , data=dtf) # Here, cs and rtr are crossed random effects. cs 1-5 are of type TRUE, cs 6-10 are of type FALSE, so cs is nested in trth, which is fixed. So for cs I should get a fit for 1-5 and 6-10. This appears to be the case from the random effects: mean( ranef(mod1)$cs[[1]][1:5] ) [1] -2.498002e-16 var( ranef(mod1)$cs[[1]][1:5] ) [1] 23.53083 mean( ranef(mod1)$cs[[1]][6:10] ) [1] 2.706169e-16 var( ranef(mod1)$cs[[1]][6:10] ) [1] 1.001065 However VarCorr(mod1) gives me only a single variance estimate for the cases. How do I get the other variance estimate? Thanks for any help. -Frank My fake data set: --- data: $frame x rtr trth cs 1 -4.4964808 1 TRUE 1 2 -0.6297254 1 TRUE 2 31.8062857 1 TRUE 3 42.7273275 1 TRUE 4 5 -0.6297254 1 TRUE 5 6 -1.3331767 1 FALSE 6 7 -0.3055796 1 FALSE 7 81.3331767 1 FALSE 8 90.1574314 1 FALSE 9 10 -0.1574314 1 FALSE 10 11 -3.0958803 2 TRUE 1 12 12.4601615 2 TRUE 2 13 -5.2363532 2 TRUE 3 14 1.5419810 2 TRUE 4 15 7.7071005 2 TRUE 5 16 -0.3854953 2 FALSE 6 17 0.7673098 2 FALSE 7 18 2.9485984 2 FALSE 8 19 0.3854953 2 FALSE 9 20 -0.3716558 2 FALSE 10 21 -6.4139940 3 TRUE 1 22 -3.8162344 3 TRUE 2 23 -11.0518554 3 TRUE 3 24 2.7462631 3 TRUE 4 25 16.2543990 3 TRUE 5 26 -1.7353668 3 FALSE 6 27 1.3521369 3 FALSE 7 28 1.3521369 3 FALSE 8 29 0.2054067 3 FALSE 9 30 -1.7446691 3 FALSE 10 31 -6.7468356 4 TRUE 1 32 -11.3228243 4 TRUE 2 33 -18.0088554 4 TRUE 3 34 4.6264891 4 TRUE 4 35 9.2973991 4 TRUE 5 36 -4.1122576 4 FALSE 6 37 -0.5091994 4 FALSE 7 38 1.2787085 4 FALSE 8 39 -1.6867089 4 FALSE 9 40 -0.5091994 4 FALSE 10 __ 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 Graphics: Saving PDF and other formats from Windows Graphic Device for LaTeX
On 10/4/2006 1:11 PM, Anupam Tyagi wrote: Hello, I can't seem to save (or find the default location) when I use the Window Graphic Device's pull down menu. It does not seem to save to the directory I have set using setwd(...). How do I make the pull down menu's work? If you want the best quality results, don't use the Save menu at all. Instead, write directly to a graphics device like pdf(). What is the best format to save R graphics for inclusion into a LaTeX documents? I will use PdfTex, or LaTeX - PS - PsToPdf to generate the final PDF file. Which is likely to give the best graphics quality in the final PDF document? The final graphs will be about 3x3 inch (fit in a column in two-column format). I will be grateful if someone can share their experience. The postscript and pdf formats both give good results. Depending on your Latex setup, sometimes only one or the other will be supported. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A more efficient code using whole object approach?
Dear All,
I have the following code which works fine but takes 16+ hours to run and I
was hoping someone could give me a hint as to how I could make it more
efficient.
Let me explain what the code is supposed to do. Each single row of the m.o.f
matrix (n*p dim) has to go through the following operation Dm*m.o.f[i]^alpha1m
where both Dm and alpha1m have n*1 dimensions. Each row of the m.o.f is to be
evaluated n times for the different values of alpha1m and Dm. My code changes
the Dm and alpha1m (n*1) matrices into (n*p) matrices (not shown below, done
only 1 time) and also change the (1*p) m.o.f row into a m.o (n*p) matrix (shown
below, done n times). For each of the n rows of the m.o.f matrix we repeat this
operation which we record in the temp matrix. The third line of the loop
multiplies for each row, the columns of the matrix and takes the resultant mean
of the vector.
I know I should use the whole object approach somehow but after many tries I
gaave up for the long approach. I know the explanation above is rather long and
I apologize for that, any hint/help will be greatly appreciated.
for (i in 1:numrows)
{
mo.o-t(array(m.o.f[i,],dim=c(numcols,numrows)))
t-Dm*m.o^alpha1m
l1[i]-mean(apply(t,1,prod))
}
Best Regards,
-
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[R] concordance measures
Dear all, I have a question about concordance measures. I have n itens which are measured by 4 subjects. The outcomes are discrete. What is the appropriated test to verify the concordance between the subjects? Best Regards. _ Inscreva-se no novo Windows Live Mail beta e seja um dos primeiros a testar as novidades-grátis. Saiba mais: __ 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.
[R] discarding 'levels'
Ok, so I am using read.table to read a .txt file and put it into a matrix. There are some values that are 'NA'. If I use read.table with as.is =FALSE, then some of the entries in the matrix return this: data[1,3] [1] 0 Levels: 0 1 NA and if I do data[1,3]==0 it returns FALSE. It's a zero, it's not false! If I set as.is=TRUE, I don't get the levels problem, but in those entries where I did get the levels problem, this happens: data[1,3] [1] 0 This time, it keeps it as a string. I can use as.numeric to fix it now, but I'm just curious as to why this happens. Thanks -- View this message in context: http://www.nabble.com/discarding-%27levels%27-tf2384152.html#a6645474 Sent from the R help mailing list archive at Nabble.com. __ 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 Graphics: Saving PDF and other formats from Windows GraphicDevice for LaTeX
If you plan to include your graphics in LaTeX files then you should really look at the Sweave function in the utils package. This approach may work better for you and make these questions not matter anymore. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Anupam Tyagi Sent: Wednesday, October 04, 2006 11:11 AM To: r-help@stat.math.ethz.ch Subject: [R] R Graphics: Saving PDF and other formats from Windows GraphicDevice for LaTeX Hello, I can't seem to save (or find the default location) when I use the Window Graphic Device's pull down menu. It does not seem to save to the directory I have set using setwd(...). How do I make the pull down menu's work? What is the best format to save R graphics for inclusion into a LaTeX documents? I will use PdfTex, or LaTeX - PS - PsToPdf to generate the final PDF file. Which is likely to give the best graphics quality in the final PDF document? The final graphs will be about 3x3 inch (fit in a column in two-column format). I will be grateful if someone can share their experience. Anupam. __ 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. __ 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] ciclo for in matrix construction ( matlab - R )
The help page for 'for' warns:
Note that it is a common mistake to forget to put braces ('{ ..
}') around your statements, e.g., after 'if(..)' or 'for()'.
In particular, you should not have a newline between '}' and
'else' to avoid a syntax error in entering a 'if ... else'
construct at the keyboard or via 'source'. For that reason, one
(somewhat extreme) attitude of defensive programming is to always
use braces, e.g., for 'if' clauses.
Also this is illustrated in R FOR OCTAVE USERS
http://cran.r-project.org/doc/contrib/R-and-octave.txt
in the section starting:
MULTILINE FOR STATEMENTS:
On Wed, 4 Oct 2006, massimodisasha wrote:
hi,
i'm new to R
i have a little script in matlab
now i'm porting it to R but i've some problem.
how can i write in R language this
matlab/octave code:
LX = L ; L is a matrix
ss = size(LX,1);
E_N_2 = zeros(ss,2);
for i = 1:ss
E_2 = E_0 + LX(i,1)*C(3)+LX(i,2)*C(4); E_0 , C(3), c(4)
are costant
N_2 = N_0 + LX(i,2)*C(3)-LX(i,1)*C(4);
r=[ E_2,N_2];
E_N_2(i,:)=r;
end
E_N_2
i'm try so :
library(matlab)
LX - L
ss - dim(LX)
ss - ss[1]
E_N_2 - zeros(ss,2)
for(i in 1:ss)
.
.?
thanks for any help :-)
Massimo
my mayor problem is to know how the cicle for works
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
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Re: [R] A more efficient code using whole object approach?
A couple of thoughts (hopefully others will have even better
suggestions):
1. Could you do a some of the computations on the log scale? This would
turn exponents into multiplications and multiplications into additions
and may turn a lot of the work into matrix multiplications.
2. It does not appear that the order matters (i=1, 2, ...), so this
could be easily parallelized, the nws package allows a fairly straight
forward way to do this if you have access to multiple computers (I for
one don't have a problem stealling cycles from my coworkers computers
when they are not doing computationally intesive things).
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Muzaffer Musal
Sent: Wednesday, October 04, 2006 11:36 AM
To: r-help@stat.math.ethz.ch
Subject: [R] A more efficient code using whole object approach?
Dear All,
I have the following code which works fine but takes 16+ hours to run
and I was hoping someone could give me a hint as to how I could make it
more efficient.
Let me explain what the code is supposed to do. Each single row of the
m.o.f matrix (n*p dim) has to go through the following operation
Dm*m.o.f[i]^alpha1m where both Dm and alpha1m have n*1 dimensions. Each
row of the m.o.f is to be evaluated n times for the different values of
alpha1m and Dm. My code changes the Dm and alpha1m (n*1) matrices into
(n*p) matrices (not shown below, done only 1 time) and also change the
(1*p) m.o.f row into a m.o (n*p) matrix (shown below, done n times). For
each of the n rows of the m.o.f matrix we repeat this operation which we
record in the temp matrix. The third line of the loop multiplies for
each row, the columns of the matrix and takes the resultant mean of the
vector.
I know I should use the whole object approach somehow but after many
tries I gaave up for the long approach. I know the explanation above is
rather long and I apologize for that, any hint/help will be greatly
appreciated.
for (i in 1:numrows)
{
mo.o-t(array(m.o.f[i,],dim=c(numcols,numrows)))
t-Dm*m.o^alpha1m
l1[i]-mean(apply(t,1,prod))
}
Best Regards,
-
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Re: [R] Possible bug?
On Thursday 05 October 2006 00:14, ronggui wrote: Yes, the installer missed some file(s) in RHOME/bin. When I choose Message translations, the /bin directory contains the following files. -- snip -- I meant to mention that when I used the installer I didn't have to choose Message translations, it was ticked by default. HTH, Ray Brownrigg __ 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.
[R] Suitability of R for Algorithm simulations
Greetings, Sorry for the basic question, but I am trying to find out if R is a suitable platform for what I want to do... I am interested in creating simulations of distributed algorithms (i.e. team formation, Byzantine Generals , P2P communication modeling, mobile networks) that would be represented in GUIs. I would like to be able to instantiate an object for each node in my simulated (stand alone, one computer) distributed environment and then proceed by (a) adding message exchange functionality and (b) algorithm behavior to each node. The simulation results are represented on a GUI that looks like a grid with each node being a dot. As the algorithm progresses, different formations and messages are exchanged between the nodes. I am in a bit of a desperate situation as I am trying to get away from MATLAB (too expensive, no longer available to me) and at the same time would like to avoid developing the infrastructure from scratch (i.e in Java) to run these simulations. Is R suitable for what I am trying to do? I looked around but have not been able to determine if R is the appropriate platform. Your help, comments or suggestion of alternatives and pontification is welcome. Thank you, Ethan B. Finn - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] complex plots using layout()
Hi Lu, Jiang Jane wrote: Dear Dr. Murrell, Thank you very much for your suggestion. I have successfully produced the ideal plot following your advice. Please see the attached PDF file (layouttest.pdf) for results. However, I do not understand why the left and right outer margins are so big that it occupies almost half of the page. I did not specify any outer margins in my program, which I attached to this email at the end. Any comment is appreciated. The blank space is there because the layout has 'respect=TRUE', which means that a column width of 1 has the same physical size as a row height of 1 (i.e., the scatterplots are square and, more importantly, the two marginal histograms are the same height). Overall, the layout is square, but the page is rectangular, so the layout cannot use all of the page. Try removing the 'respect=TRUE' (I doubt you'll like the result). You could try partial respect, for example ... layout(matrix(c(2,0,0,1,3,7,5,0,0,4,6,8), nrow=4, ncol=3, byrow=TRUE), widths=c(3,1,3), heights=c(1,3,1,3), respect=matrix(c(0,1,0,0,0,0,0,1,0,0,0,0), nrow=4, ncol=3, byrow=TRUE)) ... (again, untested) just to enforce the histogram heights, but it can take a bit of experimenting to understand what is going on with partial respect. BTW, I think your par(mar)'s are not quite right (the marginal histograms stick out beyond the edges of the scatterplot). I think something like ... par(mar=c(5,5,1,1)) plot(x, y1, xlim=xrange, ylim=y1range, xlab=predtname[1], ylab=MJI) lines(lowess(x[is.na(x)==FALSE],y1[is.na(x)==FALSE]),col=2,lwd=3) par(mar=c(0,5,5,1)) barplot(xhist$counts, axes=FALSE, ylim=c(0, top1), space=0,main=paste(Correlation Coeffcient = ,y1corr)) par(mar=c(5,0,1,1)) barplot(y1hist$counts, axes=FALSE, xlim=c(0, top1), space=0, horiz=TRUE) ... would be better. Paul = y1 - demograc$MYOJEOP y2 - log(demograc$ntotles) x - demograc$agebl xc - demograc$AGECAT predtname - c(Age,Categorical Age) prdtlevel - list(ctnage=0, ftage=c(50,50-59,60-69,=70)) postscript(file=C:/Lu/MyR/Trials/Layout/testlayout.eps,horizontal=TRUE ) xhist - hist(x, plot=FALSE) y1hist - hist(y1, plot=FALSE) y2hist - hist(y2, plot=FALSE) top1 - max(c(xhist$counts, y1hist$counts)) top2 - max(c(xhist$counts, y2hist$counts)) xrange - range(x,na.rm=TRUE) y1range - range(y1,na.rm=TRUE) y2range - range(y2,na.rm=TRUE) y1corr - round(cor(x,y1,use=complete.obs),2) y2corr - round(cor(x,y2,use=complete.obs),2) def.par - par(no.readonly = TRUE) # save default, for resetting... nf - layout(matrix(c(2,0,0,1,3,7,5,0,0,4,6,8),nrow=4,ncol=3, byrow=TRUE),widths=c(3,1,3),heights=c(1,3,1,3),respect=TRUE) par(mar=c(5,5,1,1)) plot(x, y1, xlim=xrange, ylim=y1range, xlab=predtname[1], ylab=MJI) lines(lowess(x[is.na(x)==FALSE],y1[is.na(x)==FALSE]),col=2,lwd=3) par(mar=c(0,3,5,1)) barplot(xhist$counts, axes=FALSE, ylim=c(0, top1), space=0,main=paste(Correlation Coeffcient = ,y1corr)) par(mar=c(3,0,1,1)) barplot(y1hist$counts, axes=FALSE, xlim=c(0, top1), space=0, horiz=TRUE) par(mar=c(5,5,1,1)) plot(x, y2, xlim=xrange, ylim=y2range, xlab=predtname[1], ylab=log(Numer of Lesions)) lines(lowess(x[is.na(x)==FALSE],y2[is.na(x)==FALSE]),col=2,lwd=3) par(mar=c(0,3,5,1)) barplot(xhist$counts, axes=FALSE, ylim=c(0, top2), space=0,main=paste(Correlation Coeffcient = ,y2corr)) par(mar=c(3,0,1,1)) barplot(y2hist$counts, axes=FALSE, xlim=c(0, top2), space=0, horiz=TRUE) y1pvalue - round(anova(lm(y1~factor(xc)))[1,5],3) y2pvalue - round(anova(lm(y2~factor(xc)))[1,5],3) par(mar=c(4,5,2,2)) boxplot(y1~xc,varwidth=TRUE,main=paste(p-value of t test or ANOVA = ,y1pvalue), names=prdtlevel[[2]],ylab='MJI',xlab=predtname[2],na.action=na.omit) boxplot(y2~xc,varwidth=TRUE,main=paste(p-value of t test or ANOVA = ,y2pvalue), names=prdtlevel[[2]],ylab='log(Number of Lesions)',xlab=predtname[2],na.action=na.omit) par(def.par) dev.off() Jiang Lu BARI 2D Coordinating Center University of Pittsburgh 130 DeSoto Street, 127 Parran Hall Pittsburgh, PA 15261 Tel: (412)624-5219 -Original Message- From: Paul Murrell [mailto:[EMAIL PROTECTED] Sent: Tuesday, October 03, 2006 8:50 PM To: Lu, Jiang Jane Cc: r-help@stat.math.ethz.ch Subject: Re: [R] complex plots using layout() Hi Lu, Jiang Jane wrote: Dear r-help, I am trying to plot several scatter plots with marginal histograms on one page. Ideally, a page is equally divided into 4 figure regions. Within each figure region, a scatter plot with marginal histograms will be plotted. I followed Dr. Paul Murrell's code released online to successfully plot the scatter plot with marginal histograms. The code applies layout() to partition the page. Right now,
[R] convert vector to matrix
Hi All, I have vector containing 10 elements(odservations). I need to put this into a matrix, where the matrix should contain only one column. I need this to be done using the cbind command because in the final table I should have a column of attributes( from adifferent vector) and a column of vectors from the matrix above Please suggest me how this can be done Thanks and Regards, Pratap - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert vector to matrix
On Wed, 2006-10-04 at 21:50 +0100, nalluri pratap wrote: Hi All, I have vector containing 10 elements(odservations). I need to put this into a matrix, where the matrix should contain only one column. I need this to be done using the cbind command because in the final table I should have a column of attributes( from adifferent vector) and a column of vectors from the matrix above Please suggest me how this can be done Thanks and Regards, Pratap Did you even try to use cbind on your vector? I guess not as, vec - 1:10 mat - cbind(vec) mat vec [1,] 1 [2,] 2 [3,] 3 [4,] 4 [5,] 5 [6,] 6 [7,] 7 [8,] 8 [9,] 9 [10,] 10 class(mat) [1] matrix clearly shows it is possible. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% *Note new Address and Fax and Telephone numbers from 10th April 2006* %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC [f] +44 (0)20 7679 0565 UCL Department of Geography Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street London, UK[w] http://www.ucl.ac.uk/~ucfagls/cv/ WC1E 6BT [w] http://www.ucl.ac.uk/~ucfagls/ %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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.
[R] Spearman correlation test confidence intervals
Hello, How does one calculate the confidence levels for a spearman correlation test? I noticed cor.test(x,y) gives the confidence levels only for pearson test. Thank you for the suggestions, in advance. Best Regards, Mahesh Krishnan __ 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] convert vector to matrix
Gavin Simpson wrote: Did you even try to use cbind on your vector? I guess not as, vec - 1:10 mat - cbind(vec) mat Why does mat remain a matrix instead of losing one dimension? I am reading the FAQ at... http://cran.us.r-project.org/doc/FAQ/R-FAQ.html#Why-do-my-matrices-lose- dimensions_003f ... and it seems that anything you do to mat should turn it back into a one-dimensional vector. Alberto Monteiro __ 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.
[R] RODBC: longest string is truncated
Hello R community:
I'm encountering unexpected behaviour as I download string data from
MySQL using the RODBC package. The unexpected behaviour is that the last
character of the string is truncated. As far as I can see, this happens
when some strings are of length 501 or more.
Here's how to reproduce this behaviour.
## In MySQL, pick a database and run this:
CREATE TABLE test (
v1 text NOT NULL
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
INSERT INTO test
set v1=concat(repeat('a',499),'1'); # length 500
INSERT INTO test
set v1=concat(repeat('a',499),'12'); # length 501
INSERT INTO test
set v1=concat(repeat('a',499),'123'); # length 502
## In R, first setup a channel to connect to your MySQL database.
# library(RODBC)
# channel - odbcConnect(mydb)
## Now run this:
sqlQuery(channel, select * from test, as.is=T)$v1
You'll see the entire strings, except for the last character of the 3rd
record, which is 3. Strange enough, if I remove the last record from
the MySQL table and reload the data in R, I see that the 2 of the 2nd
record is truncated. Looks like only the string with greatest length is
truncated.
Can you reproduce this behaviour? Is this a bug? Can someone please
explain why the last character is truncated?
Many thanks for your help.
Jerome
OS: RHEL 4 AS
R version 2.3.1
RODBC version 1.1-7
--
Jerome Asselin, M.Sc., Agent de recherche, RHCE
CHUM -- Centre de recherche
3875 rue St-Urbain, 3e etage // Montreal QC H2W 1V1
Tel.: 514-890-8000 Poste 15914; Fax: 514-412-7106
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Re: [R] convert vector to matrix
cbind always produces a matrix or data frame. What the FAQ says is that a subsetting operation *on* a matrix will result in redundant dimensions being dropped, not that you can't get a matrix with a redundant dimension as a result of a function. So, vec-1:10 vec [1] 1 2 3 4 5 6 7 8 9 10 cbind(vec) vec [1,] 1 [2,] 2 [3,] 3 [4,] 4 [5,] 5 [6,] 6 [7,] 7 [8,] 8 [9,] 9 [10,] 10 mat-cbind(vec) dim(mat) [1] 10 1 mat[,1] [1] 1 2 3 4 5 6 7 8 9 10 takes us back to a vector again. On 04/10/06, Alberto Monteiro [EMAIL PROTECTED] wrote: Gavin Simpson wrote: Did you even try to use cbind on your vector? I guess not as, vec - 1:10 mat - cbind(vec) mat Why does mat remain a matrix instead of losing one dimension? I am reading the FAQ at... http://cran.us.r-project.org/doc/FAQ/R-FAQ.html#Why-do-my-matrices-lose- dimensions_003f ... and it seems that anything you do to mat should turn it back into a one-dimensional vector. Alberto Monteiro __ 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. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ 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] discarding 'levels'
From TFM of read.table: as.is: the default behavior of 'read.table' is to convert character variables (which are not converted to logical, numeric or complex) to factors. The variable 'as.is' controls the conversion of columns not otherwise specified by 'colClasses'. Its value is either a vector of logicals (values are recycled if necessary), or a vector of numeric or character indices which specify which columns should not be converted to factors. You may have some blanks in the third column. Factor levels whose character representation happens to be a numeral don't necessarily compare equal to the integer with the same character representation (if you get my drift...). You can use as.numeric, but better would be to use colClasses in read.table. Regards, Mike On 10/4/06, hoopz [EMAIL PROTECTED] wrote: Ok, so I am using read.table to read a .txt file and put it into a matrix. There are some values that are 'NA'. If I use read.table with as.is =FALSE, then some of the entries in the matrix return this: data[1,3] [1] 0 Levels: 0 1 NA and if I do data[1,3]==0 it returns FALSE. It's a zero, it's not false! If I set as.is=TRUE, I don't get the levels problem, but in those entries where I did get the levels problem, this happens: data[1,3] [1] 0 This time, it keeps it as a string. I can use as.numeric to fix it now, but I'm just curious as to why this happens. Thanks -- View this message in context: http://www.nabble.com/discarding-%27levels%27-tf2384152.html#a6645474 Sent from the R help mailing list archive at Nabble.com. __ 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. -- Regards, Mike Nielsen __ 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.
[R] compiling rgdal package on windows / macos
Greetings: As I am not a windows user, I cannot try this: is it possible to install rgdal on windows without having to compile it from source ? Compilation on MacOS is within my abilities, however each time i try and install the rgdal package it dies complaining that it cannot find gdal-config --- which was recently installed with GRASS. I have updated my PATH environment variable, logged out, but R still cannot find the gdal-config program. any tips on getting the rgdal package up and running on MacOS or Windows would be greatly appreciated. Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ 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-2.4.0 is released
On Tue, 3 Oct 2006 20:30, Peter Dalgaard wrote: o load()ing an object saved in one of the formats used prior to R 1.4.0 is deprecated. Such objects should be re-saved in the current format. Is there some property of old .RData files that I could use with find on linux to detect and update them? I suppose I could use the last modified date, but it would be nice to detect the format? Robert. -- Robert King, Statistics, School of Mathematical Physical Sciences, University of Newcastle, Australia Room V133 ph +61 2 4921 5548 [EMAIL PROTECTED] http://tolstoy.newcastle.edu.au/~rking/ Verbogeny is one of the pleasurettes of a creatific thinkerizer. - Peter da Silva [EMAIL PROTECTED] in alt.sysadmin.recovery __ 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] Spearman correlation test confidence intervals
Mahesh Krishnan [EMAIL PROTECTED] writes: Hello, How does one calculate the confidence levels for a spearman correlation test? I noticed cor.test(x,y) gives the confidence levels only for pearson test. Thank you for the suggestions, in advance. You can't. Not easily anyway. The distribution of the Spearman correlation is known under the null hypothesis of independence (through symmetry considerations), but not otherwise. In largish samples, I suppose that resampling techniques could be employed. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert vector to matrix
On Wed, 2006-10-04 at 19:55 -0200, Alberto Monteiro wrote: Gavin Simpson wrote: Did you even try to use cbind on your vector? I guess not as, vec - 1:10 mat - cbind(vec) mat Why does mat remain a matrix instead of losing one dimension? I am reading the FAQ at... http://cran.us.r-project.org/doc/FAQ/R-FAQ.html#Why-do-my-matrices-lose- dimensions_003f ... and it seems that anything you do to mat should turn it back into a one-dimensional vector. Dear Alberto, That FAQ is referring to subsetting a matrix, and as yet, the code above has not subsetted mat at all - indeed, we have only created it and then examined it's class, if we were to now look at rows 2:5, then we'd see that mat loses a dimension and reverts to a vector: vec - 1:10 mat - cbind(vec) mat vec [1,] 1 [2,] 2 [3,] 3 [4,] 4 [5,] 5 [6,] 6 [7,] 7 [8,] 8 [9,] 9 [10,] 10 mat[2:5,] [1] 2 3 4 5 vec[2:5] [1] 2 3 4 5 class(mat[2:5,]) [1] integer class(vec[2:5]) [1] integer all.equal(mat[2:5,], vec[2:5]) [1] TRUE To preserve dimensions, we use drop = FALSE, as discussed in the FAQ you quote: mat[2:5, , drop = FALSE] vec [1,] 2 [2,] 3 [3,] 4 [4,] 5 class(mat[2:5, , drop = FALSE]) [1] matrix HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% *Note new Address and Fax and Telephone numbers from 10th April 2006* %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC [f] +44 (0)20 7679 0565 UCL Department of Geography Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street London, UK[w] http://www.ucl.ac.uk/~ucfagls/cv/ WC1E 6BT [w] http://www.ucl.ac.uk/~ucfagls/ %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] compiling rgdal package on windows / macos
I just tried the PackagesInstall package(s).. menu item on my fresh R-2.4.0-patched and rgdal just shows up on the list of packages to install, so I am not sure what the problem is. Alternatively, you can download the Windows *.zip file from any CRAN repository and install it from your hard drive. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Dylan Beaudette dylan.beaudette@ gmail.com To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] compiling rgdal package on 10/04/2006 05:46 windows / macos PM Please respond to [EMAIL PROTECTED] mail.com Greetings: As I am not a windows user, I cannot try this: is it possible to install rgdal on windows without having to compile it from source ? Compilation on MacOS is within my abilities, however each time i try and install the rgdal package it dies complaining that it cannot find gdal-config --- which was recently installed with GRASS. I have updated my PATH environment variable, logged out, but R still cannot find the gdal-config program. any tips on getting the rgdal package up and running on MacOS or Windows would be greatly appreciated. Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ 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. __ 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] treatment effect at specific time point within mixed effects model
Consider the following modification of your example: fm1a = lme(z ~ (factor(Time)-1)*drug, data = data.grp, random = list(Patient = ~ 1) ) summary(fm1a) snip Value Std.Error DFt-value p-value factor(Time)1 -0.6238472 0.7170161 10 -0.8700602 0.4047 factor(Time)2 -1.0155283 0.7170161 10 -1.4163256 0.1871 factor(Time)30.1446512 0.7170161 10 0.2017405 0.8442 factor(Time)40.7751736 0.7170161 10 1.0811105 0.3050 factor(Time)50.1566588 0.7170161 10 0.2184871 0.8314 factor(Time)60.0616839 0.7170161 10 0.0860286 0.9331 drugP1.2781723 1.0140139 3 1.2605077 0.2966 factor(Time)2:drugP 0.4034690 1.4340322 10 0.2813528 0.7842 factor(Time)3:drugP -0.6754441 1.4340322 10 -0.4710104 0.6477 factor(Time)4:drugP -1.8149720 1.4340322 10 -1.2656424 0.2343 factor(Time)5:drugP -0.6416580 1.4340322 10 -0.4474502 0.6641 factor(Time)6:drugP -2.1396105 1.4340322 10 -1.4920240 0.1666 Does this answer your question? Hope this helps. Spencer Graves Afshartous, David wrote: All, The code below is for a pseudo dataset of repeated measures on patients where there is also a treatment factor called drug. Time is treated as categorical. What code is necessary to test for a treatment effect at a single time point, e.g., time = 3? Does the answer matter if the design is a crossover design, i.e, each patient received drug and placebo? Finally, what would be a good response to someone that suggests to do a simple t-test (paired in crossover case) instead of the test above within a mixed model? thanks! dave z = rnorm(24, mean=0, sd=1) time = rep(1:6, 4) Patient = rep(1:4, each = 6) drug = factor(rep(c(I, P), each = 6, times = 2)) ## P = placebo, I = Ibuprofen dat.new = data.frame(time, drug, z, Patient) data.grp = groupedData(z ~ time | Patient, data = dat.new) fm1 = lme(z ~ factor(time) + drug + factor(time):drug, data = data.grp, random = list(Patient = ~ 1) ) __ 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. __ 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] Suitability of R for Algorithm simulations
[Ethan B. Fini] I would like to be able to instantiate an object for each node in my simulated (stand alone, one computer) distributed environment and then proceed by (a) adding message exchange functionality and (b) algorithm behavior to each node. Not so long ago, I quickly glanced at Eiffel after an enthusiastic friend told me about it, and while I do not think I will soon use it for myself, Eiffel might be the right choice for you, being strong on light-weight processes and message passing, from what I've read... If I had a simulation problem to tackle nowadays, I'd likely consider Python supplemented with greelets from the pylib library, mainly because I'm fond on Python legibility, and have a reasonably good confidence in people having implemented greenlets. The simulation results are represented on a GUI [...] The GUI aspects of Eiffel are unknown to me, I did not dive deep enough to touch them. For Python, I'd use pygtk, but there are many toolkits to choose from. Is R suitable for what I am trying to do? I looked around but have not been able to determine if R is the appropriate platform. R libraries are especially good at statistics and graphics. The language in itself is much oriented towards vectorisation, among other things, and this might be convenient for a speedy implementation of some simulation problems. If vectorisation could not be turned into an advantage for you with R, it is likely that R might be slow for such problems, and also not so well adapted to quasi-parallelism between interacting processes having each their own behaviour. Of course, seasoned R users might have much more sound opinions than mine on this topic! :-) -- François Pinard http://pinard.progiciels-bpi.ca __ 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.
[R] help with script
Hello,
I wrote the function, below, in the hope of _quickly_ generating a
sliding-window time series of the mean, sd, median, and mad values
from a matrix of data. The script below is anything but quick; it has
been working away on a 2500 x 2500 matrix with a sliding window of 100
x 100 for five days, with no end in sight. Obviously, I am not the
best of programmers. Can anyone offer suggestions as to how I might
optimize this script.
Thank you,
John
common.ground-function(inMatrix,window){
cleanMatrix-as.matrix(inMatrix)
diag(cleanMatrix)-NA
outMatrix-matrix(0,dim(inMatrix)[1]-window,4)
colnames(outMatrix)-c(mean,SD, median,mad)
for(i in 1:dim(outMatrix)[1]){
for(j in window:dim(cleanMatrix)[2]){
outMatrix[i,1]-mean(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
outMatrix[i,2]-sd(c(cleanMatrix[c(i:j),c(i:j)]),na.rm=TRUE)
outMatrix[i,3]-median(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
outMatrix[i,4]-mad(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
}
}
return(outMatrix)
}
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Re: [R] help with script
See:
http://tolstoy.newcastle.edu.au/R/help/04/10/5161.html
On 10/4/06, JOHN VOIKLIS [EMAIL PROTECTED] wrote:
Hello,
I wrote the function, below, in the hope of _quickly_ generating a
sliding-window time series of the mean, sd, median, and mad values
from a matrix of data. The script below is anything but quick; it has
been working away on a 2500 x 2500 matrix with a sliding window of 100
x 100 for five days, with no end in sight. Obviously, I am not the
best of programmers. Can anyone offer suggestions as to how I might
optimize this script.
Thank you,
John
common.ground-function(inMatrix,window){
cleanMatrix-as.matrix(inMatrix)
diag(cleanMatrix)-NA
outMatrix-matrix(0,dim(inMatrix)[1]-window,4)
colnames(outMatrix)-c(mean,SD, median,mad)
for(i in 1:dim(outMatrix)[1]){
for(j in window:dim(cleanMatrix)[2]){
outMatrix[i,1]-mean(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
outMatrix[i,2]-sd(c(cleanMatrix[c(i:j),c(i:j)]),na.rm=TRUE)
outMatrix[i,3]-median(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
outMatrix[i,4]-mad(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
}
}
return(outMatrix)
}
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[R] Bug in 2.4.0 Windows menu setup
I've tracked down where this is occurring, but I don't know how to fix it. Here's a summary: If the language in Windows is set to simplified Chinese (i.e. Chinese (PRC)) and message translations are installed, then on startup Rgui crashes when it tries to install the console popup menu. The crash comes when it gets an error trying to do a conversion using mbrtowc, and tries to report it using error(); but the R symbol table is needed for that, and it hasn't been set up yet. I'm not sure which menu entry causes the crash, but I think it's not the first, so conceivably this is caused by an error in one of the translation files. Indeed, setting the language to Chinese (Taiwan) works. I don't know how to debug the translation files, so I'm going to have to leave this one for now. I think Brian Ripley is the only one who understands all the details of what goes on in the translations, and he's away until Oct 9. Duncan Murdoch On 10/3/2006 9:00 PM, ronggui wrote: This morning I downloaded R-2.4.0 and install in under Windows. I customized the installation and choose Message translations,but I could not launch Rgui.exe successfully( Rterm.exe worked fine). If I did't choose Message translations, Rgui.exe worked fine. Message translations is Simplified Chinese. version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) __ 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. __ 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] help with script
Also see package caTools.
On 10/4/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
See:
http://tolstoy.newcastle.edu.au/R/help/04/10/5161.html
On 10/4/06, JOHN VOIKLIS [EMAIL PROTECTED] wrote:
Hello,
I wrote the function, below, in the hope of _quickly_ generating a
sliding-window time series of the mean, sd, median, and mad values
from a matrix of data. The script below is anything but quick; it has
been working away on a 2500 x 2500 matrix with a sliding window of 100
x 100 for five days, with no end in sight. Obviously, I am not the
best of programmers. Can anyone offer suggestions as to how I might
optimize this script.
Thank you,
John
common.ground-function(inMatrix,window){
cleanMatrix-as.matrix(inMatrix)
diag(cleanMatrix)-NA
outMatrix-matrix(0,dim(inMatrix)[1]-window,4)
colnames(outMatrix)-c(mean,SD, median,mad)
for(i in 1:dim(outMatrix)[1]){
for(j in window:dim(cleanMatrix)[2]){
outMatrix[i,1]-mean(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
outMatrix[i,2]-sd(c(cleanMatrix[c(i:j),c(i:j)]),na.rm=TRUE)
outMatrix[i,3]-median(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
outMatrix[i,4]-mad(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
}
}
return(outMatrix)
}
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[R] littler release 0.0.6
What ? -- We are pleased to announce version 0.0.6 of littler What's new ? This version includes a bug fix or two as well as a number of small enhancements to the documentation. For OS X and the r/R confusion, our recommended suggestion is to call configure using either the --program-suffix=X or --program-prefix=Y option to have the binary and manual page renamed when 'make install' runs. In this example, r would be renamed to rX and Yr, resptively. Suitable choices of X and Y are left to the user. Where ? --- You can find the source tarball at both http://dirk.eddelbuettel.com/code/littler/ and http://biostat.mc.vanderbilt.edu/LittleR Comments are welcome, as are are suggestions, bug fixes, or patches. - Jeffrey Horner [EMAIL PROTECTED] - Dirk Eddelbuettel [EMAIL PROTECTED] -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ 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] ciclo for in matrix construction ( matlab - R )
massimodisasha wrote: hi, i'm new to R i have a little script in matlab now i'm porting it to R but i've some problem. how can i write in R language this matlab/octave code: LX = L ; L is a matrix ss = size(LX,1); E_N_2 = zeros(ss,2); for i = 1:ss E_2 = E_0 + LX(i,1)*C(3)+LX(i,2)*C(4); E_0 , C(3), c(4) are costant N_2 = N_0 + LX(i,2)*C(3)-LX(i,1)*C(4); r=[ E_2,N_2]; E_N_2(i,:)=r; end E_N_2 i'm try so : library(matlab) LX - L ss - dim(LX) ss - ss[1] E_N_2 - zeros(ss,2) for(i in 1:ss) . .? thanks for any help :-) Massimo my mayor problem is to know how the cicle for works Perhaps a more important problem is learning how to use matrix algebra. Loops are notoriously slow in R, and worth avoiding in octave as well. E_0 - 12 N_0 - 13 C3 - 21 C4 - 22 L - matrix(c(1,2,3,4,5,6,7,8,9),ncol=3) ss - dim(L)[1] LX - L[1:ss,1:2] C - matrix(c(C3,C4,-C4,C3),ncol=2) EN - matrix(rep(c(E_0,N_0),ss),ncol=2,byrow=TRUE) E_N_2 - EN + LX %*% C E_N_2 -- --- Jeff NewmillerThe . . Go Live... DCN:[EMAIL PROTECTED]Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k __ 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 Graphics: Saving PDF and other formats from Win dows Graphic Device for LaTeX
Thanks. That worked. I am using the following to set-up the device:
pdf(sgr6100.pdf, horizontal=FALSE, onefile=FALSE,
height=3, width=3, pointsize=6)
Reducing point-size below 6 does not seem to make any difference to
the size of text and symbols. Any suggestions to get smaller font sizes?
I am using WinEdt with MikTeX set-up.
Any suggestions about something, or some packages,
that might improve graphics inclusion.
Latex complains about the [scale...] part for any scale in
\includegraphics[scale=1]{}
and pauses. Suggestions will be appreciated about what is the best way to scale
R graphics for inclusion in LaTeX.
Anupam.
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[R] searching for data.frame rows / processing of rows
R 2.3.1, WinXP:
I have a puzzling problem that I suspect may be solved using
grep or a regular expression but am at a loss how to actually do it...
My data.frame looks like
Location TimeXY
--- ---
1 0 1.6 9.3
1 3 4.2 10.4
1 6 2.7 16.3
2 0 0.5 2.1
2 3 NA 3.6
2 3 5.0 0.06
2 6 3.4 14.0
and so forth. I would like to search for duplicate Time values
within a Location and take the numerical average (where possible)
of the elements in X and Y. These numerical averages should
then be used to create a single row where multiple rows once
existed. So, I would like to obtain
2 3 5.0 1.83
for the two Time = 3 rows for Location = 2 and use it to replace
these two rows. Ideally, avoiding for(i in 1:blah) loops would be
nice because the data.frame has about 10,000 rows that need to
be searched and processed. My intent is to do some comparing of
SAS to R -- the DATA step processing in SAS is quite fast and
using the RETAIN statement along with the LAG( ) function allows
this sort of thing to be done rapidly.
Thanks in advance,
Greg
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