[R] Generic distributions
Is there any class that generalizes distributions? For example, I could say x - generic_distribution(normal, list(mean=1, sigma=0.5)) and then use it like rgeneric_distribution(100, x) to get a sample of 100, or pgeneric_distribution(0.5, x) to get the pdf at (x = 0.5). In the openbugs/winbugs package, that uses a language that looks like R/S, we can do things like x ~ dnorm(mu, tau), forget that x is a normal with mean mu and variance 1/tau, and then treat it generically. Alberto Monteiro PS: this is noise... but due to spam invasion, anything that increases the nonspam/spam ratio should be welcome :-) __ 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] Subseting data frame based on column names
Hello all, I have a data frame containing 170 columns and would like to generate a new data frame containing all rows but only 67 columns selected according to column names. How can I do this? Thanks in advance, AG Lee [[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] R and SAS proc format
--- lamack lamack [EMAIL PROTECTED] wrote: Dear all, Is there an R equivalent to SAS's proc format? What does the SAS PROC FORMAT do? __ 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 and SAS proc format
Ulrike Grömping wrote: The down side to R's factor solution: The numerical values of factors are always 1 to number of levels. Thus, it can be tough and requires great care to work with studies that have both numerical values different from this and value labels. This situation is currently not well-supported by R. You can add an attribute to a variable. In the sas.get function in the Hmisc package for example, when importing SAS variables that have PROC FORMAT value labels, an attribute 'sas.codes' keeps the original codes; these can be retrieved using sas.codes(variable name). This could be done outside the SAS import context also. Frank Regards, Ulrike P.S.: I fully agree with Frank regarding the annoyance one sometimes encounters with formats in SAS! lamack lamack wrote: Dear all, Is there an R equivalent to SAS's proc format? Best regards J. Lamack _ O Windows Live Spaces é seu espaço na internet com fotos (500 por mês), blog e agora com rede social http://spaces.live.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. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] Recalling and printing multiple graphs. Is there something in the HISTORY menu that will help?
I am re-sending this Email message as it does not appear to have been received my the R mail list Daemon. My apologies of you receive two copies of this message. If you do, it will mean that the first message finally made it through cyberspace to the list server. I have written an R function that produces multiple graphs. I use par(ask=TRUE) to allow for the inspection of each graph before the next graph is drawn. I am looking for a way to recall all graphs drawn in an R session, and a method that can be used to print all the graphs at one time. I know that I could simply print each graph after I inspect the graph, but this gets tiresome if one's function produces tens of graphs. I suspect that if I knew more about the history menu (which currently has an entry RECORDING) I could get the graphs to be replayed and printed, but alas I have not been able to find instructions for using the HISTORY menu. Please take pity on my when you let me know that some easy search or command could get me the information I needed. I have looked, but clearly in the wrong places. John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition Research Unit, and Baltimore VA Center Stroke of Excellence University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) [EMAIL PROTECTED] Confidentiality Statement: This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. [[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] optim(), nlminb() and starting values
If your problem is small enough just use a grid of starting values and run your optimization on each one and then take the best. On 3/6/07, Dae-Jin Lee [EMAIL PROTECTED] wrote: Hi all ! I've been trying to maximize a likelihood using optim( ) function, but it seems that the function has several local maxima. I've tried in my algorithm with different starting values and depending on them optim obtains different results... I use the L-BFGS-B method setting the lower values as 1e-06, because my parameters must be strictly positive. Also tried a log() transformation to ensure that my parameters are positive. Don't know if this is useful in this case... (also with notLog and notExp functions of mgcv package) the function nlminb( ) also have the same problems. ¿Is there any thing I'm not considering? I mean other methods instead of L-BFGS-B? How can I do to take a strategy to begin with good starting values? Thanks in advance Dae-Jin PS: I'm trying to fit a mixed model with REML and several random effects, so I maximize over several parameters... [[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-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] Obtaining figures with exactly placed points
Dear list, I have to plot some geometrical shape given as list of points. My need is the following: let's say my shape is a 1 inch large square; how can I plot it with R in a graphic format that gives me an image *exactly* 1 inch large? I tried to set oma, mar and fin parameters, but with no success. I'm currently using the xfig driver for the final images are to be included in latex documents, so I can easily add latex mathematical text and other things; however, other formats (pdf, eps) will do. The piece of code: xfig(R2fig.fig) par(mar=c(0,0,0,0),oma=c(0,0,0,0),fin=c(1,1))#no margin, figure dimension 1x1 inch plot(0,0,n,xlim=c(0,1),ylim=c(0,1),axes=F,ann=F) rect(0,0,1,1) dev.off() gives me not what I want: $ cat R2fig.fig #FIG 3.2 Landscape Flush left Inches A4 100.00 Single -2 1200 2 # End of XFig header 2 2 0 1 0 -1 100 0 -1 4.000 0 0 -1 0 0 5 0 0 0 0 0 And this is what it should be (drawn by Xfig itself): $ cat Xfig.fig #FIG 3.2 Landscape Flush left Inches A4 100.00 Single -2 1200 2 2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5 0 0 1200 0 1200 1200 0 1200 0 0 The interesting part is the last line; 1200 is replaced by in the R ouput. Why is the R ouput still scaled? Do I miss some graphic parameter? Any tip is appreciated, marco __ 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] Question about the smooth.Pspline
Xuhong Zhu napsal(a): Hello, Everyone, I want to use the smooth.Pspline to smooth my data but R give me the error message as follows: Error in smooth.Pspline(sort.e$time, sort.e$cuff, method = 3) : X not strictly increasing my data looks like the following: id cuff time patient ... 2783 13.229608 478 6 3472 20.904825 478 7 4155 15.033727 478 8 4845 19.342963 478 9 715 8.00 479 3 1422 22.052385 479 4 2110 15.393063 479 5 2784 13.200922 479 6 3473 20.900132 479 7 ... my R codes is: e - rbind(patient.1,patient.2,patient.3,...) attach(e) sort.e - e[order(time),] plot(sort.e$time, sort.e$cuff, xlab=Time, ylab=Cuff,type=p, col=3, xlim=c(c[2],d[2]) , ylim=c(c[1], d[1]) , main=one Smooth Curve for 10 Patients) fm - smooth.Pspline(sort.e$time, sort.e$cuff, method=3) lines(fm$x, fm$y, lty=1,col=1) What I am doing here is to combine the data together and find a smooth curve. My question is if the smooth.Pspline could not be used in my data since the variable time has repeated values. Quoted from your error message: Error in smooth.Pspline(sort.e$time, sort.e$cuff, method = 3) : X not strictly increasing Quoted from help of smooth.Pspline (which, as you should have told us by the way, is contained in package pspline): Arguments: x values of the predictor variable. These must be strictly increasing, and there must be at least 2*norder + 1 of them. sm.spline provides a simplified interface, in which the x values can be unsorted, or a list with components x and y or a two-column matrix or a complex vector. Strictly increasing = no repeated values... Petr Xuhong __ 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 Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ 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] qr decomposition issue inside lm
Dear list, It's never happened to me before in such a simple exercise but is not going away and I've checked my data are good. I want a simple lm model with one response and one predictor, where N is about 4,200 * data set not exactly small. Both x and y are nice, continuous variables having NA filtered out with a call to na.omit. So I did mod = lm( y ~ x, data=x1) Then the error, Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in foreign function call (arg 4) I did a trace back and it turned out it's an error thrown by the Fortran subroutine that seems to be trying a QR decomposition, traceback() 3: .Fortran(dqrls, qr = x, n = n, p = p, y = y, ny = ny, tol = as.double(tol), coefficients = mat.or.vec(p, ny), residuals = y, effects = y, rank = integer(1), pivot = 1:p, qraux = double(p), work = double(2 * p), PACKAGE = base) 2: lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) 1: lm(log.p.sales ~ log.mktcap, data = x1) My question is why would QR fail since the default in lm.fit is 'singular.ok' ? Furthermore, is there a way to get around presumably a singularity in my design matrix? Thanks in advance. Horace W. Tso __ 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] Memory Limits in Ubuntu Linux
[EMAIL PROTECTED] wrote: I am an R user trying to get around the 2Gig memory limit in Windows, so here I am days later with a working Ubuntu, and R under Ubuntu. But - the memory problems seem worse than ever. R code that worked under windows fails, unable to allocate memory. Searching around the web, it appears that the problem may be the ability to find contguous memory for my big vectors, but a fresh boot of Ubuntu does not help either. Which way to go? 1) Try to install 64-bit version for bigger address space. Would this help? Is this workable for my Athlon 64 Dual-core? (the live cd seems to work but I never got it to boot after a disk install, but then the 386 version was no better until I learned more about Grub...I could try again if this might solve the problem) If you really have got such amounts of RAM in that machine, it should be worth trying. Uwe Ligges 2) Recompile R to get bigger memory capability? (I'll have to cross-post to some R forums too) This will be a challenge for a Linux newbie...like me. 3) Any other suggestions? My goal is to create a bigger neural network than fits in my Windows R version. __ 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] Subseting data frame based on column names
Li, Aiguo (NIH/NCI) [C] wrote: Hello all, I have a data frame containing 170 columns and would like to generate a new data frame containing all rows but only 67 columns selected according to column names. How can I do this? For date.frame d and column names in vector cn: d[,cn] Uwe Ligges Thanks in advance, AG Lee [[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-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] Substituting functions in package - Lattice
Hi, I'm trying to learn how a package works but substituting a parituclart function with my own (basically the original one with some debug statements). The package is lattice and the method is print.trellis which is a S3 method and is not visible. To replace this, i sourced a file with the rewritten print.trellis, and the old one was replaced. However, i get this error when I attempt to print a trellis object (e.g an xyplot) Error in assign(last.object, x, env = .LatticeEnv) : object .LatticeEnv not found I notice that .LatticeEnv is defined in zzz.R (in the R folder of the lattice source). My question, how does one do development on the lattice package without having to recompile everything and install a package? I read something about emacs and development (i use emacs) in the zzz.R file ## .First.lib will be used if the NAMESPACE file is missing. This is ## useful during development, thanks to C-c C-l in Emacs/ESS. It won't ## be used if a NAMESPACE file is present. Note: Due to registration ## of C functions done in the NAMESPACE file, wireframe (and possibly ## cloud) won't work in this scenario. But couldn't quite figure it out. Thanks for any help provided. Saptarshi Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha [[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] Generate random numbers up to one
On 06-Mar-07 Alberto Monteiro wrote: Ted Harding wrote: And, specifically (to take just 2 RVs X and Y), while U = X/(X+Y) and V = Y/(A+Y) are two RVs which summ to 1, the distribution of U is not the same as the distribution of X conditional on (X+Y = 1). This question Which question? There are (implicitly) two questions there! appeared in October 2006, and the answer To the second question (X conditional on X+Y=1) was the Dirichlet distribution with parameters (1,1,1...1): http://en.wikipedia.org/wiki/Dirichlet_distribution It's the distribution of uniform U1, U2, ... Un with the restriction that U1 + U2 + ... + Un = 1. Indeed, and the resulting (U1,U2,...,Un) is uniformly distributed on the simplex U1+U2+...+Un=1. For n2, however, the resulting marginal distribution of (say) U1 conditional on (U1+U2+...+Un=1) is no longer uniform (that only holds for n=2, as in my example). For n=3 this is easy to see: P[U1 u1] is the area of the triangular simplex between its vertex at (1,0,0) and the line from (u1,1-u1,0) to (u1,0,0), and this is equal to (1 - u1)^2, so the density of U1 is f(u1) = 2*(1-u1). In general, the marginal density of U1 in the n-dimensional Dirichlet is (n-1)*(1-u1)^(n-2). But the aim was to illustrate Petr Klasterecky's point that sum(x) is a random variable as well and dividing by sum(x) does not preserve the original distribution data were generated from. namely to show two ways of generating RVs distributed on U1 + U2 + ... + Un = 1, starting from independent RVs, which result on two different distributions, and to give an example where dividing by sum(x) can be seen to not preserve the distribution. Indeed, I think there is sometimes a confusion between this question and the really unrelated question: Given non-negative numbers V1, V2, ..., Vn, how can we convert then to a probability distribution? To which the answer is, of course, divide by their sum. With best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 06-Mar-07 Time: 22:01:34 -- XFMail -- __ 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] Generic distributions
I think the distr package does this. There are also packages that link to winbugs if that is what you really want to do. -- 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 Alberto Monteiro Sent: Tuesday, March 06, 2007 1:38 PM To: r-help@stat.math.ethz.ch Subject: [R] Generic distributions Is there any class that generalizes distributions? For example, I could say x - generic_distribution(normal, list(mean=1, sigma=0.5)) and then use it like rgeneric_distribution(100, x) to get a sample of 100, or pgeneric_distribution(0.5, x) to get the pdf at (x = 0.5). In the openbugs/winbugs package, that uses a language that looks like R/S, we can do things like x ~ dnorm(mu, tau), forget that x is a normal with mean mu and variance 1/tau, and then treat it generically. Alberto Monteiro PS: this is noise... but due to spam invasion, anything that increases the nonspam/spam ratio should be welcome :-) __ 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] Stangle and annotate
How exactly should I go about turning off annotation when running Stangle (Rtangle) with R CMD Stangle myfile.Rnw? Ideally I would like to be able to turn annotation off and on for individual code chunks, or maybe better, to annotate only named chunks. Are either of these things easily done? Is there some way to figure out this sort of thing without reading through the source code in Sweave.R? -- Brett Presnell Department of Statistics University of Florida __ 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] Recalling and printing multiple graphs. Is there something in the HISTORY menu that will help?
John Sorkin [EMAIL PROTECTED] wrote: I have written an R function that produces multiple graphs. I use par(ask=TRUE) to allow for the inspection of each graph before the next graph is drawn. I am looking for a way to recall all graphs drawn in an R session, and a method that can be used to print all the graphs at one time. I know that I could simply print each graph after I inspect the graph, but this gets tiresome if one's function produces tens of graphs. I suspect that if I knew more about the history menu (which currently has an entry RECORDING) I could get the graphs to be replayed and printed, but alas I have not been able to find instructions for using the HISTORY menu. Please take pity on my when you let me know that some easy search or command could get me the information I needed. I have looked, but clearly in the wrong places. John Sorkin M.D., Ph.D. I assume you are on Windows (please give OS and R version in future help requests). The code I use before starting such functions is graphics.off() windows(record=TRUE) .SavedPlots - NULL which closes existing graphics devices, opens a windows device with recording on, and deletes any existing graphics history. You can go through the history with PageUp and PageDown keys. Within your function, you can call savePlot (q.v.) to save each plot to a file just after it is generated. HTH -- Mike Prager, NOAA, Beaufort, NC * Opinions expressed are personal and not represented otherwise. * Any use of tradenames does not constitute a NOAA endorsement. __ 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] Memory Limits in Ubuntu Linux
Take a look at Windows FAQ 2.9. Following the instructions there, I was able to make WinXP use at least 3GB of RAM (physical RAM installed) with Rgui.exe. -Christos Christos Hatzis, Ph.D. Nuvera Biosciences, Inc. 400 West Cummings Park Suite 5350 Woburn, MA 01801 Tel: 781-938-3830 www.nuverabio.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, March 06, 2007 3:44 PM To: r-help@stat.math.ethz.ch Subject: [R] Memory Limits in Ubuntu Linux I am an R user trying to get around the 2Gig memory limit in Windows, so here I am days later with a working Ubuntu, and R under Ubuntu. But - the memory problems seem worse than ever. R code that worked under windows fails, unable to allocate memory. Searching around the web, it appears that the problem may be the ability to find contguous memory for my big vectors, but a fresh boot of Ubuntu does not help either. Which way to go? 1) Try to install 64-bit version for bigger address space. Would this help? Is this workable for my Athlon 64 Dual-core? (the live cd seems to work but I never got it to boot after a disk install, but then the 386 version was no better until I learned more about Grub...I could try again if this might solve the problem) 2) Recompile R to get bigger memory capability? (I'll have to cross-post to some R forums too) This will be a challenge for a Linux newbie...like me. 3) Any other suggestions? My goal is to create a bigger neural network than fits in my Windows R version. -- David Katz www.davidkatzconsulting.com 541 482-1137 [[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-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] Obtaining figures with exactly placed points
plot(0,0,n,xlim=c(0,1),ylim=c(0,1),axes=F,ann=F,xaxs='i',yaxs='i') It was exactly this! *8/100+ [1] 1199.88 Thanks, Marco __ 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] Subseting data frame based on column names
Use the subset function and the select argument of that function to specify the columns. -- 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 Li, Aiguo (NIH/NCI) [C] Sent: Tuesday, March 06, 2007 2:02 PM To: r-help@stat.math.ethz.ch Subject: [R] Subseting data frame based on column names Hello all, I have a data frame containing 170 columns and would like to generate a new data frame containing all rows but only 67 columns selected according to column names. How can I do this? Thanks in advance, AG Lee [[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-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] Obtaining figures with exactly placed points
Try: plot(0,0,n,xlim=c(0,1),ylim=c(0,1),axes=F,ann=F,xaxs='i',yaxs='i') To see if that fixes it for you (without the xaxs and yaxs arguments it adds 4% of the range to each side so that any points plotted do not fall to close to the axes. 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 Scionforbai Sent: Tuesday, March 06, 2007 2:42 PM To: r-help@stat.math.ethz.ch Subject: [R] Obtaining figures with exactly placed points Dear list, I have to plot some geometrical shape given as list of points. My need is the following: let's say my shape is a 1 inch large square; how can I plot it with R in a graphic format that gives me an image *exactly* 1 inch large? I tried to set oma, mar and fin parameters, but with no success. I'm currently using the xfig driver for the final images are to be included in latex documents, so I can easily add latex mathematical text and other things; however, other formats (pdf, eps) will do. The piece of code: xfig(R2fig.fig) par(mar=c(0,0,0,0),oma=c(0,0,0,0),fin=c(1,1))#no margin, figure dimension 1x1 inch plot(0,0,n,xlim=c(0,1),ylim=c(0,1),axes=F,ann=F) rect(0,0,1,1) dev.off() gives me not what I want: $ cat R2fig.fig #FIG 3.2 Landscape Flush left Inches A4 100.00 Single -2 1200 2 # End of XFig header 2 2 0 1 0 -1 100 0 -1 4.000 0 0 -1 0 0 5 0 0 0 0 0 And this is what it should be (drawn by Xfig itself): $ cat Xfig.fig #FIG 3.2 Landscape Flush left Inches A4 100.00 Single -2 1200 2 2 2 0 1 0 7 50 -1 -1 0.000 0 0 -1 0 0 5 0 0 1200 0 1200 1200 0 1200 0 0 The interesting part is the last line; 1200 is replaced by in the R ouput. Why is the R ouput still scaled? Do I miss some graphic parameter? Any tip is appreciated, marco __ 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] Substituting functions in package - Lattice
You need to set the environment on your version of print.trellis to match that of the original (at least that is what has worked for me when trying to do modified functions from the trellis package). Try something like: environment(print.trellis) - environment(lattice::print.trellis) 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 Saptarshi Guha Sent: Tuesday, March 06, 2007 2:55 PM To: R-Help Subject: [R] Substituting functions in package - Lattice Hi, I'm trying to learn how a package works but substituting a parituclart function with my own (basically the original one with some debug statements). The package is lattice and the method is print.trellis which is a S3 method and is not visible. To replace this, i sourced a file with the rewritten print.trellis, and the old one was replaced. However, i get this error when I attempt to print a trellis object (e.g an xyplot) Error in assign(last.object, x, env = .LatticeEnv) : object .LatticeEnv not found I notice that .LatticeEnv is defined in zzz.R (in the R folder of the lattice source). My question, how does one do development on the lattice package without having to recompile everything and install a package? I read something about emacs and development (i use emacs) in the zzz.R file ## .First.lib will be used if the NAMESPACE file is missing. This is ## useful during development, thanks to C-c C-l in Emacs/ESS. It won't ## be used if a NAMESPACE file is present. Note: Due to registration ## of C functions done in the NAMESPACE file, wireframe (and possibly ## cloud) won't work in this scenario. But couldn't quite figure it out. Thanks for any help provided. Saptarshi Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha [[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-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] Substituting functions in package - Lattice
Hi, Unfortunately, print.trellis is not exported . environment(print.trellis) - environment(lattice::print.trellis) returns Error: 'print.trellis' is not an exported object from 'namespace:lattice' I then took the environment of lattice search() #package:lattice is the 2nd element latt-as.environment(2) environment(print.trellis)-latt Yet, i get the same error as before when I run print(k), where k is a trellis object. This is the line in NAMESPACE for lattice (from the source) S3method(print,trellis) Thanks Saptarshi Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha On Mar 6, 2007, at 5:29 PM, Greg Snow wrote: You need to set the environment on your version of print.trellis to match that of the original (at least that is what has worked for me when trying to do modified functions from the trellis package). Try something like: environment(print.trellis) - environment(lattice::print.trellis) 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 Saptarshi Guha Sent: Tuesday, March 06, 2007 2:55 PM To: R-Help Subject: [R] Substituting functions in package - Lattice Hi, I'm trying to learn how a package works but substituting a parituclart function with my own (basically the original one with some debug statements). The package is lattice and the method is print.trellis which is a S3 method and is not visible. To replace this, i sourced a file with the rewritten print.trellis, and the old one was replaced. However, i get this error when I attempt to print a trellis object (e.g an xyplot) Error in assign(last.object, x, env = .LatticeEnv) : object .LatticeEnv not found I notice that .LatticeEnv is defined in zzz.R (in the R folder of the lattice source). My question, how does one do development on the lattice package without having to recompile everything and install a package? I read something about emacs and development (i use emacs) in the zzz.R file ## .First.lib will be used if the NAMESPACE file is missing. This is ## useful during development, thanks to C-c C-l in Emacs/ESS. It won't ## be used if a NAMESPACE file is present. Note: Due to registration ## of C functions done in the NAMESPACE file, wireframe (and possibly ## cloud) won't work in this scenario. But couldn't quite figure it out. Thanks for any help provided. Saptarshi Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha [[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-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] qr decomposition issue inside lm (solved)
Folks, apologize for such an obvious oversight on my part. The reason qr fails is, one of the data points has value of -Inf (response is actually the log of something, and I have a zero in the original set). That explains the error message in call to dqrls. I should have taken the mean of the response before proceeding and that would tell me right away what's wrong. Thanks. H. Horace Tso [EMAIL PROTECTED] 3/6/2007 1:45:28 PM Dear list, It's never happened to me before in such a simple exercise but is not going away and I've checked my data are good. I want a simple lm model with one response and one predictor, where N is about 4,200 * data set not exactly small. Both x and y are nice, continuous variables having NA filtered out with a call to na.omit. So I did mod = lm( y ~ x, data=x1) Then the error, Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : NA/NaN/Inf in foreign function call (arg 4) I did a trace back and it turned out it's an error thrown by the Fortran subroutine that seems to be trying a QR decomposition, traceback() 3: .Fortran(dqrls, qr = x, n = n, p = p, y = y, ny = ny, tol = as.double(tol), coefficients = mat.or.vec(p, ny), residuals = y, effects = y, rank = integer(1), pivot = 1:p, qraux = double(p), work = double(2 * p), PACKAGE = base) 2: lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) 1: lm(log.p.sales ~ log.mktcap, data = x1) My question is why would QR fail since the default in lm.fit is 'singular.ok' ? Furthermore, is there a way to get around presumably a singularity in my design matrix? Thanks in advance. Horace W. Tso __ 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] Substituting functions in package - Lattice
Hi, Got it. This worked environment(print.trellis) - getNamespace(lattice) where print.trellis is my modified print.trellis. Thanks. Regards Saptarshi Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha On Mar 6, 2007, at 5:29 PM, Greg Snow wrote: You need to set the environment on your version of print.trellis to match that of the original (at least that is what has worked for me when trying to do modified functions from the trellis package). Try something like: environment(print.trellis) - environment(lattice::print.trellis) 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 Saptarshi Guha Sent: Tuesday, March 06, 2007 2:55 PM To: R-Help Subject: [R] Substituting functions in package - Lattice Hi, I'm trying to learn how a package works but substituting a parituclart function with my own (basically the original one with some debug statements). The package is lattice and the method is print.trellis which is a S3 method and is not visible. To replace this, i sourced a file with the rewritten print.trellis, and the old one was replaced. However, i get this error when I attempt to print a trellis object (e.g an xyplot) Error in assign(last.object, x, env = .LatticeEnv) : object .LatticeEnv not found I notice that .LatticeEnv is defined in zzz.R (in the R folder of the lattice source). My question, how does one do development on the lattice package without having to recompile everything and install a package? I read something about emacs and development (i use emacs) in the zzz.R file ## .First.lib will be used if the NAMESPACE file is missing. This is ## useful during development, thanks to C-c C-l in Emacs/ESS. It won't ## be used if a NAMESPACE file is present. Note: Due to registration ## of C functions done in the NAMESPACE file, wireframe (and possibly ## cloud) won't work in this scenario. But couldn't quite figure it out. Thanks for any help provided. Saptarshi Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha [[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-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] Stangle and annotate
On 3/6/2007 5:20 PM, Brett Presnell wrote:
How exactly should I go about turning off annotation when running
Stangle (Rtangle) with R CMD Stangle myfile.Rnw?
Ideally I would like to be able to turn annotation off and on for
individual code chunks, or maybe better, to annotate only named
chunks. Are either of these things easily done?
Is there some way to figure out this sort of thing without reading
through the source code in Sweave.R?
I don't think R CMD Stangle has a way to pay attention to optional args
to Stangle, but this works:
echo Stangle('myfile.Rnw', annotate=F) | Rterm --slave
Duncan Murdoch
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Re: [R] R and SAS proc format
- Original Message - From: John Kane [EMAIL PROTECTED] To: lamack lamack [EMAIL PROTECTED]; R-help@stat.math.ethz.ch Sent: Tuesday, March 06, 2007 2:13 PM Subject: Re: [R] R and SAS proc format --- lamack lamack [EMAIL PROTECTED] wrote: Dear all, Is there an R equivalent to SAS's proc format? What does the SAS PROC FORMAT do? It formats or reformats data in the SAS system. It looks this: proc format; value kanefmt 1='A' 2='B' 3='C' 4='X' 5='Throw me out'; data temp; do i=1 to 10; kanevar=put(i,kanefmt.); output; end; proc print; run; And produces this: Obs i kanevar 1 1A 2 2B 3 3C 4 4X 5 5Throw me out 6 6 6 7 7 7 8 8 8 9 9 9 1010 10 But it is more robust than what is shown here. __ 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] Waiting for Key input
Hi, I have another question. Is there any command that waits for key input? I am running R on OS X, so getGraphicsEvents doesn't work. I have put some debug print messages in a function and would like to pause the code every time the message is printed and continue on a keypress. Thank you Saptarshi Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha [[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] Question
How can I evaluate two or more expressions to return two or more columns? eval(expression(with(bd,Var1*100),with(bd,Var2*200))) The execution is always for the last expression. I can't execute the two expressions at the same time. It is possible? How about something like this with(bd, c(Var1 * 100, Var2 * 200)) _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ 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] Estimating parameters of 2 phase Coxian using optim
Andy Fugard wrote:
Hi There,
Perhaps the problem is the line
loglik-log(p %*% expm(Q * y(i)) %*% q)
You mention that y is a vector but here you're treating it as a
function. Maybe try
loglik-log(p %*% expm(Q * y[i]) %*% q)
?
Don't have a clue about the correctness of the contents of cox2.lik...
Andy
On 6 Mar 2007, at 08:54, Laura Hill wrote:
Hi,
My name is Laura. I'm a PhD student at Queen's University Belfast
and have
just started learning R. I was wondering if somebody could help me
to see
where I am going wrong in my code for estimating the parameters
[mu1, mu2,
lambda1] of a 2-phase Coxian Distribution.
cox2.lik-function(theta, y){
mu1-theta[1]
mu2-theta[2]
lambda1-theta[3]
p-Matrix(c(1, 0), nrow=1, ncol=2)
Q-Matrix(c(-(lambda1 + mu1), 0, lambda1, -mu2), nrow=2, ncol=2)
q-Matrix(c(mu1, mu2), nrow=2, ncol=1)
for (i in 1:length(y)){
loglik-log(p %*% expm(Q * y(i)) %*% q)
return(loglik)}
sumloglik-sum(loglik)
return(-sumloglik)
}
Just to add my 2 AU cents regarding the for loop:
You're trying to create a vector of log likelihoods to sum up later, but
that's not what's happening there. Instead, assign an empty vector of
same length as y, then assign the loglik from each iteration to a
different cell.
Lastly, there's no need to return anything from a for loop, it's not a
function.
HTH,
Gad
--
Gad Abraham
Department of Mathematics and Statistics
The University of Melbourne
Parkville 3010, Victoria, Australia
email: [EMAIL PROTECTED]
web: http://www.ms.unimelb.edu.au/~gabraham
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Re: [R] R plug in for Eclipse
Hi Dominik, Yes, I am currently running Version: 3.2.2 Build id: M20070212-1330 From: Dominik Holenstein [EMAIL PROTECTED] To: Harry Ho [EMAIL PROTECTED] Subject: Re: [R] R plug in for Eclipse Date: Tue, 6 Mar 2007 23:00:29 +0100 Hi, Are you using Eclipse 3.2? semanticum 2007/3/6, Harry Ho [EMAIL PROTECTED]: Hello, Is there any R plug-in available for Eclipse other than StatET? StatET doesn't seem to work with the latest release of Eclipse properly, i.e. syntax highlighting isn't enabled for R commands. I already contacted the author some time ago, but have not yet received a response. Would also be great if somebody could tell me whether they have the same problem. I already tried installing it on two different machines so I guess it isn't a local problem, but you never know... Thx a lot _ Sie suchen E-Mails, Dokumente oder Fotos? Die neue MSN Suche Toolbar mit Windows-Desktopsuche liefert in sekundenschnelle Ergebnisse. Jetzt neu! __ 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. _ Sie suchen E-Mails, Dokumente oder Fotos? Die neue MSN Suche Toolbar mit Windows-Desktopsuche liefert in sekundenschnelle Ergebnisse. Jetzt neu! __ 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] Off topic:Spam on R-help increase?
On Tue, 2007-03-06 at 12:36 -0600, Douglas Bates wrote: On 3/6/07, Peter Dalgaard [EMAIL PROTECTED] wrote: Bert Gunter wrote: Folks: In the past 2 days I have seen a large increase of spam getting into R-help. Are others experiencing this problem? If so, has there been some change to the spam filters on the R-servers? If not, is the problem on my end? Feel free to reply privately. Martin Maechler is still walking about upside-down after the DSC, slated to return on March 8 (plus presumably a day or two to recover from the flight...). Actually he is walking around sideways at present. He's in Dubai, not New Zealand. LOLand hopefully having a great time. It is at times like these, as Uwe noted, where it becomes clear the extent and results of Martin's efforts in filtering this stuff from the lists. Martin deserves a hearty Well Done! for managing this great resource in a superior fashion. Regards, Marc __ 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] Memory Limits in Ubuntu Linux
On 6 March 2007 at 12:43, [EMAIL PROTECTED] wrote: | I am an R user trying to get around the 2Gig memory limit in Windows, so The real limit on 32bit systems is a 3gb address space. R under Windows can get there, see the R-Windows FAQ. | here I am days later with a working Ubuntu, and R under Ubuntu. But - the | memory problems seem worse than ever. R code that worked under | windows fails, unable to allocate memory. Well, maybe you had virtual memory enabled under Windows but not under Ubuntu. Or maybe you had other memory-hungry applications up under Ubuntu. There is only so much magic the OS can do. You easiest remedy will be to upgrade to 4gb. And even 8gb can useful on 32bit system, despite the fact that each individual address space can only max out at 3gb, as you may have multi-core / multi-cpu systems that allow you to multitask better. | Which way to go? | | 1) Try to install 64-bit version for bigger address space. Would this help? Yes, but you'd probably would have to buy more ram to. The main advantage is that your limit is now way above the 3gb -- and probably set by your hardware or budget. Maybe it is as high as 16gb. But again, on the _same_ box with the _same_ amount of ram that is already constrained under 32bit, you will not see any improvement. Rather the opposite as the basic building block is now 8 bytes instead of 4, you will need more memory for the same tasks. No free lunch, as they say. | 2) Recompile R to get bigger memory capability? Nope. It's what you give your OS in terms of RAM what's binding here. | 3) Any other suggestions? Different algorithms or approaches, tricks like the data.frame-in-sqlite or biglm, ... Dirk -- 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.
[R] Sigmoidal Fitting
I want to thank professor Tura for his help but the function in some cases fails to converge and I am not able to understand the reason : GAS [1] 0.8108649 1.0386906 1.1638837 2.4144286 PRESSURE [1] 0 5 15 45 model.1 - nls(GAS_PER_G ~ SSlogis(PRESSURE, ASym, xmid, scal)) model.1 - nls(GAS_PER_G ~ SSlogis(PRESSURE, ASym, xmid, scal)) Error in nls(y ~ 1/(1 + exp((xmid - x)/scal)), data = xy, start = list(xmid = aux[1], : step factor 0.000488281 reduced below 'minFactor' of 0.000976562 Massimo Cressoni __ 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] Sweave issue: quotes in verbatim-like output print incorrectly
Hi all
I love Sweave; use it all the time.
But I recently received a new computer, and ever since I
have had a problem I've never seen before.
For example, I place the following in my Snw file:
=
sms -
read.table(http://www.sci.usq.edu.au/staff/dunn/Datasets/applications/popular/smsspeed.dat;,
header=TRUE)
attach(sms)
sms.lm - lm( Time ~ Age*Phone, subset=(Age30) )
summary(sms.lm)
@
Standard stuff. The output appears in the corresponding LaTeX
file as it should, in a verbatim-like environment as it should.
But since I have had this new machine, this line of output:
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
appears in my resulting pdf document as
Signif. codes: 0 ^a˘A¨Y***^a˘A´Z0.001 ^a˘A¨Y**^a˘A´Z0.01 ^a˘A¨Y*^a
˘A´Z0.05 ^a˘A¨Y.^a˘A´Z0.1 ^a˘A¨Y^a˘A´Z1
In short, every quote is replaced by garbage. This makes my
output looks incredibly bad. (This is true for all cases; the above
is the output from my example.)
I also imagine (hope!) there is a very simple fix. Can anyone help me?
Documents which used to produce the correct output document
now do this, so it must be something to do with my machine
set up, or R set up, rather than the documents themselves, I guess.
Any help appreciated. I have no idea where to look for the solution
(the FAQ. manuals and mailing archives were no help that I could see;
happy to be corrected).
P.
version
_
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status Patched
major 2
minor 4.0
year 2006
month 11
day25
svn rev39997
language R
version.string R version 2.4.0 Patched (2006-11-25 r39997)
sessionInfo()
R version 2.4.0 Patched (2006-11-25 r39997)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=en_AU.UTF-8;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
--
Dr Peter Dunn | dunn at usq.edu.au
Faculty of Sciences, USQ; http://www.sci.usq.edu.au/staff/dunn
Aust. Centre for Sustainable Catchments: www.usq.edu.au/acsc
This email (including any attached files) is confidential an...{{dropped}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Waiting for Key input
?browser ?readline Petr Saptarshi Guha napsal(a): Hi, I have another question. Is there any command that waits for key input? I am running R on OS X, so getGraphicsEvents doesn't work. I have put some debug print messages in a function and would like to pause the code every time the message is printed and continue on a keypress. Thank you Saptarshi Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha [[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. -- Petr Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ 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] Generic distributions
Hello Alberto, hello Greg, in distr you can do: library(distr) N - Norm(mean = 1, sd = 2) p(N)(0.5) r(N)(100) !!! not: p(N, 0.5) or r(N, 100) !!! A detailed description of package distr is given in package distrDoc. library(distrDoc) vignette(distr) hth Matthias - original message Subject: Re: [R] Generic distributions Sent: Tue, 06 Mar 2007 From: Greg Snow[EMAIL PROTECTED] I think the distr package does this. There are also packages that link to winbugs if that is what you really want to do. -- 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 Alberto Monteiro Sent: Tuesday, March 06, 2007 1:38 PM To: r-help@stat.math.ethz.ch Subject: [R] Generic distributions Is there any class that generalizes distributions? For example, I could say x - generic_distribution(normal, list(mean=1, sigma=0.5)) and then use it like rgeneric_distribution(100, x) to get a sample of 100, or pgeneric_distribution(0.5, x) to get the pdf at (x = 0.5). In the openbugs/winbugs package, that uses a language that looks like R/S, we can do things like x ~ dnorm(mu, tau), forget that x is a normal with mean mu and variance 1/tau, and then treat it generically. Alberto Monteiro PS: this is noise... but due to spam invasion, anything that increases the nonspam/spam ratio should be welcome :-) __ 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. --- original message end __ 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] Autogenerate tags in tag=value pairs for
Dear list,
Is there a way to programmatically specify tag names for the ... (ellipsis)
part of the argument list to a function? In other words, a way to do this:
x - data.frame(A=1:5)
if the name A was not hardcoded but given by a variable, and without
resorting to:
x - data.frame(1:5)
names(x) - A
A longer example describing my actual problem follows. Thanks in advance for
any help.
Best regards,
Jon Olav
I want to use function transformBy() in package doBy. The key is that the ...
Further arguments of the form tag=value require tag to be specified,
otherwise the output does not include the results of my groupwise calculations.
Quoting the documentation:
transformBy(doBy)
Function to make groupwise transformations of data
by applying the transform function to subsets of data.
Usage
transformBy(formula, data, ...)
Arguments
formula A formula with only a right hand side, see examples below
data A data frame
... Further arguments of the form tag=value
### example ###
# a function to replace NAs with the last non-NA value from above
filldown - function(x) {
notna - !is.na(x) # elements with values
ix - cumsum(notna) # index to previous element (but zeros where we need NA)
ix[ix==0] - NA # use [NA] as index to produce NA in output
return(x[notna][ix]) # for each: return previous value if found, else NA
}
# illustration of how it works
tmp - c(NA,NA,1,NA,3,NA,NA)
cbind(tmp,filldown(tmp))
# I now want to apply filldown() to subsets of a data frame
# and I want it to work on several columns
# generate a data frame for illustration,
# with a few non-NA values scattered round
set.seed(5) # repeatable example
x - data.frame(id = rep(1:4,each=6), v1=NA, v2=NA)
ix - which(runif(nrow(x))0.75)
x[ix,2] - rpois(length(ix),5)
ix - which(runif(nrow(x))0.75)
x[ix,3] - rpois(length(ix),5)
x
library(doBy)
# the hard way -- works as required,
# but I would like not having to hardcode column names v1 etc.
transformBy(~id,data=x,v1.fd = filldown(v1),v2.fd = filldown(v2))
# does not work because
# output includes only columns explicitly mentioned in the ... argument
transformBy(~id,data=x,function(y) lapply(y,filldown))
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