Re: [R] [friday topic]: what exactly is statistical computing
This is indeed a "Friday" topic. I think I understand the difficulty that Wensui has. I teach two classes, each with the phrase "statistical computing" in the title, and yet they cover completely different topics. -roger Wensui Liu wrote: > Thanks for your insight, Roger. > > Actually, my question is not related to R only. > > statistical computing is a popular topic recently. However, when I > check its meaning on wikipedia/google, I couldn't find it. > > another reason why I asked is related to myself. I am very interested > in this area and maintaining a blog in this topic. however, when asked > what 'statistical computing' is, I am not able to give a > well-verbalized answer. > > > On 3/2/07, Bos, Roger <[EMAIL PROTECTED]> wrote: >> This means it comes with substantial statistical routines built-in. You >> could just as well use VBA or Java for your programming language, but >> with those you would have to write pretty much any stat routine you >> need. With R, since it is a 'statistical computing' language, you know >> that most of what you need has already been programmed, tested(?), and >> is ready to use. >> >> I have seen you on this list for a while. You already know all this. I >> am not sure why you are asking this question. >> >> Roger >> >> -Original Message- >> From: [EMAIL PROTECTED] >> [mailto:[EMAIL PROTECTED] On Behalf Of Wensui Liu >> Sent: Friday, March 02, 2007 9:43 AM >> To: r-help@stat.math.ethz.ch >> Subject: [R] [friday topic]: what exactly is statistical computing >> >> Dear List, >> on www.r-project.org, the title says 'The R Project for Statistical >> Computing'. >> >> but what exactly is the definition of statistical computing? >> >> __ >> 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. >> >> ** * >> This message is for the named person's use only. It may >> contain confidential, proprietary or legally privileged >> information. No right to confidential or privileged treatment >> of this message is waived or lost by any error in >> transmission. If you have received this message in error, >> please immediately notify the sender by e-mail, >> delete the message and all copies from your system and destroy >> any hard copies. You must not, directly or indirectly, use, >> disclose, distribute, print or copy any part of this message >> if you are not the intended recipient. >> ** >> > > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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 File IO Slow?
A 27MB .RData file is relatively big, in may experience. What do you think is slow? Maybe it's your computer that is slow? -roger ramzi abboud wrote: > Is R file IO slow in general or am I missing > something? It takes me 5 minutes to do a load(MYFILE) > where MYFILE is a 27 MB Rdata file. Is there any way > to speed this up? > > The one idea I have is having R call a C or Perl > routine, reading the file in that language, converting > the data in to R objects, then sending them back into > R. This is more work that I want to do, however, in > loading Rdata files. > > Any ideas would be appreciated. > Ramzi Aboud > University of Rochester > > > > > > > > Need Mail bonding? > > __ > 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. > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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] Large data Problem
For a CSV file I would use 'read.csv()'. I've compiled some notes on reading in large data frames into R at http://www.biostat.jhsph.edu/~rpeng/docs/R-large-tables.html. -roger Sumanta Basak wrote: > Hi R-Experts, > > > > I'm having a problem with reading a large data file which is > in .csv format and size is 120 MB (app.). I was trying to use RODBC > package but I found RODBCconnectExcel function only. And can I convert > this file to .dbf format? How can I read this file? And also let me > know if this was a file in .sas7bdat format, what should I do? Thanks in > advance. > > > > > > Sumanta. > > > [[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. > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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] Reading bzip2 and tar files in R
bzip2-ped files can be read via the bzfile() connection function. I don't think there's a way to read from tar files though. -roger DrakeGis wrote: > Is there any way to read and decompress inside R tar and bzip2 files ? > > Thanks > > D > > > - > Stay ahead of the information curve. > Receive EDA news and jobs on your desktop daily. > Subscribe today to the EDA CafeNews newsletter. > [ http://www10.edacafe.com/nl/newsletter_subscribe.php ] > It's informative and essential. > This message was sent to you from a machine at 141.211.76.26 > > __ > 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. > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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] Sweave and font problems
Try
\usepackage[noae]{Sweave}
-roger
Mark Wardle wrote:
> Dear All,
>
> Having now successfully started using Sweave, I have just noticed an odd
> side effect with fonts.
>
> Using plain LaTeX, I have had no problems using \usepackage{palatino} or
> \usepackage{times} and the font correctly changes.
>
> However, once I convert the tex document into Snw, and run it through R
> CMD SWEAVE, LaTeX seems to ignore this package directive. The LaTeX log
> suggests the font package is successfully loaded.
>
> In fact, invetigating the problem in more detail, the mere addition of
> \usepackage{Sweave} is enough to cause the \usepackage{times} or
> \usepackage{palatino} to be ignored.
>
> I suspect it is not Sweave itself, as I have seen examples in Sweave
> using Times or Palatino; it may be an issue with my local LaTeX
> installation (but that doesn't show up without using Sweave), or some
> odd interaction? Certainly, Sweave generates the correct .tex file, but
> bizarrely, the package directive is ignored.
>
> Has anyone had similar problems, or am I alone...?
>
> pdfeTeX 3.141592-1.21a-2.2 (Web2C 7.5.4)
> Installed via darwinports (macports as it is now).
>
> Mark
>
--
Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/
__
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 remove the empty element in the vector
How about x[-c(2, 3)] -roger Yanqin Yang wrote: > Hello, > > Would anyone kindly tell me how to remove the empty element in the vector > object? > For example, > > x > [1] "a" "" "" "c" "c" "c" "d" >> unique(x) > [1] "a" "" "c" "d" > How could I get the output like: "a","c","d"? > > Thanks, > > Yanqin > > > > - > Get your email and more, right on the new Yahoo.com > [[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. > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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] levels of factor when subsetting the factor
I think you want 'fact[1:6, drop = TRUE]'
-roger
Afshartous, David wrote:
>
> All,
>
> When I take a subset of a factor the reduced factor still maintains all
> the original levels of the factor when say forming the key in a plot.
> The data is correct, but the variable still "remembers" the original
> levels. See below for reproducible code. Does anyone know how to fix
> this?
> cheers,
> dave
>
> fact = as.factor(c(rep("A", 3),rep("B", 3), rep("C", 3)))
> new.fact = fact[1:6]
>> new.fact
> [1] A A A B B B
> Levels: A B C## should only show A B
>
> __
> 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.
>
--
Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/
__
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] regex scares me
You might want to try 'glob2rx()', as in
grep(glob2rx("*.tab"), x)
where 'x' is a vector of strings.
-roger
Jon Minton wrote:
> Hi, apologies if this is too simple but I've been stuck on the following for
> a while:
>
>
>
> I have a vector of strings: filenames with a name before the extension and a
> variety of possible extensions
>
>
>
> I want to select only those files with:
>
> 1) a ".tab" extension
>
> AND
>
> 2) the character sequence "lad" anywhere in the name of the file before the
> extension.
>
>
>
> Surely this won't take long to do, I thought. (But I was wrong.)
>
>
>
> What's the regexp pattern to specify here?
>
>
>
> Thanks,
>
>
>
> Jon Minton
>
>
>
>
>
>
> [[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.
>
--
Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/
__
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] plot question
Take a look at ?plot.stepfun. 'ecdf()' returns an object of class "ecdf" inheriting from class "stepfun" and 'plot.ecdf()' calls 'plot.stepfun'. -roger Catherine Carter wrote: > Hi everyone, > > I have what may appear to be a newbie question, but I have looked > everywhere I can think to look and I cannot find an answer. On page 35 > of "An Introduction to R" the following command appears: > plot(ecdf(eruptions), do.points=FALSE, verticals=TRUE). What is the > do.points argument? I know what it does (suppresses printing of the > points) but where can I find help on it? I want to be able to explain it > fully to my students. > > Thanks for your help, > Cathy > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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] big numbers
The 'gmp' package may be of use here, but I'm not sure.
-roger
Robin Hankin wrote:
> Hi
>
> Can I get R to handle really big numbers?I am not interested
> in more than (say) 10 sig figs, but I would like to deal with numbers
> up to, say, 10^1.
>
> If
>
> a <- 10^1
> b <- pi* a
>
> I would like "a+b" to return 3.1415926e1.
>
>
> Toy example, illustrating why I can't deal with log(a) and log(b),
> follows.
>
>
>
> f <- function(a,n=100){
>out <- rep(0,n)
>out[1] <- a
>for(i in 2:n){
> out[i] <- sum(exp(out[1:i])) + rexp(1)
>}
>return(log(out))
> }
>
>
> then f(1,10) has infinities in it, even though the values should be
> moderate size.
>
> What are my options here?
>
> --
> 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.
>
--
Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/
__
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] Floating point imprecision in sum() under R-2.3.1?
I think you want to look at sum(x)/2066.758 - 1 which on my Linux box is 2.2e-16. -roger Brahm, David wrote: > After upgrading to R-2.3.1 on Linux Redhat, I was suprised by this: > > R> x <- c(721.077, 592.291, 372.208, 381.182) > R> sum(x) - 2066.758 >[1] 4.547474e-13 > > Now I understand that floating point arithmetic is not precise, but > 1) the result is exactly 0 in R-2.2.1 (patched) on the same machine, > 2) .Machine$double.eps = 2.2e-16, so the error seems quite large. > > Also note I get the same result on R-2.3.1 under Windows, and that > R> (721.077 + 592.291 + 372.208 + 381.182) - 2066.758 >[1] 0 > > Is this related to the (2.3.0) NEWS item: > sum(), prod(), mean(), rowSums() and friends use a long double > accumulator where available and so may be more accurate. > and should I be concerned? Thanks. > > -- David Brahm ([EMAIL PROTECTED]) > > > Version: > platform = i686-pc-linux-gnu > arch = i686 > os = linux-gnu > system = i686, linux-gnu > status = > major = 2 > minor = 3.1 > year = 2006 > month = 06 > day = 01 > svn rev = 38247 > language = R > version.string = Version 2.3.1 (2006-06-01) > > Locale: > C > > Search Path: > .GlobalEnv, package:methods, package:stats, package:graphics, > package:grDevices, package:utils, package:datasets, Autoloads, > package:base > > __ > 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. > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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: Large datasets in R
In my experience, the OS's use of virtual memory is only relevant in the rough sense that the OS can store *other* running applications in virtual memory so that R can use as much of the physical memory as possible. Once R itself overflows into virtual memory it quickly becomes unusable. I'm not sure I understand your second question. As R is available in source code form, it can be compiled for many 64-bit operating systems. -roger Marshall Feldman wrote: > Hi, > > I have two further comments/questions about large datasets in R. > > 1. Does R's ability to handle large datasets depend on the operating > system's use of virtual memory? In theory, at least, VM should make the > difference between installed RAM and virtual memory on a hard drive > primarily a determinant of how fast R will calculate rather than whether or > not it can do the calculations. However, if R has some low-level routines > that have to be memory resident and use more memory as the amount of data > increases, this may not hold. Can someone shed light on this? > > 2. Is What 64-bit versions of R are available at present? > > Marsh Feldman > The University of Rhode Island > > -Original Message- > From: Thomas Lumley [mailto:[EMAIL PROTECTED] > Sent: Monday, July 17, 2006 3:21 PM > To: Deepankar Basu > Cc: r-help@stat.math.ethz.ch > Subject: Re: [R] Large datasets in R > > On Mon, 17 Jul 2006, Deepankar Basu wrote: > >> Hi! >> >> I am a student of economics and currently do most of my statistical work >> using STATA. For various reasons (not least of which is an aversion for >> proprietary software), I am thinking of shifting to R. At the current >> juncture my concern is the following: would I be able to work on >> relatively large data-sets using R? For instance, I am currently working >> on a data-set which is about 350MB in size. Would be possible to work >> data-sets of such sizes using R? > > > The answer depends on a lot of things, but most importantly > 1) What you are going to do with the data > 2) Whether you have a 32-bit or 64-bit version of R > 3) How much memory your computer has. > > In a 32-bit version of R (where R will not be allowed to address more than > 2-3Gb of memory) an object of size 350Mb is large enough to cause problems > (see eg the R Installation and Adminstration Guide). > > If your 350Mb data set has lots of variables and you only use a few at a > time then you may not have any trouble even on a 32-bit system once you > have read in the data. > > If you have a 64-bit version of R and a few Gb of memory then there should > be no real difficulty in working with that size of data set for most > analyses. You might come across some analyses (eg some cluster analysis > functions) that use n^2 memory for n observations and so break down. > > > -thomas > > Thomas Lumley Assoc. Professor, Biostatistics > [EMAIL PROTECTED] University of Washington, Seattle > > __ > 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. > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ 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] Date Format
Try structure(11328, class = "Date") or just class(datetest) <- "Date" -roger pierre clauss wrote: > Hi everybody, > I need your precious help for, I think, a simple request, but I do not manage > to solve this. > > When I use a "table" function with dates in the rows, the rows are coerced to > number after the table function. > > So I need to transform the row names into date format. But I do not manage. > > Therefore, for an example, I manage to write this : > > datetest<-"06/01/2001" > datetest<-as.Date(datetest,"%d/%m/%Y") > datetest<-as.numeric(datetest) > > to get 11328. > > But I do not obtain the inverse tranformation : > > datetest<-as.Date(datetest,"%d/%m/%Y") > > How do we get this please ? > > Thanks a lot for your solution. > Pierre. > > > > [[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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Possible to get a definition of a function from a package to use without invoking the package?
You should be able to download the source package from CRAN and copy the code for the 'instring()' function into your own source file. -roger Waichler, Scott R wrote: > Hi, > > I often use the mod() and instring() functions that are available in the > clim.pact package. This package has a lot of dependencies, including > installation of netCDF, and I haven't yet been able to get > library(clim.pact) to work on a Mac OS 10.4.6. A previous request for > help with the Mac problem yielded no results, so now I wonder if I could > just extract the definitions for the couple of functions that I need and > save them in my own file of R functions. I'm pretty sure that mod() and > instring() are very basic and don't have any exotic dependencies. I did > find an alternative mod() in the new matlab package, and that's fine. > Now I just need another way to get the instring() functionality. > > Thanks, > Scott Waichler > Pacific Northwest National Laboratory > scott.waichler _at_ pnl.gov > > __ > 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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] MLE maximum number of parameters
It really depends on how well-behaved your objective function is, but I've been able to fit a few models with 10--15 parameters. But I felt like I was stretching the limit there. -roger Federico Calboli wrote: > Hi All, > > I would like to know, is there a *ballpark* figure for how many > parameters the minimisation routines can cope with? > > I'm asking because I was asked if I knew. > > Cheers, > > Federico > > -- > Federico C. F. Calboli > Department of Epidemiology and Public Health > Imperial College, St. Mary's Campus > Norfolk Place, London W2 1PG > > Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 > > f.calboli [.a.t] imperial.ac.uk > f.calboli [.a.t] gmail.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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How add degree character in axis?
Take a look at ?plotmath. -roger fernando espindola wrote: > Hi user R, > > I am try to put degree character in axis x, but don't make this. I have > the next code: > > plot(mot[,5], > time1,xlim=c(-45,-10),type="l",yaxt="n",ylab="",col=1,lwd=2,xlab="",xaxt="n") > > The range of value in axis-x is -45 to -10, this values represents the > longitudes positions in space. I try to put 45°S for real value (-45) in > the axis-x, and for all elements . Anybody can give an advance in this > problems. > > Thank for all > > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] speed?
Running on 64-bit per se does not make things faster. In fact, from my experience it sometimes makes things slower. The advantage with 64-bit is the extra address space for storing things in memory. Of course, today's 64-bit chips are all faster than recent 32-bit chips, so you will get a speed improvement, but only because you're getting a better chip. -roger Kerpel, John wrote: > The benchmark report is good stuff - I've been wondering about these > speed issues recently myself. > > Has anyone tried something similar on 64-bit Linux or other OS? I'm > contemplating switching to 64-bit Linux if I'll get some dramatic cycle > time improvements. Anyone have any experience with this? > > Best, > > John > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy > Sent: Friday, June 02, 2006 10:01 AM > To: ivo welch; r-help@stat.math.ethz.ch > Subject: Re: [R] speed? > > You (and your colleague) might want to have a look at > http://www.sciviews.org/benchmark/. It's a bit dated, > but still may be a good starting point. > > Some months ago some one asked about working on getting > R to use the GPU for computation on the R-devel list. > Don't know if anything came of it. > > Cheers, > Andy > > From: ivo welch >> dear R wizards: >> >> while extolling the virtues of R, one of my young >> econometrics colleagues told me that he still wants to run ox >> because [a] his code is written in it (good reason); [b] >> because ox seems to be faster than R in most benchmarks (huh?). >> >> this got me to wonder. language speed can't matter much, so >> it must be mostly the underlying matrix algebra by now. I >> presume that nowadays most of the plain matrix operation >> speed depends primarily on which hardware features the >> library accesses. (The basic algorithms aren't so different, >> so even though the algorithm may have mattered a long time >> ago, they are probably pretty similar nowadays. hmmm...maybe >> matrix inversion still is different, but multiplication and >> adding should not be.) >> >> On x86 architecture, I believe there is a hierarchy in terms >> of raw processing power: FPU < SSE* < GPU. >> >> is it even possible to use the GPU now for math processing >> (linux or windows), and specifically in R? >> >> assuming I compile everything with the proper SSE flags and atlas, is >> SSE* fully taken advantage of? >> >> regards, >> >> /ivo >> >> __ >> R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide! >> http://www.R-project.org/posting-guide.html >> >> > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > > __ > R-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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] function environment
Try
save(A, B, file = "myfun.r")
attach("myfun.r")
Your functions will be on the search list.
-roger
Matthias Braeunig wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hi,
>
> how can I automatically access the functions that I loaded into a
> separate environment?
>
>> save(A,B,file="myfun.r")
>> load("myfun.r",envir=(ENV<-new.env()))
>> ls(ENV)
> [1] "A" "B"
>
> ?"[" turned up that I can access the functions via
>
>> ENV$A
> function ()
> {
> }
>> ENV$A()
> NULL
>
> Now, how can they be included in the search() path??
> attach() as for data.frames does not work...
>
> Furthermore, if I change a functions environment to ENV, why is it not
> listed with ls(ENV)?? Instead it still lives in .GlobalEnv
>
>> C<-function(){}
>> environment(C)<-ENV
>> ls(ENV)
> [1] "A" "B"
>> C
> function(){}
>
>> ENV
>
>
> Thanks folks!
> I enjoy reading and learning from r-help list!
>
> M
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.2.2 (GNU/Linux)
>
> iD8DBQFEgFw2XjamRUP82DkRAooRAJ9sxwERwfXF3l7pssZ081sMC1+nigCgqAPM
> OkA1tNJg6MN3l0PQFrwBlIE=
> =tGFq
> -END PGP SIGNATURE-
>
> __
> 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
>
--
Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] timeSeq and TimeDate analog in R ?
I think the 'fCalendar' package might be of help. -roger [EMAIL PROTECTED] wrote: > Hi All : I am attempting tomove a large amount of code from Splus to R and I > was hoping that there was an equivalent in R of the Splus functions timeSeq > and timeDate ? > > I did an RSiteSearch but nothing came up ? > If the equivalent functions are part of some package, that's fine. > Thanks a lot. > >Mark > > __ > 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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] iraq statistics - OT
I guess it all depends on what you include in the category of "violent death". This study is the only one I'm aware of to attempt to address this: http://www.thelancet.com/journals/lancet/article/PIIS0140673604174412/fulltext (there's a registration but I think it's free, can't remember). -roger Gabor Grothendieck wrote: > I came across this one: > > http://www.nysun.com/article/32787 > > which says that the violent death rate in Iraq (which presumably > includes violent deaths from the war) is lower than the violent > death rate in major American cities. > > Does anyone have any insights from statistics on how to > interpret this? > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Large database help
You can read fixed-width-files with read.fwf(). But my rough calculation says that your dataset will require 40GB of RAM. I don't think you'll be able to read the entire thing into R. Maybe look at a subset? -roger Rogerio Porto wrote: > Hello all. > > I have a large .txt file whose variables are fixed-columns, > ie, variable V1 goes from columns 1 to 7, V2 from 8 to 23 etc. > This is a 60GB file with 90 variables and 60 million observations. > > I'm working with a Pentium 4, 1GB RAM, Windows XP Pro. > I tried the following code just to see if I could work with 2 variables > but it seems not possible: > R : Copyright 2005, The R Foundation for Statistical Computing > Version 2.2.1 (2005-12-20 r36812) > ISBN 3-900051-07-0 >> gc() > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 169011 4.6 35 9.4 35 9.4 > Vcells 62418 0.5 786432 6.0 289957 2.3 >> memory.limit(size=4090) > NULL >> memory.limit() > [1] 4288675840 >> system.time(a<-matrix(runif(1e6),nrow=1)) > [1] 0.28 0.02 2.42 NA NA >> gc() > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 171344 4.6 35 9.4 35 9.4 > Vcells 1063212 8.23454398 26.4 4063230 31.0 >> rm(a) >> ls() > character(0) >> system.time(a<-matrix(runif(60e6),nrow=1)) > Error: not possible to alocate vector of size 468750 Kb > Timing stopped at: 7.32 1.95 83.55 NA NA >> memory.limit(size=5000) > Erro em memory.size(size) : .4GB > > So my questions are: > 1) (newbie) how can I read fixed-columns text files like this? > 2) is there a way I can analyze (statistics like correlations, cluster etc) > such a large database neither increasing RAM nor changing to 64bit > machine but still using R and not using a sample? How? > > Thanks in advance. > > Rogerio. > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] kernel smoothing of disease rates at locations
It is certainly possible to get negative values when smoothing, especially on the edges. But we cannot reproduce your problem because you did not provide any code. -roger Oarabile Molaodi wrote: > I want to do kernel smoothing on the standardised mortality rates at > specified location(x-y coordinates) and be able to produce contour map. > I've tried to use the package called fields in R (function smooth.2d) > but the problem is I get negative results after smoothing and I do not > understand why? Your contributions will be highly appreciated or if > there is any package that can do this I will be happy to know about it. > Thanks in advance for your comments. > Oarabile > > Below is how my data in R looks like > XcoordYcoord smr > 1 383894.70 653202.8 1.5816327 > 2 339053.00 631770.9 1.0003473 > 3 369164.50 609973.2 1.2943872 > 4 313477.70 640382.8 0.9443508 > 5 290748.80 695088.8 1.1662125 > 6 287547.50 679829.6 0.9433962 > 7 259031.90 704478.3 1.0184905 > 8 329107.60 585753.3 1.0445860 > 9 292170.20 578978.2 1.1287758 > 10 268330.90 564281.7 0.9805996 > 11 227395.50 561524.6 1.1947431 > 12 310130.70 689395.0 1.0991957 > 13 325756.00 696565.6 1.1734694 > 14 339427.20 713217.2 0.8724100 > 15 391752.10 805661.5 1.2483221 > 16 385935.90 851044.5 1.0558140 > 17 372471.20 826373.7 1.4220183 > 18 354901.70 791107.2 0.9175084 > 19 324944.10 842040.8 1.0447080 > 20 275672.50 802570.4 0.9899329 > 21 320750.00 954769.7 1.0866834 > 22 243489.20 832748.8 1.0995658 > 23 166559.70 786365.3 1.0401267 > 24 288160.80 846054.4 1.0299003 > 25 220347.00 869181.0 0.9529435 > 26 175863.63 822593.9 0.9902252 > 27 246114.40 938419.3 0.8909370 > 28 359070.60 669738.3 0.9883721 > 29 320614.70 670434.2 1.1288534 > 30 331414.80 659972.3 0.9070866 > 31 299336.90 666122.9 0.7969349 > 32 156965.25 708047.7 1.1410460 > 33 253867.30 674916.5 0.9256710 > 34 249188.40 674272.8 1.0869565 > 35 272463.00 679495.3 0.8576698 > 36 252643.80 611378.4 0.8615611 > 37 212637.35 643725.0 0.8596604 > 38 234751.95 691803.4 0.9706546 > 39 264856.20 644684.8 0.8468395 > 40 253949.30 653042.5 0.8106169 > 41 260412.35 663552.2 0.9253686 > 42 270807.60 657454.0 0.9002826 > 43 228477.30 670443.2 1.0782502 > 44 248215.30 641897.3 0.9240407 > 45 229797.50 596059.0 1.1579197 > 46 291725.00 635771.8 0.8908766 > 47 278012.80 667982.0 1.024 > 48 279490.80 659761.6 0.9828301 > 49 242791.70 662651.8 1.0230584 > 50 263217.20 675295.2 0.9759817 > 51 341138.80 754471.3 0.9505541 > 52 334963.00 735075.4 0.9264498 > 53 286139.70 733611.6 0.9052453 > 54 354015.60 1025696.8 0.8905506 > 55 455775.60 1201636.0 1.0862620 > 56 88429.32 854994.4 0.9577015 > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] the 'copula' package
What is the error message that you get? -roger Casey Quinn wrote: > Is anybody using the Copula package in R? The particular problem I'm > facing is that R is not acknowledging the fitCopula command/function > when I load the package and (try to) run something very simple: > > fit1 <- fitCopula(x1 = list(u11,u12,u13,u14,u15,u16,u17,u18), tCopula, > optim.control = list(NULL), method = "BFGS") > > Anybody also using it, successfully or unsuccessfully? I'd appreciate a > tip or two. > > Casey Quinn > Centre for Health Economics > University of York > York YO10 5DD > England > > Phone: +44 01904 32 1411 > Fax:+44 01904 32 1402 > Email: [EMAIL PROTECTED] > Web: http://www.york.ac.uk/inst/che/staff/quinn.htm > > __ > 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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] finding method file?
The `summary' function (i.e. the generic) is defined in the "base" package, the source code of which is in src/library/base/R in the R source tree (try the file "summary.R"). There are also a number of methods defined there. The source code is not in the R *installation*, since the code for the base/recommended packages is loaded via lazy-loaded databases. When looking for source code, it's good to check the sources, not the installation. The latest release source is at http://cran.us.r-project.org/src/base/R-2/R-2.2.1.tar.gz -roger ivo welch wrote: > dear R wizards: > > I am trying to determine how to determine (no further recursion) where > a built-in function is defined. In particular, I have decided I am > going to add sd() to the existing basic summary function, rather than > try to rewrite my own summary() function from scratch. > > So, I just installed R-2.2.1 (via gentoo; eventually I will figure out > how to get atlas/sse/sse2 working on amd64, too! PS: [a] how can I > determine whether a running S installation uses sse2, sse, and atlas? > [b] does atlas use sse2; [c] are there now modern graphics processor > routines that might speed up R, too? ok, all of these are irrelevant > sidequestions). > > then, I did a > >> summary > [not informative about which file it is defined in] > > ok, easy. Just grep. back on the unix line, > ># grep -r '1st Qu' /usr/lib/R > > which should look for this fairly unique string. to my surprise, it > was only found in R-intro.html. > > so, how would I go about looking for where R defines functions? or > has this becomes so deeply wired into fortran/C in later versions that > it can no longer be changed? > > help/advice as always appreciated. > > sincerely, > > /ivo welch > > __ > 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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] boot problem
Your 'resample' function is not written according to the help page. Try
resample <- function(x, index) { x[index, ] }
-roger
david v wrote:
> Hello,
> This is the code that is giving me problems
>
>
>>library(boot)
>>data<-read.table("test",header=FALSE,sep="\t",row.names=1)
>>data
>
> V2 V3 V4
> A 5 8 9
> B 12 54 89
> C 65 89 23
> D 32 69 44
> E 21 84 97
> F 33 59 71
> G 16 45 93
> H2 46 55
> I 22 33 88
>
>
>>resample <- function(x,index) {
>
> sample(data,replace=TRUE)
> }
> dist<-boot(data,resample,R=1000)
> Erreur : nombre d'indices incorrect sur la matrice (french)
> Error: number of indices wrong in the matrix (moreless)
>
> Can anybody help???
>
> __
> 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
>
--
Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] memory tops out at 1.84gb on OS X 10.4 machine w/ 5GB ram
I'm not completely sure, but I don't think OS X is at the point yet where it can access > 2GB of memory (like, for example, Linux on Opteron). More specifically, I'm not sure a single process image can access > 2GB of memory, but I'd welcome any corrections to that statement. To be sure, this problem is not an issue with R because R has regularly been reported to access u> 4GB of memory when the OS allows it. -roger Ken Termiso wrote: > Hi all, > > Sorry if this is a dumb question, but I am on 10.4 with R2.2, and when > loading a big text file (~500MB) with scan(file, what=character) I am > throwing malloc errors that say I am out of memory...I have 5GB on this > machine, and Activity Monitor tells me R is only up to ~1.84GB both times > this has happened (running from terminal)... > > I am wondering why this is happening when I still have >2GB of free memory > waiting to be used...? > > Any advice would be much obliged, > Ken > > __ > 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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] 32 vs 64 bit
When we first moved to 64 bit I found that certain things were slower. I believe it is because of the increased overhead for memory management. -roger Paul Gilbert wrote: > I ran R on an AMD Athlon 64 with a 32 bit Linux (by accident, I moved > the hard disk from another machine). Now, after install 64 bit Linux and > 64 bit R, I am finding some of my R tests are quite a bit slower, I > think because memory demands cause a lot of swap. Does anyone know if > extra memory usage would be mainly because of R itself, or is there a > lot of extra memory demand because of the OS, windowing system, and > other apps? > > Paul Gilbert > > __ > 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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] save to ascii
You could try using functions like 'dput()' or 'dump()'. These may or may not be equivalent to 'save()' depending on how complex the object to be saved is. -roger P.S. Asking people to respond to a different email address is not a good way to get responses! Afshartous, David wrote: > All, > > Usually when I save a variable I have ascii = FALSE since I usually > load the variable via the load(variable) command and do not need to > view the variable outside of R. > > When I set ascii = TRUE and view the variable outside of R in a text editor, > I notice additional characters (starting w/ RDA2 ...) before the first actual > value > in the vector. > > Is there are way to save to ascii such that this does not happen? > I checked the help under save and didn't see anything. I apologize > in advance for this overly simplistic question. > > Cheers, > Dave > ps - please reply directly to [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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Element-by-element multiplication operator?
What about A * B? -roger Gates, Michael BGI SF wrote: > Is there an element-by-element multiplication in R, like the .* operator in > Matlab? > > eg: A (2x3) > B (2x3) > C=A.*B > C (2x3) > C = [[a11*b11 a12*b12 a13*b13]; [a21*b21 a22*b22 a23*b23]] > > I can't find one... > > Thanks > > -Mike Gates > > __ > 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 > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to plot the circles in matrix form
Would 'symbols()' be of use? -roger shanmuha boopathy wrote: > Could you help me > to plot the circles in the form of matrix like > > O O O O > O O O O > O O O O > > thank you.. > > with regards, > boopathy. > > > Thirumalai Shanmuha Boopathy, > Zimmer no : 07-15, > Rütscher strasse 165, > 52072 Aachen . > Germany. > > Home zone : 0049 - 241 - 9813409 > Mobile zone : 0049 - 176 - 23567867 > > > > > > - > > [[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 -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] encrypted RData file?
I would be interested in that, particularly with certain kinds of confidential data. What was the approach you had in mind (if you in fact had one in mind)? -roger Na Li wrote: > Hi, I wonder if there is interest/intention to allow for encrypted .RData > files? One can certainly do that outside R manually but that will leave a > decrypted RData file somewhere which one has to remember to delete. > > Cheers, > > Michael > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > -- Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RSQLite problems
I encountered this too, and my limited investigation (both on the web and in R)
was unable to find a work around.
-roger
Na Li wrote:
> Hi, I'm experimenting with using (R)SQLite to do data management. Here are
> two little problems that I've encountered:
>
> 1. The presence of ',' in string values causes trouble since ',' is also the
>delimiter used in the SQL statement.
>
> 2. A newline '\n' line attached to the last string value of each row.
>
> Some examples:
>
>
>>library (RSQLite)
>
> Loading required package: DBI
>
>>sqlite <- dbDriver ("SQLite")
>>db <- dbConnect (sqlite, dbname = "test.dbms")
>>data (barley)
>>dbWriteTable (db, "barley", barley, overwrite = TRUE)
>
> [1] TRUE
>
>>barley[1:3,]
>
> yield variety yearsite
> 1 27.0 Manchuria 1931 University Farm
> 2 48.86667 Manchuria 1931 Waseca
> 3 27.43334 Manchuria 1931 Morris
>
>>dbReadTable (db, "barley")[1:3,]
>
> yield variety year__1 site
> 1 27.0 Manchuria1931 University Farm\n
> 2 48.86667 Manchuria1931 Waseca\n
> 3 27.43334 Manchuria1931 Morris\n
>
>
>>barley$site <- as.character (barley$site)
>>barley$site[1] <- "University, Farm"
>>dbWriteTable (db, "barley", barley, overwrite = TRUE)
>
> Error in sqliteWriteTable(conn, name, value, ...) :
> RS-DBI driver: (RS_sqlite_import: /tmp/RtmpgSNaLn/rsdbi6a5d128c line 1
> expected 5 columns of data but found 6)
>
> I'm using RSQLite 0.4.0 with R 2.1.1 on Mac OS X.
>
> Cheers,
>
> Michael
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
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Re: [R] Finding code for R functions
If you're really interested in reading the source for functions and aren't
interested in tracking down various methods (possibly hidden in namespaces) at
the R prompt, I think it's much easier to download the R source code from CRAN
and go through the original source files.
-roger
Wolfrum, Ed wrote:
> Greetings,
>
> I am trying to figure out how to find the source code for R functions. I
> am specifically interested in finding the code for the "prcomp"
> function. I know that typing the function name without parenthesis will
> lead to the code (or to a .Internal or .FORTRAN or .C call). However, I
> don't really understand what is going on. For example, typing "mean"
> gives a "UseMethod" response, while typing "mean.default" give the
> actual code:
>
>
>>mean
>
> function (x, ...)
> UseMethod("mean")
>
>
>>mean.default
>
> function (x, trim = 0, na.rm = FALSE, ...)
> ---SNIP---
> }
>
>
> Why is this? What does "mean.default" mean? I tried the same thing with
> "prcomp". With the stats package loaded, I cannot get to the source code
> for "prcomp".
>
>
>>require(stats)
>
> [1] TRUE
>
>>prcomp
>
> function (x, ...)
> UseMethod("prcomp")
>
>
>>prcomp.default
>
> Error: object "prcomp.default" not found
>
> How do I find the prcomp code? Are there general rules for finding the
> source code for functions that I should know?
>
> Thanks in Advance,
>
> Edward J. Wolfrum, Ph.D.
> National Renewable Energy Laboratory
> Golden, Colorado
>
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>
--
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http://www.biostat.jhsph.edu/~rpeng/
__
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Re: [R] Questions about readBin function (Was: dec2bin?)
I think you can use 'seek()' here, but it may not be completely reliable on all
platforms.
-roger
Tuszynski, Jaroslaw W. wrote:
> Hi,
>
> The latest version of R had some changes to functions "readbin() and
> writeBin() [which] now support raw vectors as well as filenames and
> connections.". As a result I am working on retiring "raw2bin" and "bin2raw"
> functions from "caTools" package which do exactly the same. Thanks to Prof.
> Ripley for bringing this change to my attention.
>
> Which brings me to my question: how to use readBin function to read the
> whole file or vector "con" and not just requested number of elements (n)
> from it? In other words what to do if I do not know what to set argument "n"
> to ("The (maximal) number of records to be read"), and want to read all
> records?
>
> So far the simplest solution I found is to measure vector length (or file
> size) of "con" and set n to length()%/%size. Which gets quite messy if
> "size" is not provided and have to be deduced from "what" (see code below).
> Am I missing something? Is there an easier way to read the whole file or
> vector? Shouldn't that be the default?
>
> readBin(con, what, n = 1, size = NA, signed = TRUE, endian =
> .Platform$endian)
>
> bin2raw = function(x, ...) writeBin(x, raw(), ...) # old bin2raw can be
> easily written using curent writeBin
>
> raw2bin = function(r, what, size=NA, ...)
> {
> TypeList = c("logical", "integer", "double", "complex", "character",
> "raw",
>"numeric", "int")
> if (!is.character(what) || length(what) != 1 || !(what %in% TypeList))
> what <- typeof(what)
> if (!is.vector(r) || mode(r) == "list")
> stop("raw2bin: 'r' has to be vector of type 'raw'")
> if (what=="raw") return(r)
> if (!is.na(size)) nBits=size
> else nBits = switch(match(typeof(x), TypeList), 4, 4, 8, 16, 2, 1, 8, 4)
> n = length(r)
> if (n%%nBits)
> stop("raw2bin: number of elements in 'r' is not multiple of 'size'")
> x = readBin(r, what, n = n%/%nBits, size=size, ...)
> return (x)
> }
>
> Jarek
> \
> Jarek Tuszynski, PhD. o / \
> Science Applications International Corporation <\__,|
> (703) 676-4192 "> \
> [EMAIL PROTECTED] ` \
>
> __
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> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
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http://www.biostat.jhsph.edu/~rpeng/
__
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Re: [R] wildcards and removing variables
In R 2.2.0, there is the function 'glob2rx()' which can be used for this
purpose. As in
rm(list = ls(pattern = glob2rx("results*")))
-roger
Afshartous, David wrote:
> All,
>
> Is there are a wildcard in R for varible names as in unix? For example,
>
> rm(results*)
>
> to remove all variable or function names that begin w/ "results"?
>
> cheers,
> Dave
> ps - please respond directly to [EMAIL PROTECTED]
>
> [[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
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http://www.biostat.jhsph.edu/~rpeng/
__
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Re: [R] Dummy quesion about environment
Try 'get("x", env = environment(h))'
-roger
Ron Ophir wrote:
> Hi,
> I'm trying to understand environment object in R.
> I used the example:
> f <- function(x) {
> y <- 10
> g <- function(x) x + y
> return(g)
> }
> h <- f()
> h(3)
> then i saw that f return an environment
>
>>h
>
> function(x) x + y
>
> but I coudn't access to x and y object in that environment:
> I tried
> get("x",env=h)
> I tried
> h$y
> can I access y and x?
> how can I see an environment tree? oes search does it?
> Thanks,
> Ron
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
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>
--
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__
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Re: [R] warning.expression?
You might be interested in 'tryCatch' to catch warnings.
-roger
Thomas Friedrichsmeier wrote:
> Hi!
>
> I'm trying to catch all warning-messages for special handling. It seems
> options (warning.expression=myfunc ()) can be used for that. However, the
> question is: How can I get at the actual warning in myfunc ()? Apparently in
> S, you can use .C("get_last_message") for that. Is there a similar mechanism
> in R?
>
> Thanks for your help!
> Thomas
>
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>
--
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__
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Re: [R] toLatex
Try 'methods(toLatex)'. -roger Simone Vantini wrote: > hallo! > does everybody know which kind of objects the function toLatex can manage? > thanks > simone vantini > > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Packages
What version of R are you using? 'modreg' no longer exists---its functions have been moved to the 'stats' package. -roger Amir Safari wrote: > > Hi Dear All, > I want to instal some packages, but I can not find them in both lists of > Package Index in internet ( > http://www.maths.lth.se/help/R/.R/doc/html/packages.html ) and of Instalation > of Packages window in the softwar. For example "modreg". Are they included > in larger packages ? > Thanks for your help. > Best Regards, > Amir Safari > > __ > > > > [[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 > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] problems when installing R in Fedora core 4
You are probably missing the 'devel' package for x11 which includes header files. -roger Peter Yang wrote: > Hi, I got a problem when installing R in Fedora core 4. When I ran > .configure, it gave the following error message: > > configure: error: --with-x=yes (default) and X11 headers/libs are not > available > > Could anyone tell me what's wrong? Am I missing some package in Fedora? > > Thanks a lot for your help. > > Peter > > __ > 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 > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Fwd: Documenting data sets with many variables
Have you tried using 'promptData()' on the data frame and then
just using the resulting documentation file?
-roger
Arne Henningsen wrote:
> Hi,
>
> since nobody answered to my first message, I try to explain my problem more
> clearly and more general this time:
>
> I have a data set in my R package "micEcon", which has many variables (82).
> Therefore, I would like to avoid to describe all variables in the "\format"
> section of the documentation (.Rd file). However, doing this lets "R CMD
> check" complain about "data codoc mismatches" (details see below).
> Is there a way to avoid the description of all variables without getting a
> complaint from "R CMD check"?
>
> Thanks,
> Arne
>
>
> -- Forwarded Message --
>
> Subject: Documenting data sets with many variables
> Date: Friday 05 August 2005 14:03
> From: Arne Henningsen <[EMAIL PROTECTED]>
> To: R-help@stat.math.ethz.ch
>
> Hi,
>
> I extended the data set "Blanciforti86" that is included in my R package
> "micEcon". For instance, I added consumer prices, annual consumption
> expenditures and expenditure shares of eleven aggregate commodity groups.
> The corresponding variables in the data frame are called "pAgg1",
> "pAgg2", ..., "pAgg11", "xAgg1", "xAgg2", ..., "xAgg11", "wAgg1",
> "wAgg2", ..., "wAgg11". To avoid to describe all 33 items in the "\format"
> section of the documentation (.Rd file) I wrote something like
>
> \format{
>This data frame contains the following columns:
>\describe{
> [ . . . ]
> \item{xAggX}{Expenditure on the aggregate commodity group X
> (in Millions of US-Dollars).}
> \item{pAggX}{Price index for the aggregate commodity group X
> (1972 = 100).}
> \item{wAggX}{Expenditure share of the aggregate commodity group X.}
> [ . . . ]
>}
> }
>
> and explained the 11 aggregate commodity groups only once in a different
> section (1=food, 2=clothing, ... ). However, "R CMD check" now complains
> about "data codoc mismatches", e.g.
> Code: [...] pAgg1pAgg2 pAgg3 [...]
> Docs: [...] pAggX [...]
>
> Is there a way to avoid the description of all 33 items without getting a
> complaint from "R CMD check"?
>
> Thanks,
> Arne
>
> ---
>
--
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http://www.biostat.jhsph.edu/~rpeng/
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Re: [R] use of NA's
To test for 'NA' you shouldn't use '=='. Use 'is.na()' instead.
-roger
tom wright wrote:
> Can someone please explain why this works:
>
>
>>>d<-c(0,2,3,2,0,3,4,0,0,0,0,0)
>>>d.mat<-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
>>>for(i in 1:length(d.mat[1,])){
>>
>>+ d.mat[,i][d.mat[,i]==0]<-mean(d.mat[,i][d.mat[,i]>0])
>>+ }
>
>
> Whereas:
>
>
>>d<-c(0,2,3,2,0,3,4,0,0,0,0,0)
>>d.mat<-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
>>d.mat[d.mat==0]<-NA
>>for(i in 1:length(d.mat[1,])){
>
> + d.mat[,i][d.mat[,i]==NA]<-mean(d.mat[,i],na.rm=TRUE)
> + }
> dosnt
>
> Thanks
> Tom
>
> ______
> 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
>
--
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http://www.biostat.jhsph.edu/~rpeng/
__
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Re: [R] Help: how to stop the process when there is a mishandling
On Unix you can send one of the 'USR' signals to 'kill'. See ?Signals. -roger Shengzhe Wu wrote: > Hello, > > How to stop the process when there is a mishandling making R system > frozen? If there is a way other than quitting the system when frozen > occurs? > > Thank you, > Shengzhe > > __ > 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 > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Modifying the parameters for a function
What exactly do you mean by "compile"? What compile works fine?
-roger
Philip Bermingham wrote:
> I have modified the parameters for a function (for my own use) in the
> stats package, but I assume I need to update the parameter set in
> another file as I'm getting the following error when I run R:
>
>
>
> The compile works fine so I assume there is a configuration file in the
> base package of R that needs modification.
>
>
>
> Error in parse(file, n, text, prompt) : syntax error on line 11102
>
> Error: unable to load R code in package 'stats'
>
> During startup - Warning message:
>
> package stats in options("defaultPackages") was not found
>
>
>
> Philip.
>
>
> [[alternative HTML version deleted]]
>
> __
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> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
--
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http://www.biostat.jhsph.edu/~rpeng/
__
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Re: [R] hash code for arbitrary object
You can compute MD5 and SHA1 digests with the 'digest' package. -roger Adrian Baddeley wrote: > Can anyone suggest a simple way to calculate a 'hash code' > from an arbitrary R object? > > hash(x) should return an integer or string > with the property that > if hash(x) != hash(y) then x and y are not identical > and the time to compute hash(x) should be quite short. > > Any suggestions welcome > thanks > Adrian Baddeley > > __ > 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 > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] help: how to change the size of a window after it has been created
Not sure you can do this. You might have to launch separate graphics windows. -roger wu sz wrote: > Hello, > > I wish to plot some figures in a window in turn, but the size of these > figures is different, so how can I change the size of the window by > resetting the parameters before each plotting? > > Thank you, > Shengzhe > > __ > 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 > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Plotting greek symbols in plot titles, labels, etc.
Take a look at '?plotmath'. -roger Roy Werkman wrote: > Hi, > > Can anyone please tell me how to use the escape sequences (e.g. \\*a for > alfa) for plotting Greek symbols in for example plot titles? I have read > the reference manual, but can't seem to get it to work. > > Thanx! > > Roy > > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] tcltk package
How do you know that it has disappeared? -roger Kurt Sys wrote: > Hi all, > > I have a package depending on the tcltk-package. However, I see that > this package has been disappeared... Is there a reason why package > 'tcltk' is not available anymore? Or is it replaced by another one? > > thx, > Kurt. > > __ > 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 > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Data Parsing
You can use 'subset()' if you have a data frame.
d <- read.table(...)
subset(d, Score %in% c("Passed", "Borderline"))
-roger
Bernard L. Dillard wrote:
> Hello. I have looked at R Site Search for this problem, and it didn't
> give me exactly what I needed.
>
> Consider this dataset called "results". It has the following information:
>
> Student DaySubjectScore
>
> Mary 1 Math Failed
> David 2 Science Passed
> Bob 4 Reading Passed
> Marie 4 Reading Failed
> Jesse 3 Spelling Borderline
> Et cetera
>
>
> My goal is to only do analysis of the data having to do those who passed
> or who are borderline. I want to ignore all of the data having to do with
> those who failed. I think part of the syntax is something like
> results[-c("Failed")], but I'm not getting anywhere with it.
>
> How do I create a separate data set containing all information on students
> who either passed or were borderline?
>
> Thanks.
>
> Bernard
>
--
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Re: [R] ccf
You might try passing 'na.contiguous' to the 'na.action' argument. -roger Laura De Vendictis wrote: > Hello group, > > For my research I should calculate the cross-correlation between two > time series. > I don't know if the function ccf can calculate this with series that > have NA values. > e.g. temperature: > > 15.5 > NA > 12.3 > 10.0 > NA > 14.2 > 15,3 > > > Can you help me? > Thank you very much! > > Laura > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ordinary polynomial coefficients from orthogonal polynomials?
I think this is covered in the FAQ: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Models -roger James Salsman wrote: > How can ordinary polynomial coefficients be calculated > from an orthogonal polynomial fit? > > I'm trying to do something like find a,b,c,d from > lm(billions ~ a+b*decade+c*decade^2+d*decade^3) > but that gives: "Error in eval(expr, envir, enclos) : > Object "a" not found" > > > decade <- c(1950, 1960, 1970, 1980, 1990) > > billions <- c(3.5, 5, 7.5, 13, 40) > > # source: http://www.ipcc.ch/present/graphics/2001syr/large/08.17.jpg > > > > pm <- lm(billions ~ poly(decade, 3)) > > > > plot(decade, billions, xlim=c(1950,2050), ylim=c(0,1000), > main="average yearly inflation-adjusted dollar cost of extreme weather > events worldwide") > > curve(predict(pm, data.frame(decade=x)), add=TRUE) > > # output: http://www.bovik.org/storms.gif > > > > summary(pm) > > Call: > lm(formula = billions ~ poly(decade, 3)) > > Residuals: >1 2 3 4 5 > 0.2357 -0.9429 1.4143 -0.9429 0.2357 > > Coefficients: > Estimate Std. Error t value Pr(>|t|) > (Intercept)13.800 0.882 15.647 0.0406 * > poly(decade, 3)1 25.614 1.972 12.988 0.0489 * > poly(decade, 3)2 14.432 1.972 7.318 0.0865 . > poly(decade, 3)36.483 1.972 3.287 0.1880 > --- > Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 > > Residual standard error: 1.972 on 1 degrees of freedom > Multiple R-Squared: 0.9957, Adjusted R-squared: 0.9829 > F-statistic: 77.68 on 3 and 1 DF, p-value: 0.08317 > > > pm > > Call: > lm(formula = billions ~ poly(decade, 3)) > > Coefficients: > (Intercept) poly(decade, 3)1 poly(decade, 3)2 poly(decade, 3)3 >13.80025.614 14.432 6.483 > > __ > 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 > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] load ing and saving R objects
I would suggest saving each object to an individual file with some sort of systematic file name. That way, you can implement a rudimentary key-value database and load only the objects you want. You might be interested in the 'serialize()' and 'unserialize()' functions for this purpose. If having ~15000 files is not desirable, then you need a database like GDBM. If you can live with something simpler, you might take a look at my 'filehash' package at http://sandybox.typepad.com/software/. It hasn't been tested much but it may suit your needs. -roger Richard Mott wrote: > Does anyone know a way to do the following: > > Save a large number of R objects to a file (like load() does) but then > read back only a small named subset of them . As far as I can see, > load() reads back everything. > > The context is: > > I have an application which will generate a large number of large > matrices (approx 15000 matrices each of dimension 2000*30). I can > generate these matrices using an R-package I wrote, but it requires a > large amouint of memory and is slow so I want to do this only once. > However, I then want to do some subsequent processing, comprising a very > large number of runs in which small (~ 10) random selection of matrices > from the previously computed set are used for linear modeling. So I > need a way to load back named objects previously saved in a call to > save(). I can;t see anyway of doing this. Any ideas? > > Thanks > > Richard Mott > > -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Default Format for Dates?
Is something like this what you want?
x <- as.Date("2003-06-24")
format(x, "%B %d %Y")
or perhaps
as.character(x, "%B %d %Y")
-roger
[EMAIL PROTECTED] wrote:
>
>
>
> Is there anyway to preset date formats? I have a date from a cover.dbf
> that is shown as this:
>
>>cover$FINALREPOR
>
> [1] "2003-06-24"
>
> The numeric value in cover$FINALREPOR is 12227. I'd rather not create
> another vector to hold the properly formatted date.
>
> When I put this in a WordPerfect merge, I want the date to be June 24,
> 2003. I could take care of the problem in a WordPerfect macro but I'd
> rather do it as an R default date format if possible.
>
> I researched some of this in the archives, FAQ's and manuals but didn't
> find anything that met my need. I would imagine that this type of question
> is probably an FAQ but I didn't find it.
>
> mailto:[EMAIL PROTECTED]
> Kenneth Ray Hobson, P.E.
> Oklahoma DOT - QA & IAS Manager
> 200 N.E. 21st Street
> Oklahoma City, OK 73105-3204
> (405) 522-4985, (405) 522-0552 fax
>
> Visit our website at:
> http://www.okladot.state.ok.us/materials/materials.htm
>
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>
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Re: [R] install package "snow"
I think for 'snow' you need to download the source and build it yourself. I assume you are on Windows (you didn't say!). 'snow' depends on external programs so it would seem unwise to have a binary package on CRAN. -roger Steve Adams wrote: Hi, I have difficulty in installing package "snow" from CRAN. Somehow, this package is not shown up in the available package list when I tried to use the GUI interface. So I have to go to CRAN to download the source file: snow_0.2-1.tar.gz. Then I tried to install it using the following command: install.packages(repos=NULL, pkgs='C:\Documents and Settings\Desktop\snow_0.2-1.tar.gz', type='source', lib = 'c:/program files/r/rw2010/library/') Warning message: installation of package 'C:Documents and Settingsyzhang24Desktopsnow_0.2-1.tar.gz' had non-zero exit status in: install.packages(repos = NULL, pkgs = "C:Documents and Settingsyzhang24Desktopsnow_0.2-1.tar.gz", What's the problem here, and how should I handle it? Thanks Steve __ 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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Strange characters in 2.1.0?
It may be a problem with your terminal program. Which one are you using? Does it work if you try a different terminal program? -roger Dan Bolser wrote: On Mon, 6 Jun 2005, Roger D. Peng wrote: What is your operating system? Very sorry for lack of details... I am RH 9, unix pc i386. -roger Dan Bolser wrote: Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Signif. codes: 0 <80><98>***<80><99> 0.001 <80><98>**<80><99> 0.01 <80><98>*<80><99> 0.05 <80><98>.<80><99> 0.1 <80><98> <80><99> 1 Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 hmm... they go away when I paste them in... __ 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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Strange characters in 2.1.0?
What is your operating system? -roger Dan Bolser wrote: Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Signif. codes: 0 <80><98>***<80><99> 0.001 <80><98>**<80><99> 0.01 <80><98>*<80><99> 0.05 <80><98>.<80><99> 0.1 <80><98> <80><99> 1 Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 hmm... they go away when I paste them in... __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] rbind wastes memory
Rather than 'rbind' in a loop, try putting your dataframes in a list and
then doing something like 'do.call("rbind", list.of.data.frames")'.
-roger
[EMAIL PROTECTED] wrote:
Hello everybody,
if I try to (r)bind a number of large dataframes I run out of memory because R
wastes memory and seems to "forget" to release memory.
For example I have 10 files. Each file contains a large dataframe "ds" (3500 cols
by 800 rows) which needs ~20 MB RAM if it is loaded as the only object.
Now I try to bind all data frames to a large one and need more than 1165MB (!)
RAM (To simplify the R code, I use the same file ten times):
start example 1 __
load(myFile)
ds.tmp <- ds
for (Cycle in 1:10) {
ds.tmp <- rbind(ds.tmp, ds)
}
end example 1 __
Stepping into details I found the following (comment shows RAM usage after this line
was executed):
load(myFile)# 40MB (19MB for R itself)
ds.tmp <- ds# 40MB; => only a pointer seems to be
copied
x<-rbind(ds.tmp, ds) # 198MB
x<-rbind(ds.tmp, ds) # 233MB; the same instruction a second time leads to
# 35MB more RAM usage - why?
Now I played around, but I couldn't find a solution. For example I bound each dataframe
step by step and removed the variables and cleared memory, but I still need 1140MB(!)
RAM:
start example 2 __
tmpFile<- paste(myFile,'.tmp',sep="")
load(myFile)
ds.tmp <- ds
save(ds.tmp, file=tmpFile, compress=T)
for (Cycle in 1:10) {
ds <- NULL
ds.tmp <- NULL
rm(ds, ds.tmp)
gc()
load(tmpFile)
load(myFile)
ds.tmp <- rbind(ds.tmp, ds)
save(ds.tmp,file=tmpFile, compress=T)
cat(Cycle,': ',object.size(ds),object.size(ds.tmp),'\n')
}
end example 1 __
platform i386-pc-solaris2.8
arch i386
os solaris2.8
system i386, solaris2.8
status
major1
minor9.1
year 2004
month06
day 21
language R
How can I avoid to run in that memory problem? Any ideas are very appreciated.
Thank you in advance & kind regards,
Lutz Thieme
AMD Saxony/ Product Engineering AMD Saxony Limited Liability Company & Co. KG
phone: + 49-351-277-4269 M/S E22-PE, Wilschdorfer Landstr. 101
fax:+ 49-351-277-9-4269 D-01109 Dresden, Germany
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Re: [R] .libPaths()
Did you check to make sure the new path exists?
-roger
Sebastian Leuzinger wrote:
Hello
I use the function .libPaths()
.libPaths()
[1] "/usr/local/lib/R/library"
.libPaths(c("/usr/local/lib/myRlib","/usr/local/lib/library"))
.libPaths()
[1] "/usr/local/lib/R/library"
but it simply does not pick up the new path. Can anybody help?
(The problem originates from the inability to install packages
into /usr/local/lib/R/library, running R under linux suse 9.3)
Sebastian Leuzinger
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Re: [R] installing R-2.1.0 from source on Fedora Core 3 with tcltk
I haven't had a problem building R 2.1.0 on FC3 and I've got the tcl, tcl-devl, tk, and tk-devel rpms installed (and I don't use the --with-tcltk configure switch). I've never downloaded the R_Tcl.zip file. Does 'configure' find the tcl/tk setup and then it fails to compile or does 'configure' just not find tcl/tk to begin with? Also, is this a 64-bit system? We've had trouble building R with tcl/tk support on some of our 64-bit Red Hat installations. -roger Jonathan Baron wrote: I installed from source on Fedora Core 3 starting with the command ./configure --prefix=/usr --with-tcltk (The --with-tcltk may not be necessary, but there seems to be some correlation between using it and getting it to work.) It would not compile with tcltk, even though I had both tcl and tk rpms installed. Various fooling around let me to get http://www.murdoch-sutherland.com/Rtools/R_Tcl.zip (even though it is supposedly for Windows), unzip it in the R-2.0.0/ directory (where the tar file put itself), and also install rpms for tcl-devel and tk-devel, which I did not have. When I did both of these things, it worked. Either one of them alone (the ..devel rpms or the R_Tcl.zip) did not suffice. (However, it isn't clear that a single trial experiment is sufficient to determine what works.) My own problem is solved for the moment. But others may benefit from this report, and it may be that the installation documentation needs minor tweaking. (Or it may be that I did something else wrong, but right now I doubt that.) Jon __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem with R-2.1.0: install.packages() doesn't work
What happens if you don't set the 'CRAN' option via 'options()'
first and just run 'install.packages()'?
-roger
Waichler, Scott R wrote:
I installed R-2.1.0 from source on a Linux box running Red Hat
Enterprise Linux WS release 4 but install.packages() wouldn't work (see
below). When I install R-2.0.1 from RPM on the same system, everything
is fine.
Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0
. . .
options(CRAN = "http://cran.fhcrc.org/";)
install.packages("rgenoud")
--- Please select a CRAN mirror for use in this session ---
Error in inherits(x, "factor") : Object "res" not found
Scott Waichler
Pacific Northwest National Laboratory
[EMAIL PROTECTED]
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Re: [R] Suggestion for the posting guide
You can use 'dput()' or 'dump()' to create a text representation and paste that into an email if it's small enough. Another possiblity, if you have access to a webserver, is to save a workspace file via 'save()' or 'save.image()' and post it on the web. Given the URL, users with Internet access can 'load()' it directly off the web into R. I guess one downside of that method is the example data do not get stored in the mailing list archives. -roger Bock, Michael wrote: I was preparing an e-mail for the help list and ran across a quandary. When asking for help it is useful to include the code/data so others can run your code and test it. I was running code on a data frame and wanted to include a small version of the data frame. The data frame was based on experimental data. What is the best way to do this? I didn't want to send an attachment so a wrote code to generate the data frame but it was a bit cumbersome. Everything worked as planned but then I saw my error and never had to send to e-mail (perhaps there is hope for me yet). Is there an easier way to export a SMALL data frame so you can recreate it using the example code that can be placed in the posting guide? Is it really a good idea to show people how to do this as we run the risk of someone sending a huge e-mail? Perhaps the "manual method" is really the best way to go, submitted for your consideration. Michael J. Bock, PhD. ARCADIS 24 Preble St. Suite 100 Portland, ME 04101 207.828.0046 fax 207.828.0062 [[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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Define "local" function
This came up just a few days ago on the mailing list! Check the
archives here:
https://stat.ethz.ch/pipermail/r-help/2005-April/067639.html
-roger
Fernando Saldanha wrote:
I discovered a bug in a program I am writing which was due to the
program using a global variable within a function.
For example,
myfunc <- function(x) { y}
That is, I made a mistake when defining the function and wrote "y"
when I should have written "x".
However, there was a variable y in the global environment and the
function "worked" but gave the wrong answer.
I would like to avoid this problem by defining a "local" function.
That would mean a function that only accepts as variables those that
were defined within its body or were passed as parameters, and would
generate an error when I try to define it if I am using an "external"
variable. Something like:
myfunc <- function(x, type = 'local') { y}
Error: using external variable
I read the documentation about environments (I still do not understand
a lot of it, have been working with R for four days now), and searched
the newsgroups, but I could not find the way to do this.
Thanks for any suggestions.
FS
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Re: [R] function corresponding to map of perl
I think you want 'sapply()'. -roger Wolfram Fischer wrote: Is there a function in R that corresponds to the function ``map'' of perl? It could be called like: vector.a <- map( vector.b, FUN, args.for.FUN ) It should execute for each element ele.b of vector.b: FUN( vector.b, args.for.FUN) It should return a vector (or data.frame) of the results of the calls of FUN. It nearly works using: apply( data.frame( vector.b ), 1, FUN, args.for.FUN ) But when FUN is called ele.b from vector.b is no known. Thanks - Wolfram __ 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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Is a .R script file name available inside the script?
I think you might want 'commandArgs()' which gives you the original
command line call.
-roger
Darren Weber wrote:
Hi,
if we have a file called Rscript.R that contains the following, for example:
x <- 1:100
outfile = "Rscript.Rout"
sink(outfile)
print(x)
and then we run
source("Rscript.R")
we get an output file called Rscript.Rout - great!
Is there an internal variable, something like .Platform, that holds
the script name when it is being executed? I would like to use that
variable to define the output file name.
Best, Darren
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Re: [R] bootstrap vs. resampleing
What you're describing sounds like subsampling, about which John Hartigan has written a few papers. -roger array chip wrote: Hi, I understand bootstrap can be used to estimate 95% confidence interval for some statistics, e.g. variance, median, etc. I have someone suggesting that by resampling certain proportion of the total samples (e.g. 80%) without replacement, we can also get the estimate of confidence intervals. Here we have an example of 1000 obsevations, we would like to estimate 95% confidence intervals for odds ratio for a diagnostic test, can I use resampling 80% of the observations without replacement, instead of bootstrap, to do this? If not, why is it wrong to do it this way? 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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Introduce a new function in a package?
I think the usual way is to create an R package for yourself and load it when you need it for whatever project. -roger Luis Ridao Cruz wrote: R-help, Sometimes I define functions I wish to have in any R session. The obvious thing to do is copy-paste the code The thing is that sometimes I don't know where I have the function code. My question is if somehow I could define a function and "introduce" it (let's say 'base' package ) so that could be used anytime I run a different R project. Thank you in advance __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how does predict.princomp work?
Try doing
getS3method("predict", "princomp")
-roger
ronggui wrote:
i want to know how the predict function to caculate the principal
component,especially when has the newdata argument,i try to find
out,but i fail.anyone knows?thank you!
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Re: [R] How to split a single vector into a multiple-column and multiple-row matrix
You can use 'matrix()', as in x <- 1:2000 matrix(x, nrow = 200, ncol = 10) -roger R_xprt_wannabe wrote: Dear List, I have, say, a 2000x1 numeric vector and would like to split it into, say, a 200x10 matrix. Any help is appreciated. __ 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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Will "R" work on this 64 bit machine?...
I believe R will run out of the box on your setup. I personally haven't tried the RPMs but you can always build R from the sources (fairly straightforward on a Linux box). -roger dsandif wrote: Hello, Will "R" work on this 64 bit machine?, Here are the specs. of our linux box: *Red Hat Enterprise Linux WS (v.3 Standard for AMD64 and Intel EM64T) *OS: redhat-release Release: 3WS CPU Arch: ia32e-redhat-linux (4) GenuineIntel Intel(R) Xeon(TM) CPU 3.40GHz 3399 MHZ Arch: EM64T Cache: 1024 KB Vendor:GenuineIntelMemory: 2000 MB Stepping: 1 Family:15 Swap: 4000 MB I see that you have it for Unix machines and that you have it for the following linux platforms: Red Hat i3868/9/Fedora1/Fedora2/Fedora3 Martyn Plummer x86_64 Fedora1 James Henstridge x86_64 Fedora3 Brian Ripley i386Enterprise LinuxMatthew P. Cox Could I use the Fedore 3 x86_64 version? Thanks for you attention and help. D- [[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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Maximum amount of memory
The amount of memory you can access depends on many things, most of which are not related to R. With a 64-bit processor and suitable OS we've used R on a machines with 16GB of RAM (and accessed most of it). Of course, the memory does get very expensive after a certain point -roger [EMAIL PROTECTED] wrote: Hi, I have a problem:I need to use the maximum amount of memory in order to perform a very tough analysis. By purchasing the suitable computer, what's the maximum amount of memory obtainable in R? 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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] newbie question about beta distribution
A probability density must integrate to 1. The specific values of the density can be either more or less than 1. -roger [EMAIL PROTECTED] wrote: hi everyone, I'm still a newbie in statistics, I have a question about beta distribution, that is, On the ref/tutorials I've found on the net, why beta distribution always have value p(x) more than 1? As I know, any probability density function always have value not more than 1? is there any one who can explain to me, I'm not statistics people, but I need to code that needing some of this distribution function. thx before __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] removing message: [Previously saved workspace restored]
R saves the workspace in a file called '.RData'. Simply remove this
file from your working directory. Or if you startup R and get the
message, try
unlink(".RData")
-roger
Federico Calboli wrote:
Dear All,
I saved by mistake the environment I was working in after typing q(),
and now I get the annoying message:
[Previously saved workspace restored]
I have already deleted all the objects in the environment, saving it as
an empty environment, so it's just a matter of nitpicking I suppose. The
message does not appear if I start R from any other place in the
directory tree.
I am reading ?Startup and related docs, but I am utterly failing to
understand how to remove [Previously saved workspace restored] when I
call R from the offending dir...
I am using R on Debian Sarge x86
Cheers,
Federico Calboli
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Re: [R] orientation of eps files
This is ghostscript feature, I believe. See here:
https://www.stat.math.ethz.ch/pipermail/r-devel/2003-October/027759.html
I usually do
setenv GS_OPTIONS "-dAutoRotatePages=/None"
in tcsh.
-roger
Andrew Collier wrote:
hello,
i have a problem with the orientation of eps files produced with the
postscript() command. i have generated some eps files with R using:
postscript(file = filename, horizontal = FALSE, paper = "special", onefile = F
ALSE, height = height, width = width, pointsize = pointsize)
now, when i include these eps files into a standard paper document (ie. a4
paper, portrait orientation) everything is fine.
however, i am now wanting to incorporate the same images into a presentation. i
am making a pdf file, which for presentation purposes is in landscape
orientation. i am using latex with the prosper package. images are included
with \includegraphics{} and a pdf file is generated with dvipdf. however, in
this case, when i include the eps figures the whole page suddenly gets rotated
around into portrait. eps files from other packages seem to work fine.
there is an example of the problem at ftp://chinstrap.nu.ac.za/orientation.pdf.
if you have any ideas as to what might be causing this problem, i would be
extremely happy to hear them.
best regards,
andrew.
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Re: [R] using 'nice' with R
On a Unix like system you can do `nice +19 R' or perhaps `nice +19 R CMD BATCH commands.R'. -roger Robert Burrows wrote: I would like to use the 'nice' command when running CPU-intensive R functions on a server. Will starting R with 'nice R' do the trick? -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Converting a list to a matrix - I still don't think I have it right
Does
do.call("rbind", l2)
do what you want?
-roger
michael watson (IAH-C) wrote:
Hi
We have touched on this before, but I don't think I quite got it right.
So I have a list, each element of which is a a vector of 2 numbers:
l2
$cat000_a01
[1] 0.3429944 4.5138244
$cat000_a02
[1] 0.1929336 4.3064944
$cat000_a03
[1] -0.2607796 4.1551591
What I actually want to convert this into is a matrix with the names
(cat000_a01 etc) as row names, the first element of each of the vectors
forming the first column of the new matrix, and the second element of
each of the vectors forming the second column:
cat000_a01 0.3429944 4.5138244
cat000_a02 0.1929336 4.3064944
cat000_a03 -0.2607796 4.1551591
What was suggested on the list last time was
matrix(unlist(mylist),nrow=length(mylist)). But if I do this I get:
matrix(unlist(l2),nrow=length(l2))
[,1] [,2]
[1,] 0.3429944 4.3064944
[2,] 4.5138244 -0.2607796
[3,] 0.1929336 4.1551591
Which is not what I want. Here, the second element of the first vector
in my list has gone into the first column of the new matrix, and that's
not what I want at all.
Any more help would be appreciated.
Thanks
Mick
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Re: [R] install RMySQL
R comes with it's own copy of zlib so even if it is compiled into R,
there isn't necessarily a system-wide installation of the library.
You may still need to install it.
-roger
Xander Meadow wrote:
Hi,
I've got a Dual G5 running 10.3.7 and I'm trying to install RMySQL.
I've already got R up and running. When I try the command
install.packages("RMySQL")
It downloads a few things and then produces the following error:
---
Configuration error:
Could not locate the library "libz" required by MySQL.
INSTRUCTIONS:
The "libz" library is required by the MySQL client library
in order to compress/uncompress connections between clients
and the MySQL engine.
Make sure you have "libz" installed properly and/or included
in your $LD_LIBRARY_PATH. Perhaps it is not in any of the
standard directories (e.g., /usr/lib/, /usr/local/lib)?
Aborting the installation of RMySQL.
ERROR: configuration failed for package 'RMySQL'
However, if I check for libz I get:
capabilities("libz")
libz
TRUE
I'm not sure what the problem is because R is telling me that it doesn't
know where libz is, but then it's also telling me it does know where
libz is.
Has anyone else seen this problem or know how I can get RMySQL installed
on my machine?
Just as an added note I know that install.packages works because
install.packages("DBI")
worked without a problem.
Thanks again.
-Xander
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Re: [R] how to generate a function from a linear model
I don't think there's an automatic way to do this but you might try
something like:
model <- lm(sat.d~1+sat.n+I(sat.n^2))
f <- function(x) { predict(model, data.frame(sat.n = x)) }
-roger
Tony Han Bao wrote:
Hi All,
I am trying to generate a function from a linear model. I think there
should be build-in function that perform this action but I've had no
luck finding it.
For example, I have a model created using lm().
model <- lm(sat.d~1+sat.n+I(sat.n^2))
What I would like to have is a function (similar to the one generated by
splinefun()) so that I can use it on different data-sets.
Thanks in advance for the help.
Tony Han Bao
[EMAIL PROTECTED]
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Re: [R] Handling large data sets via scan()
I can usually read in large tables by very careful usage of read.table() without having to resort to scan(). In particular, using the `colClasses', `nrows', and `comment.char' arguments correctly can greatly reduce memory usage (and increase speed) when reading in data. Converting from a list to a data frame likely requires at least two copies of the data being stored in memory. Also, are you using a 64-bit operating system? -roger Nawaaz Ahmed wrote: I'm trying to read in datasets with roughly 150,000 rows and 600 features. I wrote a function using scan() to read it in (I have a 4GB linux machine) and it works like a charm. Unfortunately, converting the scanned list into a datafame using as.data.frame() causes the memory usage to explode (it can go from 300MB for the scanned list to 1.4GB for a data.frame of 3 rows) and it fails claiming it cannot allocate memory (though it is still not close to the 3GB limit per process on my linux box - the message is "unable to allocate vector of size 522K"). So I have three questions -- 1) Why is it failing even though there seems to be enough memory available? 2) Why is converting it into a data.frame causing the memory usage to explode? Am I using as.data.frame() wrongly? Should I be using some other command? 3) All the model fitting packages seem to want to use data.frames as their input. If I cannot convert my list into a data.frame what can I do? Is there any way of getting around this? Much thanks! Nawaaz __ 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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] getting package version inside .First.lib
This is what I use for all my packages, which I believe handles multiple
versions of the same package being installed:
.First.lib <- function(lib, pkg) {
ver <- read.dcf(file.path(lib, pkg, "DESCRIPTION"), "Version")
ver <- as.character(ver)
...
}
-roger
Adrian Baddeley wrote:
Greetings -
Is it possible, inside .First.lib,
to find out the version number of the package that is being loaded?
If only one version of the package has been installed,
we could scan the DESCRIPTION file, something like
.First.lib <- function(lib, pkg) {
library.dynam("spatstat", pkg, lib)
dfile <- system.file("DESCRIPTION", package="spatstat")
ttt <- scan(dfile, what="", sep="^M", quiet=TRUE)[2]
vvv <- strsplit(ttt," ")[[1]][2]
cat("spatstat version number",vvv,"\n")
}
but even this does not seem very safe (it makes assumptions about the
format of the DESCRIPTION file).
Is there a better way?
thanks
Adrian Baddeley
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Re: [R] using eval() with pre-built expression inside function
If you look at the beginning of lm(), you'll see that match.call() is
used and name of the function (in this case "f1") is replaced with
"model.frame". Does something like this work?
f1 <- function(formula, data) {
mf <- match.call(expand.dots = FALSE)
mf[[1]] <- as.name("model.frame")
eval(mf, parent.frame())
}
-roger
Heather Turner wrote:
I'm trying to evaluate a pre-built expression using eval(), e.g.
dataset <- data.frame(y = runif(30, 50,100), x = gl(5, 6))
# one like this
mf <- expression(model.frame(y~x))
eval(mf, dataset, parent.frame())
# rather than this
eval(expression(model.frame(y~x)), dataset, parent.frame())
In the example above there is no problem, the problem comes when I try to do a
similar thing within a function, e.g.
f1 <- function(formula, data) {
mt <- terms(formula)
mf <- as.expression(as.call(c(as.name("model.frame"), formula = mt)))
eval(mf, data, parent.frame())
}
f1(formula = y ~ x, data = dataset)
Error in eval(expr, envir, enclos) : Object "y" not found
I can get round this by building a call to eval using paste, e.g.
f2 <- function(formula, data) {
mt <- terms(formula)
mf <- as.expression(as.call(c(as.name("model.frame"), formula = mt)))
direct <- parse(text = paste("eval(expression(", mf,
"), data, parent.frame())"))
print(direct)
eval(direct)
}
f2(formula = y ~ x, data = dataset)
expression(eval(expression(model.frame(formula = y ~ x)), data,
parent.frame()))
y x
1 92.23087 1
2 63.43658 1
3 55.24448 1
4 72.75650 1
5 67.58781 1
...
but this seems rather convoluted. Can anyone explain why f1 doesn't work (when
f2 does) and/or suggest a neater way of dealing with this?
Thanks
Heather
Mrs H Turner
Research Assistant
Dept. of Statistics
University of Warwick
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Re: [R] Hardware Suggestions
We've been running servers with AMD Opterons (both duals and 4-ways) using SuSE SLES 8 and Fedora Core 2 and 3 (64 bit). All work well and R can access up to ~15GB of RAM on our 4-way machine (which has 16GB installed). One of the Red Hat Enterprise Linux versions comes with a buggy compiler but I can't remember which version (there is some discussion on the R-devel mailing list archives). Watch out for that. I think using gcc 3.4.x solves that problem. R pretty much compiles out of the box on AMD Opteron/Fedora Core 3 (64-bit) Linux. We've been very happy with our R experience so far. -roger Jon Dressel wrote: We are currently running R under Windows 2000 on a server box running with 2 1.2 GHZ Intel Pentium III Processors. We would like to run this on a new computer running Linux and receive a significant speed increase over our current implementation. Could anyone provide some suggestions for a fast 64 BIT Intel based processor computer with a recommendation for memory and speed/type/number of processors. Also which version of R would install "out-of-the-box" easily on this computer and what version of Linux should be used? Thanks in advance for any help. Jon Dressel, MCSE MCSA MCP A+ Applications Supervisor SurroMed, Inc. 1430 O'Brien Drive Menlo Park, CA 94025 Phone: 650.470.2322 Fax: 650.470.2400 email: [EMAIL PROTECTED] [[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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing R on Xandros 3.0
I'm guessing this is a Linux based system. Does ./configure make make install work? -roger Thomas W Volscho wrote: Dear List, After obtaining a second-hand PC and because XP costs too much, I installed Xandros 3.0 (based on Debian) but pretty easy to use if migrating from WinXP. Does anyone know how to install R on this OS? Thank you for your time, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ 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 -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] install.packages() for local source file
By the way, do you get this error in a recent version of R (say >= 1.9.1). I
believe install.packages() has changed since 1.9.0. For example, see the thread
starting here
https://stat.ethz.ch/pipermail/r-help/2004-July/053001.html
-roger
Paul Roebuck wrote:
Wish to install a local source package on Un*x platform from
within R. Same thing as I can accomplish from cmdline as
$ export R_LIBS=~/R/library
$ cd /path/to/pkg
$ R CMD INSTALL -l $R_LIBS
So, how do you go about this anyway?
And isn't this a bug in 'install.packages'?
---
$ R
R : Copyright 2004, The R Foundation for Statistical Computing
Version 1.9.0 (2004-04-12), ISBN 3-900051-00-3
file.pkg <- "mypkg_0.1.tar.gz"
path.pkg <- file.path(path.expand("~"), "cvknn", file.pkg)
file.exists(path.pkg)
[1] TRUE
uri.pkg <- paste("file://", path.pkg, sep = "")
install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
Error in file.info(x) : Object "tmpd" not found
traceback()
4: file.info(x)
3: dirTest(destdir)
2: download.packages(pkgs, destdir = tmpd, available = available,
contriburl = contriburl, method = method)
1: install.packages(contriburl = uri.pkg, lib = Sys.getenv("R_LIBS"))
version
_
platform sparc-sun-solaris2.9
arch sparc
os solaris2.9
system sparc, solaris2.9
status
major1
minor9.0
year 2004
month04
day 12
language R
--
SIGSIG -- signature too long (core dumped)
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Re: [R] Export the R object
If you want to export data frame, you can use write.table() to write out a CSV (comma separated value) file, which you can then read into Excel. -roger Ko,Younhee wrote: Hi, I just have a quick question. If I got some result as the result of R, how can I export the result object? I mean, if I want to use the result object in Excel or other program in order to more specific investigation, how can I export it? If I just list the result and copy, The result is like this.. [586] "BB170029A10B06" "BB170029A20E06" First column, automatically show the number of result and other result also include the "". If I want to use this result, I have to manipulate the result by myself(I mean e.g remove " and remove [586] like this way)? Or there is any good way to export this result object to other program? Please help me. Thanks in advance. Younhee Ko([EMAIL PROTECTED]) http://comedu.korea.ac.kr/~unygo contact : 217-417-4868 Graduate Student in Dept. of Computer Science University of Illinois at Urbana-Champaign __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] outer(-x, x, pmin) cannot allocate
Actually, I believe it's 8 bytes for double precision. -roger Berton Gunter wrote: David: In general, this is not a good question to ask, as one needs to go into the bowels of R to find an answer. But note that 8000 x 8000 x 4 bytes for double precision = 256 mb. Now look at the code of outer(). Two vectors of this size are created = 512mb. Then copies of these must be created to be passed into pmin, I believe, as R passes by value. That's 1gb. My guess is that "+", as an internal function, avoids the final doubling. Corrections/clarifications by knowledgeable R experts cheerfully welcomed. I'm on thin ice here. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA "The business of the statistician is to catalyze the scientific learning process." - George E. P. Box -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Brahm, David Sent: Wednesday, December 22, 2004 12:11 PM To: [EMAIL PROTECTED] Subject: [R] outer(-x, x, pmin) cannot allocate R> x <- 0. + 1:8000 R> y <- outer(-x, x, pmin) Error: cannot allocate vector of size 100 Kb Why does R need to allocate a gigabyte to create an 8000 x 8000 matrix? It doesn't have any trouble with outer(-x, x, "+"). Thanks. -- David Brahm ([EMAIL PROTECTED]) Version: platform = i686-pc-linux-gnu arch = i686 os = linux-gnu system = i686, linux-gnu status = major = 2 minor = 0.1 year = 2004 month = 11 day = 15 language = R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] reading svm function in e1071
The predict method for class `svm' is hidden in a namespace. Try
getS3method("predict", "svm")
-roger
Rajdeep Das wrote:
Hi,
If I try to read the codes of functions in e1071 package, it gives me following
error message.
library(e1071)
svm
function (x, ...)
UseMethod("svm")
predict.svm
Error: Object "predict.svm" not found
Can someone help me on this how to read the codes of the functions in the
e1071 package?
Thanks.
Raj
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Re: [R] make check-all failed on SLES8 for x86_64
Martin Maechler brought this up a while back (and added the regression
test). I believe it was a compiler problem and upgrading to gcc 3.4.1
fixed it.
See the thread starting here:
https://stat.ethz.ch/pipermail/r-devel/2004-July/030260.html
-roger
Liaw, Andy wrote:
Hi all,
I've only now noticed that on our Opteron boxes running Suse Enterprise
Server 8 that R-2.0.1 did not pass make chek-all. It bombed in
tests/lapack.R at:
eigenok <- function(A, E, Eps = 1000 * .Machine$double.eps) {
V <- E$vect
lam <- E$values
stopifnot(abs(A %*% V - V %*% diag(lam)) < Eps, [TRUNCATED]
Ceigenok <- function(A, E, Eps = 1000 * .Machine$double.eps) {
V <- E$vect
lam <- E$values
stopifnot(Mod(A %*% V - V %*% diag(lam)) < Eps, [TRUNCATED]
sm <- cbind(1, 3:1, 1:3)
eigenok(sm, eigen(sm))
Error: abs(A %*% V - V %*% diag(lam)) < Eps is not TRUE
This is using:
~/R-2.0.1> gcc -v
Reading specs from /opt/gcc33/lib64/gcc-lib/x86_64-suse-linux/3.3/specs
Configured with: ../configure --enable-threads=posix --prefix=/opt/gcc33
--with-local-prefix=/usr/local --infodir=/opt/gcc33/share/info
--mandir=/opt/gcc33/share/man --libdir=/opt/gcc33/lib64
--enable-languages=c,c++,f77,objc,java,ada --disable-checking
--enable-libgcj --with-gxx-include-dir=/opt/gcc33/include/g++
--with-slibdir=/lib64 --with-system-zlib --enable-shared
--enable-__cxa_atexit x86_64-suse-linux
Thread model: posix
gcc version 3.3 20030312 (prerelease) (SuSE Linux)
compiled with the following setting:
R is now configured for x86_64-unknown-linux-gnu
Source directory: .
Installation directory:/usr/local
C compiler:gcc -g -O2
C++ compiler: g++ -g -O2
Fortran compiler: g77 -g -O2
Interfaces supported: X11, tcltk
External libraries:readline
Additional capabilities: PNG, JPEG
Options enabled: R profiling
Recommended packages: yes
Actually, I've only noticed this when the samething happens on a RH-based
box (same hardware), using:
$ gcc -v
Reading specs from /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--disable-checking --with-system-zlib --enable-__cxa_atexit
--enable-languages=c,c++,objc,java,f77 --host=x86_64-redhat-linux
Thread model: posix
gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-24)
I'd very much appreciate any pointers!
Best,
Andy
Andy Liaw, PhD
Biometrics Research PO Box 2000, RY33-300
Merck Research Labs Rahway, NJ 07065
andy_liaw merck.com 732-594-0820
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Re: [R] "non-visible" functions in return to methods()
"non-visible" functions are hidden in a namespace. You can view the code by using getS3method(). -roger steve houghton wrote: Please point me to the documentation explaining why some of the functions returned by calling methods() are marked as "non-visible" and whether there is indeed no way of viewing the R code of such functions thanks Steve _ Stay in touch with absent friends - get MSN Messenger http://www.msn.co.uk/messenger __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to insert one element into a vector?
?append --- look at the `after' argument. -roger jing tang wrote: suppose I want to insert 5 into the vector (1,2,3,4,6) between 4 and 6. thx! __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Running sum
You could try using embed(), but I doubt it's faster.
-roger
Sean Davis wrote:
I have vector X of length N that I want to have a running sum for
(called Y). I just need max(Y). I do this with a "for" loop like so:
Y <- vector(length=N)
Y[1] <- X[1]
for (i in 2:N) {
Y[i] <- Y[i-1]+X[i]
}
return(max(Y))
Is there a faster way to do this?
Thanks,
Sean
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Re: [R] glm with Newton Raphson
There are some examples of how to approach this in Modern Applied Statistics with S, 4th ed. (chap. 16) by Venebles & Ripley. It's not Newton-Raphson but I think the code can be adapted. -roger Valeska Andreozzi wrote: Hi, Does anyone know if there is a function to find the maximum likelihood estimates of glm using Newton Raphson metodology instead of using IWLS. Thanks Valeska Andreozzi Department of Epidemiology and Quantitative Methods FIOCRUZ - National School of Public Health Tel: (55) 21 2598 2872 Rio de Janeiro - Brazil __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Enormous Datasets
It depends on what you mean by 'handle', but probably not. You'll likely have to split the file into multiple files unless you have some rather high end hardware. However, in my limited experience, there's almost always a meaningful way to split the data (geographically, or by other categories). A few things I've learned recently working with large datasets: 1. Store files in .rda format using save() -- the load times are much faster and loading takes up less memory 2. If your data are integers, store them as integers! 3. Don't store character variables in dataframes -- use factors -roger Thomas W Volscho wrote: Dear List, I have some projects where I use enormous datasets. For instance, the 5% PUMS microdata from the Census Bureau. After deleting cases I may have a dataset with 7 million+ rows and 50+ columns. Will R handle a datafile of this size? If so, how? Thank you in advance, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] hashing using named lists
You could try using environments: > e <- new.env(hash = TRUE) > e$new <- 1:4 > ls(e) [1] "new" > e$new [1] 1 2 3 4 > e$ne NULL -roger ulas karaoz wrote: hi all, I am trying to use named list to hash a bunch of vector by name, for instance: test = list() test$name = c(1,2,3) the problem is that when i try to get the values back by using the name, the matching isn't done in an exact way, so test$na is not NULL. is there a way around this? Why by default all.equal.list doesnt require an exact match? How can I do hashing in R? thanks. ulas. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] deleting a file
You may be interested in one of dir.create(), file.exists(), or unlink().
-roger
Roger Gill wrote:
Dear all,
I have a very simple question. Simple, that is, if you know the answer.
I wish to delete a file in a given directory after having first checked its
existence. I issue the following commands
path<-'c:example/R/'
Thus creating the directory.
indicator<-length(grep(filename,path))
If indicator is greater than zero then the file exists. Now I wish to
remove this file. However, I would like to make the code compatible for
Linux/Windows and Macs.
In Linux I would issue the command
system('rm paste(path,'filename',sep='')')
and this works just fine. It does not however work for windows, and I have
no idea whether it would work on a mac.
Is there a single command thay escapes me?
Best Wishes
Roger Gill
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Re: [R] R on 64-bit Linux machine
I've built (and routinely use) 64 bit R on the following platforms: Red Hat Enterprise Linux AS release 3 (AMD Opteron 848) Fedora Core 2 x86_64 (AMD Athlon 64 3800+) SuSE SLES 8 (AMD Opteron 248) One problem that has come up is that if you want to link R with ATLAS, you need to build shared ATLAS libraries (rather than static). This requires some modifications to the configuation files for ATLAS. But my experience shows that R itself builds out of the box on these systems. -roger Vadim Ogranovich wrote: Hi, We are planning to buy a 64-bit Linux machine which will mainly run R. There was an interesting thread on 64-bits on r-help back in April that basically confirmed that the 64-bit R is fine as long as the length of an atomic object is less than 2^31 - 1. My specific question is on which 64-bit Linux distros (SUSE or RedHat) and processors R is *known* to build out-of-box and run well. Ease of maintenance is essential here. We have RedHat 7.3 on other (32-bit) machines and would try not to proliferate the OS-s. Your information will be highly appreciated, Thanks, Vadim [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems installing ncdf package into R
Did you look at
http://cran.us.r-project.org/bin/windows/contrib/2.0/ReadMe
?
-roger
[EMAIL PROTECTED] wrote:
Hello
Can someone please look into the problem with installing ncdf package into R.
I get this message when I try install it:
install.packages("ncdf")
trying URL `http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 22827 bytes
opened URL
downloaded 22Kb
Warning message:
No package "ncdf" on CRAN. in: download.packages(pkgs, destdir = tmpd,
available = available,
I checked with the homepage cran.r-project.org, and the package is there. I
have installed packages earlier into R with no problems.
In advance, thanks for all help!
Best Wishes
Dag Johan Steinskog
Bjerknes Center of Climate Research - University of Bergen, Norway
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Re: [R] expressions and paste
Can you be a bit more specific? Exactly what kind of symbol are you
trying to put in the title?
-roger
Emily Baldock wrote:
I have written a function to plot data which will be used for various different chemistries.
A simplified version is:
plot_data <- function(risk,levels,chem,sd2,measure){
plot(risk, levels,main=paste ("per", sd2, measure, "\n in usual", chem))
}
The problem is with the title.
This works fine if the variable "chem" is just text, but if it is an expression then obviously it won't work.
I have experimented with various things and I am at a complete loss for how to insert an expression into the middle of
a title.
If the expression was going in directly I would use main=expression(paste("text ", expression, " text")) but again this
doesn't work.
Can anyone help?
thanks
Emily.
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Re: [R] Logical "and"
Try setdiff(a, b) -roger Alexander Sokol wrote: Hello, I have the following very simple problem: Say I have two vectors, a<-c(1,7,4,5,9,11) b<-c(7,4,9) I would like to create a vector containing the elements in a which are not in b. Obviously, this is possible by writing a[a!=b[1] & a!=b[2] & a!=b[3]] But I would like a solution which is applicable to the situation where the number of elements in b is unknown. I have looked in the R manuals, the FAQ and the mailing lists, but have been unable to find a solution. Thank you for your replies, Alexander __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R works on Fedora Core 3
I've run into this title bar problem on FC1 and FC2 (not tried FC3 yet) when I compile from sources. I figured it was just a weird window manager bug. I find that if I maximize the window (Alt-F10, on my system) and then restore the window to its original size (Alt-F5), I get the title bar back. -roger Gavin Simpson wrote: Martyn Plummer wrote: On Wed, 2004-11-10 at 09:19 +0100, Martyn Plummer wrote: An RPM for Fedora Core 3 should be on a CRAN mirror near you by the weekend. This fixes the printcmd bug. The X11() window is the right size for me, but it doesn't have a title bar, which is a nuisance. Martyn I have this "problem" with both your rpm on FC2 and when compiled from sources (1.9.1-patched 2.0.0-patched [now 2.0.1 beta]). The title bar comes and goes, seemingly at random (I've not systematically test this so I haven't found an underlying cause) when a new X11() device is started. Mainly a more complex plot (over several lines and commands) will fail to produce the title bar, if I then close that device and open another using something simple, say plot(1:10) then I more often than not get the title bar. I say more often than not, because sometimes I have to run that command a few times, closing the opened faulty device window in between to get the title bar to appear. Same result running R from within xemacs/ess. Gav -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] substitute/paste question for using Greek in plot titles
This is not a bug. The object passed to `main' should be either character or an
expression (documented in ?title). substitute() returns neither a character
object nor an expression -- it return a call object. This is documented in
?substitute:
Substituting and quoting often causes confusion when the argument
is 'expression(...)'. The result is a call to the 'expression'
constructor function and needs to be evaluated with 'eval' to give
the actual expression object.
What you want, I think, is
label <- substitute(expression(paste("A vaue for ",phi," = ",phival)),
list(phival=phi.1))
plot(0 ~ 0, main = eval(label))
-roger
Sundar Dorai-Raj wrote:
Peter Dunn wrote:
Hi all
I am having troubles making sense of why code (1)
below fails but code (2) below works.
Code (1):
> phi.1 <- 1
> plot(0 ~ 0,
+ main=substitute(paste("A vaue for ",phi," = ",phival),
list(phival=phi.1)) )
Error in paste("The two deviances for ", phi, " = ", 2) :
Object "phi" not found
But this works:
Code (2):
> plot(0,0,
+ main=substitute(paste("A value for ",phi," = ",phival),
list(phival=phi.1)) )
>
It appears that if the plot command takes the formula style entry,
the substitue/paste fails.
Is this documented as a feature (I couldn't find it if that is the
case), or is it a bug? If it is a feature, it is a subtle difference
between (1) and (2) that has potential to be quite frustrating!
Perhaps I should just upgrade to version 2.0.0, though I can't see
anything in the Release Notes that might cause this.
Thanks.
P.
> version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major1
minor9.1
year 2004
month06
day 21
language R
Peter,
Because in the first couple of lines of plot.formula we see this:
dots <- m$...
dots <- lapply(dots, eval, data, parent.frame())
which for your case is equivalent to:
expr <- substitute(paste("A vaue for ",phi," = ",phival),
list(phival=phi.1))
eval(expr)
which returns an error saying "phi" cannot be found which is the correct
behaviour of eval. I'll let others comment on whether or not this is a
bug in plot.formula but you can always get around it by calling title:
plot(0 ~ 0)
title(main = expr)
which is exactly what your second example is doing in plot.default.
HTH,
--sundar
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