Re: [R] Excel (off-topic, sort of)
Take a look at Mathematica or Maple. This is the kind of thing you do with these languages. Best, Philippe Grosjean Alberto Monteiro wrote: Chris wrote: Typically, people in the R community are not used to the spreadsheet paradigm and need some time to be able to take advantage of automatic recalculation, (...) Do you know what's in my wish list? I wish spreadsheets and computer languages had gone one step further. I mean, it's nice to define Cell X to be equal to Cell Y + 10, and then when we change Cell Y, magically we see Cell X change. But why can't it be the reverse? Why can't I change Cell X _and see the change in Cell Y_? Maybe I'll write a letter to Santa Claus [there are people who write to congressman; they must have more faith than me]. I wish a language where I can write a = b + 10 and then when I write a = 20 the language automatically assigns b = 10. There's a way to simulate this in any computer language, or even in Excel: instead of variables or cells, we have structures with value and a flag. The flag dictates if it's input, undefined or calculated. And then there's a list of relations. So the program/language/spreadsheed loops through the list of relations, detects whenever we can infer a new calculated value, and calculates it, until there's nothing else to do or a contradiction is found. Alberto Monteiro __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-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] Excel
I think that one big problem of Excel regarding readability of the calculation done is its non linear nature: mixing data and calculation on a 2D grid could look nice at first sight, but indeed, it turns into a nightmare to understand all the calculations actually done. On the counterpart, reading a R script is like reading a book: providing you understand the language, the R script tells you a story from the beginning (reading of the raw data) to the end (final graphs and tables) in a linear way. Thus, it is the concept of Excel itself (the 2D/3D interactive spreadsheet) that makes it confusing. All the nice things you can do with Excel will never save it for the time lost to understand what a spreadsheet does (and thus, to debug it, or slightly change its calculation). Best, Philippe Grosjean Frank E Harrell Jr wrote: Rolf Turner wrote: On 30/08/2007, at 8:49 AM, Greg Snow wrote: Erich Neuwirth said: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Erich Neuwirth Sent: Wednesday, August 29, 2007 12:43 PM To: r-help Subject: Re: [R] Excel Excel bashing can be fun but also can be dangerous because you are makeing your life harder than necessary. My experience differs, so far using excel (other than as a table layout program) has made my life harder more times than it has made it easier. Remainder of message deleted. Bravo!!! Very well and very cogently expressed! cheers, Rolf Turner Yes! In addition I'd like to stress that the Excel model represents non-reproducible research. Frank Harrell __ 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] filling a list faster
If all the data coming from your iterations are numeric (as in your toy example), why not to use a matrix with one row per iteration? Also, do preallocate the matrix and do not add row or column names before the end of the calculation. Something like: m - matrix(rep(NA, 3*10^5), ncol = 3) system.time(for(i in (1:10^5)) m[i, ] - c(i,i+1,i)) user system elapsed 1.362 0.033 1.424 That is, about 1.5sec on my Intel Duo Core 2.33Mhz MacBook Pro, compared to: l - list(1-c(1,2,3)) system.time(for(i in (1:10^5)) l[[length(l)+1]] - c(i,i+1,i)) user system elapsed 191.629 49.110 248.454 ... more than 4 minutes for your code. By the way, what is your very fast machine, that is actually four times faster than mine (gr!)? Best, Philippe Grosjean ..∞})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Balazs Torma wrote: hello, first I create a list: l - list(1-c(1,2,3)) then I run the following cycle, it takes over a minute(!) to complete on a very fast mashine: for(i in (1:10^5)) l[[length(l)+1]] - c(i,i+1,i) How can I fill a list faster? (This is just a demo test, the elements of the list are calculated iteratively in an algorithm) Are there any packages and documents on how to use more advanced and fast data structures like linked-lists, hash-tables or trees for example? Thank you, Balazs Torma __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to activate the R commands in SciViews
As explained on the web page from where you downloaded SciViews 0.8-9, this version is not compatible with R 2.5.0. Best, Philippe Grosjean ..∞})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Liviu Andronic wrote: Hello everybody, I have a problem similar to that reported by Felipe. I installed R 2.5.0, Rcmdr from CRAN and SciViews-R 0.8-9 (with all the required and optional components). When accessing the R Commander menu from within SciViews, the links cannot be clicked. When pointing at them, the mouse transforms in a hand (as it normally does, similar to Internet hyperlinks). However, the links cannot be activated. I had the impression that in some way SciViews makes use of Internet Explorer in its GUI, and that the problem was somewhere there. But I could not get to the bottom of it. Is there any way to make SciViews correctly use Rcmdr functionality? Thanks in advance, Liviu On 6/20/07, Felipe Carrillo [EMAIL PROTECTED] wrote: Please help, I have SciViews(svGUI) and Rcmdr but when the SciViews Console opens the R commander menu don't work. Any ideas anybody? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [Fwd: Re: How to activate the R commands in SciViews]
Well.. plans are there from a long time to rewrite SciViews completely and make it platform independent (to work on Linux/Unix and MacOS X, as well as Windows). I have done some work in this direction when time permitted, but I am pretty busy with other work. During the holidays, I will continue to work in this direction. I will try to package a first running version of SciViews compatible with latest R and Rcmdr for Windows and Linux for next September. At least, I *have* to do so, because I *need* it for one of my teachings which will be done in a different University (where all machines are running with Linux)! So, my advice would be to check the web site again in September/October for some news. Unfortunately, I cannot promise more. Sorry for the long delays. I do my best, and the second programmer (Eric Lecoutre) has left the project a long time ago... so, I am alone on this! Best, Philippe Grosjean ..∞})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Liviu Andronic wrote: Thank you for the pointer. On the SciViews official site (http://www.sciviews.org/SciViews-R/index.html) I could not find any indications on this incompatibility. At any rate, I would have two questions related to the future of SciViews-R. Are there any developments planned in some near future that would make SciViews compatible with recent versions of R and Rcmdr? At the Unviversity of Social Sciences of Toulouse, for example, the most recent version of R is installed. And for statistics introductory classes, SciViews would be an important advantage. R should be downgraded to which version for the two to be compatible? Secondly, is there any chance that SciViews become available on Linux, again in some not so distant future? That is, would the tcltk2 package be ported to other OS's and would SciViews be subsequently enhanced to build on such systems? Last time I checked the net, no interesting information was available as to such developments. Maybe there is some beta version of tcltk2 that I don't know of.. Regards, Liviu On 7/12/07, Philippe Grosjean [EMAIL PROTECTED] wrote: As explained on the web page from where you downloaded SciViews 0.8-9, this version is not compatible with R 2.5.0. Best, Philippe Grosjean ..∞})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Liviu Andronic wrote: Hello everybody, I have a problem similar to that reported by Felipe. I installed R 2.5.0, Rcmdr from CRAN and SciViews-R 0.8-9 (with all the required and optional components). When accessing the R Commander menu from within SciViews, the links cannot be clicked. When pointing at them, the mouse transforms in a hand (as it normally does, similar to Internet hyperlinks). However, the links cannot be activated. I had the impression that in some way SciViews makes use of Internet Explorer in its GUI, and that the problem was somewhere there. But I could not get to the bottom of it. Is there any way to make SciViews correctly use Rcmdr functionality? Thanks in advance, Liviu On 6/20/07, Felipe Carrillo [EMAIL PROTECTED] wrote: Please help, I have SciViews(svGUI) and Rcmdr but when the SciViews Console opens the R commander menu don't work. Any ideas anybody? -- ..∞})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. __ 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] Me again, about the horrible documentation of tcltk
For those who are interested, I just cook a little tcltkHelp() function to ease access to the Tcl/Tk documentation under Windows. This is on the Wiki discussion of the TkCommands help page at: http://wiki.r-project.org/rwiki/doku.php?id=rdoc:tcltk:tkcommands Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Duncan Murdoch wrote: On 06/07/2007 3:51 AM, Mike Meredith wrote: I think it would help if the tcl/tk manuals were added to the RGui Help menu. Why google when they are on your hard drive already? I'd say they are too specialized for that. There are dozens of topics that are as important as this, but a GUI menu with more than a few entries is just unwieldy. We do have a text reference to the help files in the ?tcltk topic. Duncan Murdoch Cheers, Mike Mike Prager wrote: Alberto Monteiro [EMAIL PROTECTED] wrote: How on Earth can I know what are the arguments of any of the functions of the tcl/tk package? [...] My impression is that you as supposed to look in tck/tk manuals. For example, Googling on tk tck getopenfile pointed to this Web page: http://www.tcl.tk/man/tcl8.5/TkCmd/getOpenFile.htm Hope that helps. -- Mike Prager, NOAA, Beaufort, NC * Opinions expressed are personal and not represented otherwise. * Any use of tradenames does not constitute a NOAA endorsement. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Question concerning pastecs package
Hello, I already answered privately to your question. No, there is no translation of pastecs.pdf. The English documentation is accessible, as usual, by: ?turnpoints Regarding your specific question, 'info' is the quantity of information I associated with the turning points: I = -log2 P(t) where P is the probability to observe a turning point at time t under the null hypothesis that the time series is purely random, and thus, the distribution of turning points follows a normal distribution with: E(p) = 2/3*(n-2) var(p) = (16*n - 29)/90 with p, the number of observed turning points and n the number of observations. Ibanez (1982, in French, sorry... not my fault!) demonstrated that P(t) is: P(t) = 2*(1/n(t-1)! * (n-1)!) As you can easily imagine, from this point on, it is straightforward to construct a test to determine if the series is random (regarding the distribution of the turning points), more or less monotonic (more or less turning points than expected), See also the ref cited in the online help (Kendall 1976). References: --- Ibanez, F., 1982. Sur une nouvelle application de la théorie de l'information à la description des séries chronologiques planctoniques. J. Exp. Mar. Biol. Ecol., 4:619-632 Kendall, M.G., 1976. Time-series, 2nd ed. Charles Griffin Co, London Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Rainer M. Krug wrote: Hi I just installed the pastecs package and I am wondering: is there an english (or german) translation of the file pastecs.pdf? If not, is there an explanation somewhere of the object of type 'turnpoints' as a result of turnpoints(), especially the info field? Thanks, Rainer __ 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 Wiki down?
The site is up again. This was a wrong manipulation. Sorry. ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Martin Maechler wrote: Talbot == Talbot Katz [EMAIL PROTECTED] on Thu, 03 May 2007 12:35:27 -0400 writes: Talbot Hi. I can't access the site Talbot http://wiki.r-project.org/. I didn't find any Talbot notice about this on http://www.r-project.org/. Talbot Does anyone have any more information about the R Talbot Wiki status? Thanks! Yes, it is currently down. Thanks for the note. It's maintainer has hereby __ CC __ be notified as well. Regards, Martin Maechler ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Get the difference between two matrices with different length
Hello, The answer is in one page of the R Wiki (just created to address such a question, by the way): http://wiki.r-project.org/rwiki/doku.php?id=tips:data-manip:calc_on_two_tables ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Felix Wave wrote: Hello, I have got two matrices with different length. The matrices have 3 columuns. The first two are coordinates. The third is a measurement. Now I want to get a subtraction between every single value of the third column (between matrix1 and matrix2), but only if the two first coordinates in matrix1 and matrix2 are the same. I tried FUN=? in aggregate and ave, but I don't know the command for such a subtraction? Thank's a lot. Felix --- The matrixes (examlple): 1 0.1 0.0042 1 0.2 0.00423 1 0.4 0.00467 1 0.5 0.00518 1 0.6 0.0061 1 0.1 0.0043 1 0.2 0.00442 1 0.3 0.00433 1 0.4 0.0045 1 0.5 0.00524 1 0.7 0.006 My aim: --- 1 0.1 -0.0001 1 0.2 -0.00019 1 0.4 0.00017 1 0.5 -0.6 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A problem with svIDE in Tinn-R?
Hello, I konw I have some corrections to do in svIDE,... I simply don't have the time right now. Will try next week. Thank for reporting the problem. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Prof Brian Ripley wrote: It is a warning, and a warning about a long-standing error in svIDE. This is not to do with Tinn-R except perhap that the message gets mangled. I get from command-line R 1: '\A' is an unrecognized escape in a character string 2: unrecognized escape removed from ;for Options\AutoIndent: 0=Off, 1=follow language scoping and 2=copy from previous line\n Of course, a \ needs to be doubled in R character strings. That has always been the case, but the warning is new. Please take it up with the svIDE maintainer. On Sun, 29 Apr 2007, Kenneth Cabrera wrote: Hi R users: I want to know if any one of you had the problem with Tinn-R, when you call the library svIDE on the new R 2.5.0, (because in the old R 2.4.1 works with out any problem). I got this message: library(svIDE) Loading required package: tcltk Loading Tcl/Tk interface ... done Warning messages: 1: '\A' is an unrecognized escape in a character string 2: no se reconoce el valor 'save' Is it a critical warning? What would work and what not? What is it new in the new version that is not in the old version that makes this message appears? Thank you for your 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] regular expression help
gsub(^.*([[:alpha:]]).*$, \\1, vzor) ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Petr PIKAL wrote: Dear all as usual I am again lost in virtues of regular expressions. I have such character vector named vzor: [365] 61A 62C/27 65A/27 66C/29 69A/29 70C/31 73A/31 74C/33 77A/33 81A/35 82C/37 85A/37 86C/39 [378] 89A/39 90C/41 93A/41 94C/43 97A/43 98C/45 101A/45 102C/47 105A/47 106C/49 109A/49 110C/51 113A/51 and I want only letters from it. I tried gsub([[:alpha:]], \\1,vzor) Error in gsub([[:alpha:]], \\1, vzor) : invalid backreference 1 in regular expression gsub([:alpha:], \\1,vzor) gives me the same vector There is probably very simple solution to it which I overlooked and examples in help page did not help me to find it. Thank you Best regards Petr Pikal [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] software comparison
Hello, I just read this paper, and was surprised by: This study performs a comparison of the latest versions of nine different statistical software packages using StRD. These packages are SAS (9.1), SPSS (12.0), Excel (2003), Minitab (14.0), Stata (8.1), Splus (6.2), R (1.9.1), JMP (5.0), and StatCrunch (3.0). For a paper published in 2007, and submitted in April 2005, this is still surprising. If I my calculation is correct, in 2004, they would have used R 2.2.x, or something,... not 1.9.1? Anyway, does someone know if there is a chance 2.5.0 provides some improvements in some of the difficult cases for R 1.9.1 (for instance, improvement of the algorithms for calculating autocorrelation, ANOVA, linear regression or non linear regression)? Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Robert McFadden wrote: Dear R Users, May be you are interested in an article that compares 9 statistical softwares (including R). Any comments are appreciate. Article: Keeling, Kellie B.; Pavur, Robert J.A comparative study of the reliability of nine statistical software packages Computational Statistics and Data Analysis, Volume: 51, Issue: 8, 2007, pp. 3811-3831 Abstract The reliabilities of nine software packages commonly used in performing statistical analysis are assessed and compared. The (American) National Institute of Standards and Technology (NIST) data sets are used to evaluate the performance of these software packages with regard to univariate summary statistics, one-way ANOVA, linear regression, and nonlinear regression. Previous research has examined various versions of these software packages using the NIST data sets, but typically with fewer software packages than used in this study. This study provides insight into a relative comparison of a wide variety of software packages including two free statistical software packages, basic and advanced statistical software packages, and the popular Excel package. Substantive improvements from previous software reliability assessments are noted. Plots of principal components of a measure of the correct number of significant digits reveal how these packages tend to cluster for ANOVA and nonlinear regression. Best, Rob __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Abundance data ordination in R
Gavin Simpson wrote: On Sun, 2007-04-01 at 09:20 -0700, Milton Cezar Ribeiro wrote: Dear R-gurus I have a data.frame with abundance data for species and sites which looks like: mydf-data.frame( sp1=sample(0:10,5,replace=T), sp2=sample(0:20,5,replace=T), sp3=sample(0:4,5,replace=T), sp4=sample(0:2,5,replace=T)) rownames(mydf)-paste(sites,1:5,sep=) I would like make an ordination analysis of these data and my worries is about the zeros (absence of species) into the matrix. Up to I read (Gotelli - A primir of ecological statistics, 2004), when I have abundance data I cant compute Euclidian Distances because the zeros have the meaning of absence of the species and not as zero counting. Gotelli suggests one make principal coordinates analysis. I would like to here from you what you think about and what is the best packages and functions to I compute my distance matrices and do my ordination analysis. Can I considere zero as NA on my data.frame? Is there a good PDF book available about Multivariate Analysis for abundance data available on the web? In addition to the other suggestions, there is a Task View on CRAN for the topic of Environmetrics. This has a section describing the various ordination techniques available in R as well as functions to calculate distance/dissimilarity matrices: http://cran.r-project.org/src/contrib/Views/Environmetrics.html G ... And here are a couple of other suggestions: 1) Use a distance that does not take couples of zero as information. Typically, the Bray-Curtis distance is one of the most commonly used in such a case. 2) Possibly transform your data first, depending on the relative importance you want to give to rare species (typically, a log, or double square root transformations increase importance of rare species relative to abundant ones). 3) One approach is to use MultiDimensional Scaling (see MASS package) on the distance matrix to make the ordination in two or three dimensions. See the Venables Ripley's MASS book for details. 4) Another alternative is to use correspondence analysis, which uses the Chi2 distance and is adapted to abundances (it is designed to analyze contingency tables, but table of abundances, station versus species, could be considered as such a double entry contingency table in a way). Best, Philippe Grosjean Kind regards Miltinho Brazil __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Wikibooks
Bert Gunter wrote: Question: Many (perhaps most?) questions on the list are easily answerable simply by checking existing R Docs (Help file/man pages, Intro to R, etc.). Why would a Wiki be more effective in deflecting such questions from the mailing list than them? Why would too helpful R experts be more inclined to refer people to the Wiki than the existing docs? Bottom line: it's psychology at issue here, I think, not the form of the docs. Answer: The online help, vignettes and manuals have a very intimidating (i.e., technical) presentation for people that tend to be afraid of such a crude presentation. It is apparently not your case, and this is probably why you even don't realize this could be a problem for a non negligible fraction of R. The Wiki was primarily targeted to them. As you say: it's psychology at issue here. As other have pointed out, the main reason for the lack of success of the R Wiki is that the mailing lists, particularly R-Help, are sooo successful. However, I continue to consider that the mailing list is suboptimal in two cases: (1) when text is not enough to express the idea, and (2) for frequent questions that would certainly deserve a good compilation on a wiki page and a redirection to it everytime the question is asked. Best, Philippe Grosjean -- ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Disclaimer 1: None of this is meant to reflect one way or ther other on the usefulness of Wikis as a documentation format -- only their ability to change the Help list culture. Disclaimer 2: Others have repeatedly made similar comments (asking us to refer people to the docs rather than providing explicit answers, I mean). Cheers, Bert Gunter Genentech Nonclinical Statistics South San Francisco, CA 94404 650-467-7374 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Frank E Harrell Jr Sent: Thursday, March 29, 2007 3:32 PM To: Ben Bolker Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Wikibooks Ben Bolker wrote: Alberto Monteiro albmont at centroin.com.br writes: As a big fan of Wikipedia, it's frustrating to see how little there is about R in the correlated project, the Wikibooks: http://en.wikibooks.org/wiki/R_Programming Alberto Monteiro Well, we do have an R wiki -- http://wiki.r-project.org/rwiki/doku.php -- although it is not as active as I'd like. (We got stuck halfway through porting Paul Johnson's R Tips to it ...) Please contribute! Most of the (considerable) effort people expend in answering questions about R goes to the mailing lists -- I personally would like it if some tiny fraction of that energy could be redirected toward the wiki, where information can be presented in a nicer format and (ideally) polished over time -- rather than having to dig back through multiple threads on the mailing lists to get answers. (After that we have to get people to look for the answers on the wiki.) I would like to strongly second Ben. In some ways, R experts are too nice. Continuing to answer the same questions over and over does not lead to a better way using R wiki. I would rather see the work go into enhancing the wiki and refactoring information, and responses to many r-help please for help be see wiki topic x. While doing this let's consider putting a little more burden on new users to look for good answers already provided. Frank Just my two cents -- and I've been delinquent in my wiki'ing recently too ... Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Wikibooks
..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Dieter Menne wrote: Ben Bolker bolker at zoo.ufl.edu writes: Well, we do have an R wiki -- http://wiki.r-project.org/rwiki/doku.php -- although it is not as active as I'd like. (We got stuck halfway through porting Paul Johnson's R Tips to it ...) Please contribute! I once tried: http://wiki.r-project.org/rwiki/doku.php?id=guides:lmer-tests but I don't think I will do this again on the existing Wiki. I am a frequent Wikipedia-Writer, so I know how it works, but this was discouraging. 1) The structure of the Wiki was and is still incomprehensibly to me. I needed too much time to find out how to put the stuff into it. Really bad. This was the best design we obtained after a hard work of several tens of people. Sorry for you. By the way, did you ever noticed that Wikipedia basically has NO structure? It is intended to be mostly accessed by KEYWORDS. On the main page, you have: main (that page), then content (explanation and general links to the whole content), plus a couple of selected content links (featured, recent, random). So, if you like this structure, that is, basically, no structure and access through keywords... why not to do the same with the R Wiki? Just type your keyword in the top-right text entry and click search. Then, you don't need to care about that structure that is still incomprehensible to you. 2) I decided to use the large guides section, because I wanted the thread transcript to be one one page. If you check the revision history, you will find that I needed more than three hours to get it working. The main reason is the sluggish response, and the incomprehensible error messages or the lack of it when some was not matched or whatever (Thanks, Ben, for correcting the remaining errors). This is a problem of the Wiki software used, other Wikis such as Media(pedia) are much more tolerant or informant. As I said, sluggish response is probably due to a combination of a slow Internet communication from your computer to the server at the time you edited your page, the edition of a too large page, and lack of edition section per section (you can edit each paragraph separately). I already made some corrections on the Wiki when I was in USA (the server is in Belgium, Europe), and it was not sluggish at all... On other circumstances, I noted a much slower reaction, too. That's Internet! DokuWiki is NOT slower than Mediawiki, especially with an underused Wiki site as R wiki is currently. Then, Philippe Grosjean informed me: Your page is way too long and is a rather crude copy and paste from the long thread in the mailing list. Yes, I still believe so. Wiki pages are more effective when they are kept short. I disagree. Why do you have a large guides section? And taking into account the amount of work I put into reformatting the transcript, I decided it was my first and last contribution to the Wiki. The large guides section is for ... large guides, of course... but who said that they should be all contained in a single page??? Just quoting http://wiki.r-project.org/rwiki/doku.php?id=guides:guides: If it is a larger contribution with many pages, create a dedicated subsection in tutorials (like “stats-with-r”, for instance). The key is there: a large guide should better be represented by several wiki pages collected together in a dedicated subsection. Is it that hard to understand? Philippe Grosjean Dieter Menne __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fanny Clustering
1) Reduce the size of your sample (random or stratified subsampling), 2) Increase the memory of your computer available to R. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Sergio Della Franca wrote: Dear R-Helpers, I'd like to develop a fanny clustering on my data set(70.000 rows), but when i run the procedure i obtain this error: error in vector(double, lenght): too big dimension for the selected vector. How can i solve this problem? Thank you in advance. Sergio Della Franca. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fanny Clustering
Sergio Della Franca wrote: Ok, How can i increase the memory of your computer available to R? Well, if you would like to increase memory of MY computer... you are welcome to do so... but I doubt it would be of any use for you ;-) You don't tell us how much RAM you have currently, which platform you use, etc... The general approach is to use a computer with more RAM, up to the limit permitted by a 32-bit system for R, and then, to switch to a 64-bit version under Linux, if you need even more RAM. The other proposed solution is not stupid. With 70.000 cases, you have a fairly large dataset. You don't tell use how many groups you expect from your clustering, but it is often better to use a couple of tens, or hundreds of representative cases for each group, no more. In supervised classification, it is easier to build such a training set with relatively balanced number of items in each group, because targeted classification is known a priori from the manual classification provided. With unsupervised classification, you could either try a pure random subsampling, or select your subsample based on similarity according to a given distance measurement. I did something like that using a Malahanobis distance, MDS, and then, stratified subsampling inside a regular grid placed on top of the MDS plot. Otherwise, I am not a specialist of unsupervised classification, and other people here could have better suggestion. Best, Philippe Grosjean 2007/3/29, Philippe Grosjean [EMAIL PROTECTED]: 1) Reduce the size of your sample (random or stratified subsampling), 2) Increase the memory of your computer available to R. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Sergio Della Franca wrote: Dear R-Helpers, I'd like to develop a fanny clustering on my data set(70.000 rows), but when i run the procedure i obtain this error: error in vector(double, lenght): too big dimension for the selected vector. How can i solve this problem? Thank you in advance. Sergio Della Franca. [[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. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] non-linear curve fitting
Hello, If a least-square criterion is fine for you, you should use nls(). For the logistic curve, you have a convenient self-starting model available: SSlogis(). Look at: ?nls ?SSlogis Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Hufkens Koen wrote: Hi list, I have a little curve fitting problem. I would like to fit a sigmoid curve to my data using the following equation: f(x) = 1/(1 + exp(-(x-c)*b)) (or any other form for that matter) Where x is the distance/location within the dataframe, c is the shift of the curve across the dataframe and b is the steepness of the curve. I've been playing with glm() and glm.fit() but without any luck. for example the most simple example x = -10:10 y = 1/(1 + exp(-x)) glm(y ~ x, family=binomial(link=logit)) I get a warning: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) and some erratic results This is the most simple test to see if I could fit a curve to this perfect data so since this didn't work out, bringing in the extra parameters is a whole other ballgame so could someone give me a clue? Kind regards, Koen __ 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] listing all functions in R
Hello,
First, regarding GeSHi syntax highlighting for R, I have done one for
the R Wiki (plus the R function that generates the list of keywords
automatically). I will attach it to a second email send privately to
you, since the mailing list do not accept attachments.
For the problem of keeping web pages up-to-date with R code, I am also
considering this problem with the R Wiki. Although I still do not have a
completely working solution, the approach is similar to Sweave. I have a
function which extracts the R code from wiki pages (that is, it
'Stangles' the wiki page, in the Sweave terminology). I can get, thus,
the R code from all wiki pages in turn, test them and write a report
with a couple of R code lines. Here is are my functions:
getWikiRcode - function(wikipage, url = http://wiki.r-project.org/rwiki;,
strip.empty.lines = TRUE, strip.output = FALSE) {
# Read the raw wiki page
Url - paste(url, /doku.php?id=, wikipage, do=export_raw, sep =)
Raw - readLines(Url)
# Get only code r /code chunks from this page
Codestart - grep(^\\s*code, Raw)
Codeend - grep(^\\s*/code, Raw)
# A little bit of checking first
if (length(Codestart) != length(Codeend) || any(Codeend = Codestart))
stop(Malformed wiki page (wrong code... /code sections))
# Get only r code sections (those starting with code r from the list
Rstart - grep(^\\s*code r, Raw)
if (length(Rstart) == 0) return(character(0)) # no R code in this page
isRsection - Codestart %in% Rstart
Rend - Codeend[isRsection]
# Construct the list of text lines related to r code
R - data.frame(Start = Rstart, End = Rend)
Seq - function(x) seq(from = x[1], to = x[2])
Rrows - c(apply(R, 1, Seq), recursive = TRUE)
Rcode - Raw[Rrows]
# Eliminate code r and /code tags
Rcode - gsub(^\\s*/?code( r)?.*$, , Rcode)
# Eliminate prompt from R code ' ', or '+ ' at the begining of a line
Rcode - sub(^[+] , , Rcode)
# Possibly eliminate empty lines
if (strip.empty.lines) Rcode - Rcode[Rcode != ]
# Possibly eliminate output (lines starting with '#!')
if (strip.output) {
Routput - grep(^\\#\\!, Rcode)
if (length(Routput) 0) Rcode - Rcode[-Routput]
}
# Return the R code
return(Rcode)
}
rcode - getWikiRcode(tips:data-frames:merge)
rcode
sourceWikiRcode - function(wikipage, echo = TRUE, url =
http://wiki.r-project.org/rwiki;,
strip.empty.lines = TRUE, strip.output = FALSE, ...) {
# Call getWikiRcode() to extract r code from wiki pages
Rcode - getWikiRcode(wikipage = wikipage, url = url,
strip.empty.lines = strip.empty.lines, strip.output =
strip.output)
if (length(Rcode) == 0) {
warning(No r code in this page!)
} else {
Con - textConnection(Rcode)
source(Con, echo = echo, ...)
close(Con)
}
}
sourceWikiRcode(tips:data-frames:merge)
# Here, the last part of this page is not directly executable (data1 is
not defined)
# but the rest is fine!
This is suboptimal, and I am considering rewriting it in PHP to return R
code only from the wiki server.
Best,
Philippe Grosjean
Gavin Simpson wrote:
On Sat, 2007-01-06 at 10:58 -0500, Gabor Grothendieck wrote:
The arguments to the functions can differ too even if they
exist on multiple platforms. system() on Windows has the
input= argument but not on UNIX.
That's a good point Gabor, and one I hadn't considered as yet. As I'm
only just setting out on the road to providing R help resources for the
wider world (rather than the limited environs of the courses I have
run), I tend to not have thought about these things much - though I
guess I have a few gotchas waiting to bite me in the ass before too
long.
I am just starting to think about the best way to organise the snippets
of code to allow me to keep them up-to-date with current R and changes
in package code that the snippets use. Dropping the code verbatim into
PHP scripts isn't a good idea. At the moment I intend to store all
snippets in individual *.R files and read them into to variables within
the PHP scripts, from where they will be highlighted and formatted for
display.
It would be reasonably easy to write an R script to source all *.R files
in a directory to look for errors and problems. And having them all as
separate files means I can still use Emacs/ESS to prepare, format, and
run the code through R, which is my preferred environment.
All the best,
G
On 1/6/07, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 1/6/2007 9:25 AM, Gavin Simpson wrote:
On Sat, 2007-01-06 at 13:48 +, Prof Brian Ripley wrote:
Could you tell us what you mean by
Thank you for your reply, Prof
[R] How to detect if R is running on Mac OS X?
This question is probably trivial, but I don't find the answer. I have code that is different for Windows, Unix/Linux and Mac OSX. The man page of .Platform tells that .Platform$OS.type is the right way to test for it... but it also tels that it returns either windows or unix. Is Mac OS X reported as unix? If yes, how do I make the difference? Thanks, Philippe Grosjean __ 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] A question about R environment
Please, don't reinvent the wheel: putting functions in a dedicated
environment is one of the things done by R packages (together with a
good documentation of the function, and making them easily installable
on any R implementation). So, this is probably the time for you to read
the Writing R extensions manual, and to start implementing your own R
package!
Best,
Philippe Grosjean
François Pinard wrote:
[Tong Wang]
I created environment mytoolbox by : mytoolbox -
new.env(parent=baseenv()). Is there anyway I put it in the search
path? In a project, I often write some small functions, and load them
into my workspace directly, so when I list the objects with ls(), it
looks pretty messy. So I am wondering if it is possible to creat an
environment, and put these tools into this environment. For example,
I have functions fun1(), fun2() ... and creat an environment mytoolbox
which contains all these functions. And it should be somewhere in the
search path: .GlobalEnv mytoolbox package:methods.
Here is a trick, shown as a fairly simplified copy of my ~/.Rprofile.
It allows for a few simple functions always available, yet without
having to create a package, and leaving ls() and any later .RData file
unencumbered.
The idea is to use local() to prevent any unwanted clutter to leak out
(my real ~/.Rprofile holds more than shown below and use temporary
variables), to initialise a list meant to hold a bunch of functions or
other R things, and to save that list on the search path.
This example also demonstrate a few useful functions for when I read the
R mailing list. I often need to transfer part of emails containing
code excerpts within the window where R executes, while removing
quotation marks, white lines and other noise. I merely highlight-select
part of the message with the mouse, and then, within R, do things like:
xs() source the highlighted region
xd() read in a data.frame
xm() read in a matrix
xe() evaluate and print an expression
xv() read a list of values as a vector
The list above in decreasing order of usefulness (for me). Except for
xs(), which has no automatic printout, you may either let the others
print what they got, or assign their value to some variable. Arguments
are also possible, for example like this:
xd(T) read in a data.frame when the first line holds column names
if (interactive()) {
local({
fp.etc - list()
fp.etc$xsel.vector - function (...) {
connexion - textConnection(xselection())
on.exit(close(connexion))
scan(connexion, ...)
}
fp.etc$xsel.dataframe - function (...) {
connexion - textConnection(xselection())
on.exit(close(connexion))
read.table(connexion, ...)
}
fp.etc$xsel.matrix - function (...) {
connexion - textConnection(xselection())
on.exit(close(connexion))
data.matrix(read.table(connexion, ...))
}
fp.etc$xsel.eval - function (...) {
connexion - textConnection(xselection())
on.exit(close(connexion))
eval(parse(connexion, ...))
}
fp.etc$xsel.source - function (...) {
connexion - textConnection(xselection())
on.exit(close(connexion))
source(connexion, ...)
}
fp.etc$xselection - function ()
{
lignes - suppressWarnings(readLines('clipboard'))
lignes - lignes[lignes != '']
stopifnot(length(lignes) != 0)
marge - substr(lignes, 1, 1)
while (all(marge %in% c('', '+', ':', '|'))
|| all(marge == ' ')) {
lignes - substring(lignes, 2)
marge - substr(lignes, 1, 1)
}
lignes
}
fp.etc$xv - fp.etc$xsel.vector
fp.etc$xd - fp.etc$xsel.dataframe
fp.etc$xm - fp.etc$xsel.matrix
fp.etc$xe - fp.etc$xsel.eval
fp.etc$xs - fp.etc$xsel.source
attach(fp.etc, warn=FALSE)
})
}
# vim: ft=r
__
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] nonlinear quantile regression
You must specify starting conditions.
PhG
Ricardo Bessa wrote:
Hello, I’m with a problem in using nonlinear quantile regression, the
function nlrq.
I want to do a quantile regression o nonlinear function in the form
a*log(x)-b, the coefficients “a” and “b” is my objective. I try to use the
command:
funx - function(x,a,b){
res - a*log(x)-b
res
}
Dat.nlrq - nlrq(y ~ funx(x, a, b), data=Dat, tau=0.25, trace=TRUE)
But a can’t solve de problem, How I put the formula “y ~ funx(x,a,b)”?
_
MSN Busca: fácil, rápido, direto ao ponto. http://search.msn.com.br
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Colour-coded Editor for R Code
Hello, You have a rather large list of editor that support R syntax highlighting listed in: http://www.sciviews.org/_rgui/projects/Editors.html. Best, Philippe Grosjean Dan Bebber wrote: Jon, are you using Windows? If so, try WinEdt with library(RWinEdt). It has all the features you want and need. For Linux/Unix use EMACS. There is a section on CRAN about editors. Cheers, Dan Bebber Department of Plant Sciences University of Oxford __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Progress Monitor in R / looping
This question is regularly asked. Have a look at progress() in svMisc()
package (SciViews bundle).
Best,
Philippe Grosjean
Barry Rowlingson wrote:
Xiaofan Cao wrote:
Hi there,
I'm writing a program in R that has a few nested loops. I'd like to
monitor the progress when the program is running and be able to estimate
the remaining time.
A long time ago I started writing some code to give R something like
an 'iterator' object. You could do this:
ml=loop(5)
while(iterate(ml))
+ {cat(doing ,iteration(ml), of ,N(ml),\n,Ending at
,predictEnd(ml),\n);sleep(5)}
doing 1 of 5
Ending at Wed 25 Oct 2006 11:00:05 BST
doing 2 of 5
Ending at Wed 25 Oct 2006 11:00:20 BST
doing 3 of 5
Ending at Wed 25 Oct 2006 11:00:20 BST
doing 4 of 5
Ending at Wed 25 Oct 2006 11:00:20 BST
doing 5 of 5
Ending at Wed 25 Oct 2006 11:00:20 BST
you use loop(N) to construct a 1:N loop object, while(iterate(ml)) to
loop round it, iteration(ml) to get the current iteration number, N(ml)
to get the iteration limit, and predictEnd(ml) to guess when the whole
thing will finish.
All the information about the loop is encapsulated in the ml object.
It needs a chunk of polishing up and nobody seemed that interested in
it last time I mentioned it. My particular application was to MCMC,
where you could have an MCMC iterator object that was a subclass of my
simple loop class, and then you could have methods like if(isBurnIn(ml))
to decide when to start taking samples, or if(!isThinned(ml)) to decide
whether to store a sample from a thinned chain. Again, all the info
encapsulated in the loop object.
Another advantage is that unlike for(i in 1:1000) it doesn't
create a vector of 1000 objects...
If anyone thinks this is worth me working on then I'll try and find
some spare time (hah!) to fix it up. Or if anyone wants to take over, I
can throw my code at you at see if it sticks.
Barry
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Re: [R] ts vs zoo
Schweitzer, Markus wrote: Hello, I have lots of data in zoo format and would like to do some time series analysis. (using library(zoo), library(ts) ) My data is usually from one year, and I try for example stl() to find some seasonalities or trends. I have now accepted, that I might have to convert my series into ts() but still I am not able to execute the comand since stl() is not satisfied x-zoo(rnorm(365), as.Date(2005-01-01):as.Date(2005-12-31)) x-as.ts(x) #x-as.ts(x, frequency=12) #this has no effect frequency is not taken stl(x) Fehler in stl(x) : series is not periodic or has less than two periods Please, read the error message carefully: ... has less than two periods... And you say you have series of one year. stl() cannot be used with so short series. Otherwise, you must take care to define the time unit as year for using stl(), since it assumes that the periodic signal it extracts is of frequence one. Best, Philippe Grosjean I googled for an answer but I couldn t find any. Is it really necessary to transform my zoo objects to ts? how can I fix the frequency-problem. I hope you can help me. Thank you very much in advance and best regards, Markus [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ts vs zoo
Schweitzer, Markus wrote: thank you very much for the information. I guess I should have been more clear here. I was looking for the monthly or weekly trends within this one year period. Then, always keep in mind that stl() is looking for periodic component of a frequency = 1. This means you have to define the time unit so that you catch it. For monthly periodic component, use month as time unit. For weekly periodic component, use week as time unit. You must convert your data accordingly. Also keep in mind that stl() decomposes your series into a general trend, a periodic trend of frenquency 1, and noise, using an ADDITIVE model. So, if the components are multiplicative, you should use a different model. Otherwise, there is much more than stl() in R! In particular, you could look at any significant periodic component in your series by using spectrum(), for instance... still considering that your series is long enough, which is probably the case for looking at weekly periodic signals on a one-year long series. Best, Philippe Grosjean to get there I now only took the zoo object x and made x-as.ts(x) x-ts(x, frequency=7) #to get 52 weeks(Periods) with 7 days each - to get 12 periods e.g. months with 29,30 or 31 days, I guess I can only choose frequency=30 I then can run stl It is just a pitty, that the labeling (jan 2005, feb 2005 ..) has gone. So thank you for your hint with barplot and rollmean best regards, markus -Original Message- From: Achim Zeileis [mailto:[EMAIL PROTECTED] Sent: Donnerstag, 12. Oktober 2006 12:15 To: Schweitzer, Markus Cc: R-help@stat.math.ethz.ch Subject: Re: [R] ts vs zoo Markus, several comments: I have lots of data in zoo format and would like to do some time series analysis. (using library(zoo), library(ts) ) The ts package has been integrated into the stats package for a long time now... My data is usually from one year, and I try for example stl() to find some seasonalities or trends. As pointed out by Philippe, this is not what STL is made for. In STL you try to find seasonality patterns by loess smoothing the seasonality of subsequent years. If you have observations from just one year, there is just one seasonality pattern (at least if you look for monthly or quaterly patterns). I have now accepted, that I might have to convert my series into ts () but still I am not able to execute the comand since stl() is not satisfied And there are reasons for this: you need to have a regular time series with a certain frequency so that STL is applicable. (One could argue that ts is not the only format for regular time series but typically you can easily coerce back and forth between ts and zoo/zooreg. x-zoo(rnorm(365), as.Date(2005-01-01):as.Date(2005-12-31)) I don't think that this is what you want. Look at time(x). I guess you mean x - zoo(rnorm(365), seq(from = as.Date(2005-01-01), to = as.Date(2005-12-31), by = 1 day)) x-as.ts(x) #x-as.ts(x, frequency=12) #this has no effect frequency is not Here, it seems to me that you want to aggregate to monthly data, this can be done via x2 - aggregate(x, as.yearmon, mean) This is now (by default) a regular series with frequency 12 frequency(x2) and hence it can be easily coereced to ts and back (with almost no loss of information): as.zoo(as.ts(x2)) However, calling stl(as.ts(x2)) still complains that there are not enough periods because this is just a single year, i.e., only a single seasonality pattern. To look at this, you could do barplot(x2) For looking at the trend you could use a simple running mean plot(x) lines(rollmean(x, 14), 2) or you could also use loess() or some other smoother... For more details on the zoo package, see vignette(zoo, package = zoo) Best, Z __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [Fwd: Re: Block comments in R?]
Ooops! Sorry, I send it only to Uwe Ligges the first time.
Best,
Philippe Grosjean
This is perhaps another solution, more elegant in the way the block
comment is written... but it requires to redefine `!` and slows it a
little bit because it tests first its arguments before calling
.Primitive(!):
It takes advantage of `!` being not defined for character arguments:
!2
[1] FALSE
!some text
Error in !some text : invalid argument type
So, now, we will define it for character arguments (invisibly returns
the argument)
`!`- function(x)
+ if (inherits(x, character) == FALSE)
+ .Primitive(!)(x) else invisible(x)
Now, `!` can be used to construct a block comment:
A R script with block comments =
1+1 # This is a line comment
!'
This is a block comment spread
on several lines...
'
ls()
!!'
This is another block comment, possibly of higher
importance than the previous one
'
search()
!!!'
For color syntax highlighting and to better detect
the end of block comments, one may also decide to
use the same code for opening and closing the comments
like it is the present case
!!!'
!'
Note that the only constraint is to escape single quotes
in block comments (or not to use single quotes)
Of course, one could also decide to use double quotes
instead of single quotes
!'
!'
Now, it would be nice to have a little patch of .Primitive(!)
that simply displays no error message in case the argument of
`!`is a character sting. So, the hock would not be required
any more
!'
And of the R script =
Best,
Philippe Grosjean
Uwe Ligges wrote:
Robin Hankin wrote:
On 5 Oct 2006, at 10:05, Uwe Ligges wrote:
Wee-Jin Goh wrote:
Hello list,
Is there any way to perform a block comment in R? In C++, anything in
between a /* and */ is considered a comment, and it allows
programmers to comment out chunks of code for testing and debugging.
Is there such a feature in R?
This has frequently been asked on the list. Try to google for it. You
will find answers like
if(FALSE){
code block
commented
}
That method doesn't work for me:
if(FALSE){
if(12)
print(12)
else
print(12)
}
Use an editor that comments out a whole block which is what I do all the
time, e.g. use Tinn-R, Emacs or WinEdt, to mention just a few of them.
Or you can go ahead and use
if(FALSE){
if(12)
print(12)
else
print(12)
}
or
if(FALSE){'
if(12)
print(12)
else
print(12)
'}
Uwe
returns an error. How would I comment out that block of (incorrect) code?
or use a good editor that supports commenting and uncommenting blocks.
Uwe Ligges
--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
tel 023-8059-7743
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Re: [R] Maximum length of R GUI input line?
You should put your SQL query in a variable, and use this variable in your call. Something like: MyQuery - bla bla bla MyQuery - paste(MyQuery, more bla bla) # doMyRequest(MyQuery) Best, Philippe Grosjean Eric Fegraus wrote: Hello, I'm using R 2.3.1 on Windows. I'm generating some very long SQL statements. I do this by using paste() which will contain many strings and variables. I'm getting an error when the the total line length is longer than about 1013 characters. For example, it works with the line containing 1013 characters and not when it is 1059. I've looked into adjusting the options(width) and a handful of other settings. I have a feeling there is some other setting i'm missing that i can adjust. Any ideas? Thanks! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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] classification tables
x - c(1,2,3,4,2,3,3,1,2,3) y - c(2,1,3,4,1,3,3,2,2,3) table(x, y) y x 1 2 3 4 1 0 2 0 0 2 2 1 0 0 3 0 0 4 0 4 0 0 0 1 ?table Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Taka Matzmoto wrote: Dear R-users I have two vectors. One vector includes true values and the other vector has estimated values. Values are all integers from 1 to 4. For example, x - c(1,2,3,4,2,3,3,1,2,3) y - c(2,1,3,4,1,3,3,2,2,3) I would like to a classfication table x by y. With the table, I would like to calculate what percentage is correct classfication. Which R function do I need to use for creating a 4 * 4 classification table? Thank you. Taka, __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R and DDE (Dynamic Data Exchange)
Richard M. Heiberger wrote: I am thrilled to learn tcltk2 has DDE capability. It is the piece I have been needing to make ESS work directly with the RGUI on Windows. GNU emacs on Windows has a ddeclient, but no access to COM. So if R, or tcltk2 talking in both directions to R, has a ddeserver, all should be possible. I will be reading the documentation closely in a few weeks to tie it together and then intend to make it happen. Do you, or any other list member, have a sense of the size, complexity, ease, magnitude of the task I just defined? Any advice as I get started on it? Rich Well, to be honest, DDE is an old exchange protocol (the first one proposed by M$ in Windows version 1 or 2). It is not that reliable. In practice, when the communication is working fine, you have no problems with it. But if something fails in either the server or the client, you got a very bad behaviour sometimes. I think there is some interest to have DDE available for R (WinEdt uses DDE, I think... Uwe???), together with (D)COM, and socket server. Currently, I am improving the socket server build in svSocket (SciViews bundle) because it is the communication protocol we decided to push forward in Tinn-R, but there are other implementations out there. I think that using a socket server is more reliable and it is also a cross-platform solution. So, I would personnally prefer that solution. Best, Philippe Grosjean __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R and DDE (Dynamic Data Exchange)
Gabor Grothendieck wrote: You can access DDE via COM as in this example which uses DDE to open an Excel file. Note that Excel also supports COM directly and normally one would use COM with Excel, not DDE, so you might check if your application also supports COM. # opens an excel spreadsheet c:\test.xls using dde library(RDCOMClient) sh - COMCreate(Shell.Application) sh$Namespace(C:\\)$ParseName(test.xls)$InvokeVerb(Open) Well, I think you are really using COM here, not DDE. M$ implemented the same DDE commands in Excel and Word in COM to ease upgrading from DDE to COM... but the internal is completelly different! Best, Philippe Grosjean Also if you are going to access DDE via COM or just COM also check out the rcom package which is similar to RDCOMClient. On 7/17/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: R and DDE (Dynamic Data Exchange) Dear Rusers, I run an application (not mine) which acts as a DDE server. I would like to use R to get data from this application, say once per minute, and do some processing on it. I didn't find much info on the R DDE abilities, apart the tcltk2 package in which I will try to go deeper. I would be very thankful for any info, pointer or advice about the good ways to make R program get online data from a DDE server. Thanks Vincent __ 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 and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R and DDE (Dynamic Data Exchange)
Hello Vincent, I think there is not much else than tcltk2. It is a complete implementation of DDE (client/server), so it should fit your needs. There are lots of examples on the man page. Please, if you think it could be helpful for other users, do submit examples. I think real-time acquisition of data through DDE under Windows would interest a couple of users (including myself). Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. [EMAIL PROTECTED] wrote: R and DDE (Dynamic Data Exchange) Dear Rusers, I run an application (not mine) which acts as a DDE server. I would like to use R to get data from this application, say once per minute, and do some processing on it. I didn't find much info on the R DDE abilities, apart the tcltk2 package in which I will try to go deeper. I would be very thankful for any info, pointer or advice about the good ways to make R program get online data from a DDE server. Thanks Vincent __ 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 and provide commented, minimal, self-contained, reproducible code.
Re: [R] cat and positioning of the output
=?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
Hello R users!
I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression Reading row: i in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter i.
In package svMisc (SciViews bundle):
?progress
example(progress)
Best,
Philippe Grosjean
for(i in 1:header$M){
cat(Reading row: , i)
SparseIndex[[i]] - readBin( con, integer(), n=MIndexNumber[i], size=4 )
SparseSignal[[i]] - readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}
Many thanks
J?rn Schulz.
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Re: [R] cat and positioning of the output
Dan Gunter wrote:
=?ANSI_X3.4-1968?Q?J=3Frn_Schulz?= wrote:
Hello R users!
I like to use cat in a loop. I know, loops are not the best way in R ... but
my question: It is possible to overwrite the expression Reading row: i in
each iteration of the loop (print out in the below loop on the screen) or
more particulary to overwrite the counter i.
for(i in 1:header$M){
cat(Reading row: , i)
SparseIndex[[i]] - readBin( con, integer(), n=MIndexNumber[i], size=4 )
SparseSignal[[i]] - readBin( con, numeric(), n=MIndexNumber[i], size=4 )
}
Many thanks
J?rn Schulz.
On a UNIX terminal, adding '\r' will cause the cursor to go back to the
beginning of the same line. I can't speak for Windows.
e.g.
for ( i in 1:10 ) { cat(Number,i,\r); Sys.sleep(1) }; cat(\n)
-Dan
It works, but I don't like much strange things that can happen with \r
because the caret is located at the beginning of the line. Look at what
happens if you forgot the latests 'cat(\n)'. Also, note that for RGui
under windows, you must use flush.console(). So:
for (i in 1:10) {
cat(Number,i,\r)
flush.console()
Sys.sleep(1)
}
cat(\n)
does the job. The alternative is to use \b repeatedly, which is done
in progress() indeed.
Best,
Philippe Grosjean
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Re: [R] Continuation and parse
Well, you haven't used the search engines with the right key: the magic words are: RSiteSearch(incomplete line) With the first document being my query (almost two years ago), and the second one being Peter Dalgaard answer. You must adapt it to cope with internationalization, but basically, you could use something like: grep(\n2:,try(parse(textConnection(ls))), silent = TRUE)) numeric(0) grep(\n2:,try(parse(textConnection(ls()), silent = TRUE)) [1] 1 Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Jim Lemon wrote: Hi gurus, After an unsuccessful scrabble through the documentation and Jon's excellent search facility, I am no wiser as to how R recognizes an incomplete command line and politely raises its hand for more. The help page for parse gives no indication that it does anything more than spit the dummy when fed an incomplete command line, but something in there must recognize such ellipsis. Any hints? Jim __ 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] R Reporting - PDF/HTML mature presentation quality package?
Frank E Harrell Jr wrote: zubin wrote: Hello, searching for the key packages so i can output, Text, Tables ,and Graphics into a HTML or PDF report - have R create these reports in an easy and efficient way without LaTeX - I have searched the R pages but don't see any mature packages - anyone have any advice on a easy to use R package one can use for generating publication quality reports? Outputting HTML or PDF. Doing this without LaTeX is like doing statistical analysis without linear models and the Wilcoxon test. It depends the complexity of formatting and the intended use of the report. If required formatting is just title, bold, italic, etc. + tables and graphs inserted in the same page to be viewed in a web browser, HTML (or xHTML/CSS, to be more precise) can do a pretty good job (and it can do even much more). Of course, LaTeX + Sweave = PDF is another solution, richer in functionnalities, but more complex to install, especially on Windows. Zubin, you ask for mature package. You should look at R2HTML + svViews (from the SciViews bundle) that work hand in hand to generate chunks of xHTML/CSS elements from R objects (the so called, views), or complete HTML page collecting together several of these views (reports). Depending on the degree of maturity that is acceptable for you, you should perhaps plan a beta test and expect some code adaptation, as it is usual with any R package that is not intensively used. If you prefer dynamic reports, there are many approaches, but I tend to consider Rpad (also on CRAN) as one of the better solution out there. Note that it also uses R2HTML for R objects formatting, although Tom Short customized some of the R2HTML functions for a better use in Rpad. You should probably also customize and/or contribute to the development of R2HTML if you want a solution that best fits your own needs in any case. Best, Philippe Grosjean __ 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] R Reporting - PDF/HTML mature presentation quality package?
Jim Lemon wrote: I heartily second Phillipe's response. I just started a new job and the first thing required was a neat stats report for a dataset. I thought I would give R2HTML a try and about 5 minutes after downloading it, I was looking at the first draft of the report. I did have to do a bit of hacking on the graphics, but it was easy and I can now present the report first thing in the morning. Had I not been able to do this, I probably would have been told, You'll have to use SPSS. I was so impressed by R2HTML that I began writing a primitive HTML generator that will scan an R script and do something like R2HTML. I couldn't find anything like this as the svMisc package seems to have disappeared. No, it is still in the SciViews bundle. Tell me if you have problems with it. Best, Philippe Grosjean If anyone knows of something like this or is working on it, I'd appreciate knowing about it. Jim __ 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] R Wiki - official launch!
Hello all, We are pleased to announce the official launch of the R Wiki at http://wiki.r-project.org. Although there are already many sources of R documentation, this R Wiki is a complementary tool, in the sense that users become R documentation authors, a little bit like users become developers for R code. = The main sections are: - Getting Started: dedicated to very R beginners, - Guides: a section for books, tutorials and demos in Wiki format, - Tips: this is a large section with many small tipstricks, initially based on the excellent Paul Johnson's Rtips (http://pj.freefaculty.org/R/Rtips.html), - Links: users can contribute links about R here, - R Graph Gallery: an addition to discuss graphs in the Romain François' R Graph Gallery site (http://addictedtor.free.fr/graphiques/index.php), - R packages: packages authors/maintainers are free to add related material; R package users can also contribute package-specific material here. - R documentation: the wiki version of all R documentation (wikified Rd files), with the possibility for everybody to comment, add examples or anything else useful. Note that there are still some little formatting and navigation problems here, but they will be solved soon (do not report bugs yet, please!) - Users: sections where R users can create their own public page. It is also the place where everybody can comment on R events, like useR!2006 (see http://wiki.r-project.org/rwiki/doku.php?id=users:user-2006) - Wiki and playground: sections to learn how to write wiki pages and to exercise. As a R documentation reader, you could be interested by the additional information in the R Wiki. To be informed of new items added to the R Wiki, you have RSS feed available (see http://wiki.r-project.org/rwiki/doku.php?id=wiki:usage) If you have something interesting to share with other R users, this is the place to publish it. Here, you will receive the support of other people to enhance and keep your document up-to-date with the rapidly evolving R. Here are a couple of suggested uses: 1) If you feel there is an interesting thread on this R-Help mailing list, summarize and illustrate it in the right subsection of 'Tips'. That way, one could answer Please, visit Wiki page for further similar questions on the mailing list. The rich-formatted presentation of a R Wiki page is much easier to read that a mailing list thread in the archives, 2) Contribute to the official R documentation by adding material at the end of the wikified man pages in the R documentation section. Most valuable addition will eventually flow into to official documentation in subsequent R versions. 3) As a package author/maintainer, allow users to contribute various material (examples, comments, tutorials, ...) by creating a Wiki page dedicated to your package, and by adding its link in the 'URL' section of your description file. 4) Add a link to your own R-related web site in the 'Links' section. 5) Consider to publish your R tutorial / demo / course / book in the Guides section. The main advantage to publish it on the Wiki is the possibility to get help from your readers to keep this material updated (most of such contributed documents, including those on CRAN, are *not* regularly updated, if published elsewhere and if you do not revise them yourself regularly, that is, every six months!) 6) Start a page in the 'Users' section to share material under development. 7) As a R beginner, share your experience with other beginners in the 'Getting started' section. 8) For a little bit more fun, participate, or propose a new challenge. A challenge consists in solving a problem with optimized R code (optimization for speed is easy to quantify, but do not forgot to improve readability and style of your code!). We would like to advertise R Wiki challenges from time to time on this mailing list. No prize here,... just the satisfaction to have written the better code to solve a given problem. There are numerous other ways to use the R Wiki. Browse it to discover how useful it can be for you. There is also a mailing list dedicated to R Wiki developments: R-SIG-WIKI (https://stat.ethz.ch/mailman/listinfo/r-sig-wiki). On behalf of the R Wiki creators, Philippe Grosjean -- ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Mons, Belgium ( ( ( ( (web: http://www.umh.ac.be/~econum ) ) ) ) ) http://www.sciviews.org ( ( ( ( ( .. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
Re: [R] Functions starting with underscores
It is not allowed to start a variable name with an underscore. So, you
must use ` to call this non-conventional name:
'_foo' - function(x) 1
attr('_foo', 'bar') - 'pow'
Error: target of assignment expands to non-language object
attr(`_foo`, 'bar') - 'pow'
'_foo'
[1] _foo
`_foo`
function(x) 1
attr(,bar)
[1] pow
Best,
Philippe Grosjean
Joseph Wang wrote:
I'm having problems with functions starting with underscores
'_foo' - function(x) {1}
seems to work
but I can't assign an attribute to this function
attr('_foo', 'bar') - 'pow'
Any way of doing this? This is for a C++ - R wrapping system so I'd like to
keep the C++ names which start with underscores.
(please cc: responses to me personally)
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Re: [R] SciViews and R-2.3.0; does it work yet?
David Foreman wrote: Following upgrading to R-2.3.0 SciViews generates 2 warning messages (I suspect 1 for each dock) saying 'null environment deprecated', and the R Commander menu simply returns a 'file-name not found' error. I've had to go back to 2.2.1 for the moment (where everything works fine), hence relying on my memory for the error messages. Do I need to wait for a SciViews upgrade, or is it something else? Yes, I need to fix these problems before that SciViews-R is fully compatible with R 2.3.0. I'll do it as soon as possible, which means: not before then end of June, as I don't have much free time for now. Best, Philippe Grosjean __ 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] R pour débutant
Hello, You send this email to a miling list where language is English. Please, read the posting guide. Bon, je vais vous répondre en français cette fois (mais je ne sais pas à QUI ce mail est réellement adressé)! Vous trouverez des documents d'introduction à R en français dans la section documentation contributed du site http://cran.r-project.org. Vous y trouverez trois très bon documents d'introduction à R par Emmanuel Paradis, Yves Brostaux et Vincent Goulet. Tous trois sont de très bon niveau, mais le dernier est le plus récent. Donc, il est plus à jour par rapport à la version actuelle de R. Bien à vous, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Denis POIGNONEC wrote: Bonjour, Je suis actuellement doctorant (en fin de thèse) et je vais avoir besoin de me servir de R. Devant apprendre R tout seul, je suis tombé sur un mail de vous disant que vous aviez réaliser un tutorial sur ce logiciel pour des 100% débutant comme moi J'aurai essentiellement à utiliser des algo de clustering (SOM ou Nuée dyna) sur des matrices pouvant faire 41x230 Cependant je n'ai pas réussi à télécharger ce tutoriel. Le lien founi ne semble plus être actif. Vous serez t il possible de m'envoyer en copie ce document ou bien tout autre document ou lien susceptible de faciliter cet apprentissage ? Pour être honnête, je n'étais pas sensé avoir à utiliser ce logiciel, mais pour quelques raison d'encadrement', je me retrouve à 3 mois de la fin de ma thèse à commencer a analyser mes données. Par conséquent, tout conseil, remarque ou aide sera vraiment la bienvenue Je vous remercie sincèrement par avance Denis __ Denis POIGNONEC http://denis.poignonec.free.fr IRD CoRéUs BP A5 98848 Nouméa Cedex Nouvelle Calédonie mob: +(687) 92.09.17 __ 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] Rcmdr problem - SciViews R
Dear Saschin, As John told you, you should better make sure that Rcmdr works fine with R. I have seen a similar message once. It was due to missing libraries required by Rcmdr that could not be installed for some obscure reasons under SciViews-R. Once all required libraries were installed manually under R, everything worked fine. I was indeed not able to spot the problem, but at least, I found a solution. Look at all required libraries for Rcmdr in his DESCRIPTION file, and install them manually (Packages - Install package(s)...). Best, Philippe Grosjean John Fox wrote: Dear Saschin, Does the Rcmdr package load properly from the standard R for Windows SDI console? BTW, the reinstall of the Rcmdr package didn't go through (see your listing) because the package was apparently already loaded. Regards, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sachin J Sent: Tuesday, May 02, 2006 8:46 AM To: R-help@stat.math.ethz.ch Subject: [R] Rcmdr problem - SciViews R Hi, I am getting following error messages while using SciViews R. It displays a message saying: Package or Bundle Rcmdr was not found in C:\Software\R-22.1.1\Library would you like to install now?. However the Rcmdr package is there in the library. I reinstalled Rcmdr but still gives me same error message every time I try to use one of the GUI functions. Any pointers would be of great help. ERROR: Loading required package: datasets Loading required package: utils Loading required package: grDevices Loading required package: graphics Loading required package: stats Loading required package: methods Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: R2HTML Loading required package: svMisc Loading required package: svIO Loading required package: svViews Loading required package: Rcmdr Loading required package: car Error in .Tcl.args.objv(...) : argument default is missing, with no default Error: .onLoad failed in 'loadNamespace' for 'Rcmdr' trying URL 'http://www.sciviews.org/SciViews-R/Rcmdr_1.1-2.zip' Content type 'application/zip' length 788628 bytes opened URL downloaded 770Kb package 'Rcmdr' successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package 'Rcmdr' The downloaded packages are in C:\Documents and Settings\Local settings\Temp\Rtmp2g5Kpb\downloaded_packages updating HTML package descriptions Loading required package: Rcmdr Error in .Tcl.args.objv(...) : argument default is missing, with no default Error: .onLoad failed in 'loadNamespace' for 'Rcmdr' Error in .Tcl.args.objv(...) : argument default is missing, with no default Error: .onLoad failed in 'loadNamespace' for 'Rcmdr' TIA. Sachin - [[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] Rcmdr problem - SciViews R
John Fox wrote: Dear Philippe and Sachin, The only packages that Rcmdr absolutely needs are tcltk and car; if other packages (with the exception of rgl) are missing, then it will offer to install them, so a manual install shouldn't be necessary. That works fine under R, but as I said, for obscure reasons, it sometimes fails under SciViews-R. PhG Another possible source of problems, apparently, can be a saved workspace that is automatically reloaded when R starts up. Regards, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Philippe Grosjean Sent: Tuesday, May 02, 2006 3:43 PM To: John Fox Cc: R-help@stat.math.ethz.ch Subject: Re: [R] Rcmdr problem - SciViews R Dear Saschin, As John told you, you should better make sure that Rcmdr works fine with R. I have seen a similar message once. It was due to missing libraries required by Rcmdr that could not be installed for some obscure reasons under SciViews-R. Once all required libraries were installed manually under R, everything worked fine. I was indeed not able to spot the problem, but at least, I found a solution. Look at all required libraries for Rcmdr in his DESCRIPTION file, and install them manually (Packages - Install package(s)...). Best, Philippe Grosjean John Fox wrote: Dear Saschin, Does the Rcmdr package load properly from the standard R for Windows SDI console? BTW, the reinstall of the Rcmdr package didn't go through (see your listing) because the package was apparently already loaded. Regards, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sachin J Sent: Tuesday, May 02, 2006 8:46 AM To: R-help@stat.math.ethz.ch Subject: [R] Rcmdr problem - SciViews R Hi, I am getting following error messages while using SciViews R. It displays a message saying: Package or Bundle Rcmdr was not found in C:\Software\R-22.1.1\Library would you like to install now?. However the Rcmdr package is there in the library. I reinstalled Rcmdr but still gives me same error message every time I try to use one of the GUI functions. Any pointers would be of great help. ERROR: Loading required package: datasets Loading required package: utils Loading required package: grDevices Loading required package: graphics Loading required package: stats Loading required package: methods Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: R2HTML Loading required package: svMisc Loading required package: svIO Loading required package: svViews Loading required package: Rcmdr Loading required package: car Error in .Tcl.args.objv(...) : argument default is missing, with no default Error: .onLoad failed in 'loadNamespace' for 'Rcmdr' trying URL 'http://www.sciviews.org/SciViews-R/Rcmdr_1.1-2.zip' Content type 'application/zip' length 788628 bytes opened URL downloaded 770Kb package 'Rcmdr' successfully unpacked and MD5 sums checked Warning: cannot remove prior installation of package 'Rcmdr' The downloaded packages are in C:\Documents and Settings\Local settings\Temp\Rtmp2g5Kpb\downloaded_packages updating HTML package descriptions Loading required package: Rcmdr Error in .Tcl.args.objv(...) : argument default is missing, with no default Error: .onLoad failed in 'loadNamespace' for 'Rcmdr' Error in .Tcl.args.objv(...) : argument default is missing, with no default Error: .onLoad failed in 'loadNamespace' for 'Rcmdr' TIA. Sachin - [[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 __ 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] www.r-project.org
Romain, The R Web site is working fine. Even if it is not relifted from a long time, it is functional. So, this is the point... and it should remain, at least, as functional as it is. One aspect that could be easily relooked is the CSS file. I would definitely be in favor of a more styled CSS. I mean, there are now new fonts around that are designed to be more readable than Times, Helvetica and Courrier on the screen, and equally fine on the printed material. With CSS, it is always possible to define several fonts for one style, so that the style degrades nicely in case of missing fonts. So, such kind of change is safe, even for very old computers. It would be wonderful if we could get a more actual CSS file for R doc, for the Web site, and I would use the same for the R Wiki. That way, we will got homogeneity in the presentation. So, I definitely encourage you for (microchirurgical) propositions to actualize the presentation of the R Web site, and I will follow the decision of the R Core Team on this topic to make the R Wiki looking similar. Best, Philippe Grosjean Romain Francois wrote: Dear R users and developpers, My question is adressed to both of you, so I choose R-help to post it. Are there any plans to jazz up the main R website : http://www.r-project.org The look it have now is the same for a long time and kind of sad compared to other statistical package's website. Of course, the comparison is not fair, since companies are paying web designers to draw lollipop websites ... My first idea was to organize some kind of web designing contest. But, I had a small talk with Friedrich Leisch about that, who said that I shouldn't expect too many competitors. So, what about creating a small team, create a home page project and then propose it to the core team. It goes without saying it : The core team has the final word. What do you think ? Who would like to play ? Romain __ 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] www.r-project.org
OK, I try... What do you think about the fonts and styles of titles versus text in... http://wiki.r-project.org? This is obviously in the line of: would we change the styles in the CSS file (while we are replacing frames with appropriate styles too)? May be am I a little confused. Normal. After 14 hours continuous programming on R, I think that everybody starts to present serious troubles :-( OK... back to work. I still have 3 or 4 hours to finish this $¤!§çà program... Philippe Grosjean Jonathan Baron wrote: I volunteer to attempt this, but only after I get my grades in (May 8). If it gets done by someone else before that, I'll be happy. Don't worry. It won't look like my personal page, or even my R page. But I do know quite a bit about CSS. On 04/25/06 12:37, Dirk Eddelbuettel wrote: On 25 April 2006 at 13:18, Jonathan Baron wrote: | The only thing I might change is to replace the frames with some | sort of CSS-based positioning. Yes please! Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison I love this quote. He really did say something like it. 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] Considering port of SAS application to R
Please, read the R Data Import/Export manual provided with any version of R, and come back with more specific questions. In general, R cannot deal with datasets as large as those handled by SAS. But this is true only when you use standard R functions, like read.table(), which are not written to save memory and load very large datasets (other aspects are optimized). I would advise to put your data in a database and then access to it piece-by-piece using SQL queries. There are very little cases where you actually need the whole dataset in memory at once. A simple database system, if you just need to access those data (no complex database operations required) is SQLite. There is an R package to connect to such a database without extra software needed. Thus, very convenient. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. Werner Wernersen wrote: Hi there! I am considering to port a SAS application to R and I would like to hear your opinion if you think this is possible and worthwhile. SAS is mainly used to do data management and then to do some aggregations and simple computations on the data and to output a modified data set. The main problem I see is the size of the data file. As I have no access to SAS yet I cannot give real details but the SAS data file is about 7 gigabytes large. (It's only the basic SAS system without any additional modules) What do you think, would a port to R be possible with reasonable effort? Is R able to handle that size of data? Or is R prepared to work together with some database system? Thanks for your thoughts! Best regards, Werner - [[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] cat(), Rgui, and support for carriage return \r...
Prof Brian Ripley wrote: On Tue, 28 Mar 2006, Duncan Murdoch wrote: On 3/28/2006 11:00 AM, Prof Brian Ripley wrote: Rgui now supports \r in the same way as rterm. I notice that there's a slight change to the colour scheme: now the prompt is in foreground colour, rather than user colour. This might make sense (it's printed by the system, after all), but it looks a little strange at first. Yes, it was intentional. The problem is that you can now do cat(abcde\rf) and then the next line will be f de Actually, there is an interest to do so with GUIs, like R Commander or SciViews-R (although R commander uses its own in/out window by default). The idea is to work with commands constructed by the GUI, and report the corresponding command to the console, but to flag them with a special prompt, telling it is different from what the user actually entered. Something like: cat(\rGUI) # Tcl-triggered instruction would give the following prompt: GUI which is nice if there is a way to append a command in user color just after it, for instance: cat(ls()\n) # Also triggered by Tcl code giving: GUI ls() with GUI in foreground colour and ls() in user color. Perhaps is it not possible, or even, not desirable to get this result for other situations. Best, philippe Grosjean with the cursor on the 'd'. There is no longer a left-right divide between system output and user input, as you can have output to the right of user input. The previous behaviour was to mark as system output all the columns up to the 'e' here, so when you started entering new input it looked very odd indeed, changing colour in mid-word. I can change to making the prompt be explicitly regarded as user input, which would be backwards compatible and less odd in cases like this. Duncan Murdoch On Sun, 19 Mar 2006, Duncan Murdoch wrote: On 3/18/2006 2:39 PM, Duncan Murdoch wrote: On 3/17/2006 9:44 AM, Jeffrey Racine wrote: Hi, and thanks in advance for your time. Background - I am working on a package and wish to have a routine's progress reported. The routine can take some time, and I would like to inform the user about the routine's progress. I have scoured the archives but to no avail, so would like to solicit input from this list. I am successfully using cat(\rBootstrap replication , i, of , boot.num,) flush.console() # To flush stdout on windows systems which works as expected on *NIX systems and using Rterm under windows. However, under Rgui the carriage return \r is ignored, and I certainly don't want to use the newline escape sequence \n. Under Rgui it appears as Bootstrap replication 1 of 399Bootstrap replication 2 of 399Bootstrap... but I want it to function properly if at all possible. My question is simply whether there is a portable way to implement this so that it works regardless of the R platform the user may be working on? Many thanks for any/all suggestions. I've just been looking at the source code for this. I think it will be relatively easy to make \r in Rgui do a destructive CR (i.e. it will return to the start of the line, but clear any existing characters). I'll play around a bit and then do that for R-devel. Oops, this was a bad idea. I did commit the change for a while, but have reverted it now. It seems that the help system displays help pages by writing CR LF at the end of each line; the CR is \r, and my change above caused it to wipe out the line it had just written. The help pages ended up completely blank. I may look into supporting \r as a non-destructive CR, but that's harder, because it means low-level changes to the console display. Right now it only writes to the end of the text buffer; this would mean it would sometimes write to a spot before the end. I don't think it would be impossible to do, but it will take more time than I have right now. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ 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] S-PLUS 8 beta program [repost]
This is an excellent initiative! But how can you integrate GPL code in a software that is not GPL? As far as I understand it, GPL is a contaminant license, imposing to the whole software to be GPL too (or providing at least similar freedom). I have no doubt that you solved this problem. I am just curious about the solution you found. Best regards, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Pentagone (3D08) ( ( ( ( (Academie Universitaire Wallonie-Bruxelles ) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium ( ( ( ( ( ) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54 ( ( ( ( (email: [EMAIL PROTECTED] ) ) ) ) ) ( ( ( ( (web: http://www.umh.ac.be/~econum ) ) ) ) ) http://www.sciviews.org ( ( ( ( ( .. David Smith wrote: [Sorry about the duplicate posting; this one comes from the correct address. Please respond to me with any questions about this -- David.] Dear R-help readers, As Insightful announced at the DSC2005 meeting in Seattle, the next release of S-PLUS will introduce a new package system. Our goal is to provide package authors the means to create cutting-edge statistical methods currently available either as R packages or as S-PLUS library sections and deliver them to the entire community of S-PLUS and R users. In this release of S-PLUS, we plan to implement many low-level utility functions with the same API as R. Just as many R functions originated in S-PLUS, we plan on re-implementing many R functions in S-PLUS to provide S-PLUS users the ability to create packages of their work and distribute them to others as R users have done for many years. In the future, we expect package authors will be able to create a single package that will run in both environments. The actual package system would be a port of the R package system code, which furthers the exchangeability of S-PLUS and R code. The ported code will be available in a GPL library called Rcompat To demonstrate that R packages can now be ported to S-PLUS, we have - with the permissions of the authors - ported several R packages to run as S-PLUS packages. We are planning to make these packages available for download from an Insightful-hosted website (called csan.insightful.com for consistency with the CRAN site of R packages). The license terms of the source packages will always be respected, and these packages will all be available under their original open-source license. Any improvements to open-source packages, whether by Insightful or by others, will remain open-source. Our intent will be to grow the list of open-source, cross-system-compatible packages over time. While most existing R packages will not run automatically in S-PLUS, with some effort, a user should be able to port an existing R package to an S-PLUS package. More important, by using functions and interfaces now available in both systems, a user should be able to create a single package that will run in both S-PLUS and R in the future. (The judicious use of some system-specific if(is.R()) statement will help to this end.) As a proof of concept, we are developing a package that will run on both systems. In the future, we hope to post this package on both CSAN and CRAN sites. We are also working to provide S-PLUS library sections from our research group as S-PLUS packages that would also work in R. Our work on the S-PLUS package functionality is ongoing. We expect to begin beta testing in April. We invite R package authors who are interested in testing their packages in S-PLUS to participate in the beta test. As a beta participant, you will receive a beta version of S-PLUS that will be fully functional until the end of the beta period. You will also be able to send input to the development team regarding the S-PLUS package system. If you are a package author, and you are interested in participating in the beta test, see the full details on the S-PLUS 8 beta test and complete the registration form at the Insightful website: http://www.insightful.com/support/splus8beta/ Best regards from the S-PLUS product management team, Patrick Aboyoun (S-PLUS Platform) Michael O'Connell (Life Sciences) David Smith (Finance) -- David M Smith [EMAIL PROTECTED] Senior Product Manager, Insightful Corp, Seattle WA Tel: +1 (206) 802 2360 Fax: +1 (206) 283 6310 __ 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
Re: [R] S-PLUS 8 beta program [repost]
David Smith wrote: The GPL code is available as separately-downloaded packages for S-PLUS, as has been done for many years. My own Oswald library for S-PLUS was published under the GPL in 1997, for example, and many other authors produce open-source libraries for S-PLUS under a variety of licenses. The only difference is that they will be packaged as, well, packages rather than libraries. # David Smith Thank you for the explanation. The fact that GPL code is distributed *separately* from S-PLUS is the key point here. PhG __ 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 create a directoy with R
See ?dir.create, and take care at the 'recursive' argument in case you have to create several subdir levels at once. Best, Philippe Grosjean Sarah Goslee wrote: I think you need to use system(mkdir) or whatever is appropriate for your OS. Making directories is a function of the OS, not of R. If you need to make a truly cross-platform solution, you might need to check within your code what OS is being used, and call the appropriate system statement. (I think you can do this, but have never needed to.) That would be particularly important if you need to specify paths. Sarah On 3/27/06, pau carre [EMAIL PROTECTED] wrote: Hello, I am trying to create directories with R. I would like R to create directories because it is platform independent. I tried using file() and searching in R Data Import/Export but I did not succeed. I think it must be some function since exists the unlink to remove directories (and files). Pau __ 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 -- Sarah Goslee http://www.stringpage.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 __ 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] MenuRead() Question
Hi Keith,
If you want to define a Tk menu using MenuRead() and a text file to
define your menu, you have to start it with Tk.. That way, MenuRead()
recognizes that it is a Tk menu. So, rewrite your menu definition file as:
menu.txt - in RHOME
$Tk.KSesnMain
|$MenuTest
||Objects~~ ls()
||-
||Path ~~ search()
Note also that KSesnMain must point to a valid Tk window previously
constructed.
Best,
Philippe Grosjean
Keith Chamberlain wrote:
Dear List-mates,
I think the difficulty I'm having is localized to the MenuType() call made
from within MenuRead(). I'm not used to seeing text operations such as ^
or [], so am having trouble understanding what's going on.
I'm interested in understanding the regular expression:
regexpr(^[$]Tk[.].+/, menu), and why it my menus.txt file is not returning
at that point.
?regex explains that the ^ symbol excludes the text enclosed in brackets
what is in the character string in following brackets, so a bunch of
matching on string vectors going on that I don't understand well enough yet.
Do I need to install PCRE-6.6 for this to start working?
Rgds,
KeithC.
-Original Message-
From: Keith Chamberlain [mailto:[EMAIL PROTECTED]
Sent: Saturday, March 25, 2006 4:26 PM
To: 'r-help@stat.math.ethz.ch'
Cc: 'Philippe Grosjean'
Subject: MenuRead() Question
Dear List-mates,
I'm trying to read a tk window menu from a file using {svWidgets} and
'menus.txt' but am receiving Warnings without seeing the desired
consequences of the call.
library(svWidgets)
tkWinAdd(KSesnMain,title=kLab Session Manager for R, pos=+0+0)
MenuRead(file=menus.txt)
Warning messages:
1: Unrecognized menu type for $KSesnMain/MenuTest in: MenuType(menu)
2: Unrecognized menu type for $KSesnMain/MenuTest in: MenuType(menu)
3: Unrecognized menu type for $KSesnMain/MenuTest in: MenuType(menu)
4: Unrecognized menu type for $KSesnMain/MenuTest in: MenuType(menu)
menu.txt - in RHOME
$KSesnMain
|$MenuTest
||Objects ~~ ls()
||-
||Path ~~ search()
Please Advise,
KeithC.
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Re: [R] RGui: windows-record and command history
Duncan Murdoch wrote: On 3/23/2006 7:35 AM, Thomas Steiner wrote: a) How can I set the recording of all windows()-history forever to true? I want something like windows(record = TRUE) but not just for the window that opens then, but for all windows I will open ever. options(graphics.record=TRUE) will make that happen for the rest of the session. To really make it happen forever, you need to put this line in your Rprofile (see ?Rprofile for where that comes from). Watch out though: the graphics history is stored in your current workspace in memory, and it can get big. You might find you're running out of memory if you store everything, and you'll find your .RData files quite large if you save your workspace. And also, remember that a single graph history is shared by the various graph windows. This may lead to unexpected results in you work with several devices at once. On my todo list (but not for 2.3.0) is the possibility of setting a default history length, perhaps defaulting to saving the last 2 or 3 pages. That would be really great! Philippe Grosjean b) Scrolling up in RGui (windows 2000) to see past commands is nice, but: Is it possible to type eg wi and the arrow up and see the last command that started with wi (like windows()). I know this feature from Matlab (Uops, one of the forbidden words here? ;) ) and it's nice to have it. We have things like that on platforms that use the readline library for input, but Rgui doesn't. It would be nice, but it's a fair bit of work to implement properly and it's not on my todo list. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ 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] Classifying time series by shape over time
Hi, turnpoints() in library(pastecs) determines if the succession of peaks and pits is random, or not. I think that the hypothesis here is little bit stronger: it should fit a Gaussian. I just think a little bit to this problem, and I don't get a simple solution. Here is what I got, but this is subject certainly to many criticisms (feel free to do so!). The idea is to draw the cumulative distribution of the hits and fit it with a logistic curve. Then, predicted hits are back calculated (knowind that the logistic curve is symmetrical around 'xmid'), and the observed and predicted distributions of the hits are compared using a Kolmogorv-Smirnov goodness-of-fit test: # Enter example data id1 - data.frame( dates = as.Date(c(2004-12-01, 2005-01-01, 2005-02-01, 2005-03-01, 2005-04-01, 2005-05-01, 2005-06-01, 2005-07-01, 2005-08-01, 2005-09-01, 2005-10-01, 2005-11-01, 2005-12-01)), hits = c(3, 4, 10, 6, 35, 14, 33, 13, 3, 9, 8, 4, 3)) id2 - data.frame( dates = as.Date(c(2001-01-01, 2001-02-01, 2001-03-01, 2001-04-01, 2001-05-01, 2001-06-01, 2001-07-01, 2001-08-01, 2001-09-01, 2001-10-01, 2001-11-01, 2001-12-01, 2002-01-01, 2002-02-01, 2002-03-01, 2002-04-01, 2002-05-01, 2002-06-01, 2002-07-01, 2002-08-01, 2002-09-01, 2002-10-01, 2002-11-01, 2002-12-01, 2003-01-01, 2003-02-01, 2003-03-01)), hits = c(6, 5, 5, 6, 2, 5, 1, 6, 4, 10, 0, 3, 6, 5, 1, 2, 4, 4, 0, 1, 0, 2, 2, 2, 2, 3, 7)) # How does it look like? plot(id1$dates, id1$hits, type = l) plot(id2$dates, id2$hits, type = l) # Cumsum of hits and fit models id1$datenum - as.numeric(id1$dates) id1$cumhits - cumsum(id1$hits) id1.fit - nls(cumhits ~ SSlogis(datenum, Asym, xmid, scal), data = id1) summary(id1.fit) plot(id1$dates, id1$cumhits) lines(id1$dates, predict(id1.fit)) id2$datenum - as.numeric(id2$dates) id2$cumhits - cumsum(id2$hits) id2.fit - nls(cumhits ~ SSlogis(datenum, Asym, xmid, scal), data = id2) summary(id2.fit) plot(id2$dates, id2$cumhits) lines(id2$dates, predict(id2.fit)) # Get xmid and recalculate predicted values for hits xmid1 - coef(id1.fit)[xmid] id1$hitspred - predict(id1.fit, newdata = data.frame(datenum = xmid1 - abs(id1$datenum - xmid1))) plot(id1$dates, id1$hits, ylim = range(c(id1$hits, id1$hitspred))) lines(id1$dates, id1$hitspred) xmid2 - coef(id2.fit)[xmid] id2$hitspred - predict(id2.fit, newdata = data.frame(datenum = xmid2 - abs(id2$datenum - xmid2))) plot(id2$dates, id2$hits, ylim = range(c(id2$hits, id2$hitspred))) lines(id2$dates, id2$hitspred) # A two samples Kolmogorov-Smirnov test of goodness-of-fit ks.test(id1$hits, id1$hitspred) # H0 not rejected ks.test(id2$hits, id2$hitspred) # H0 rejected Best, Philippe Grosjean Kjetil Brinchmann Halvorsen wrote: Andreas Neumann wrote: Dear all, I have hundreds of thousands of univariate time series of the form: character seriesid, vector of Date, vector of integer (some exemplary data is at the end of the mail) I am trying to find the ones which somehow have a shape over time that looks like the histogramm of a (skewed) normal distribution: hist(rnorm(200,10,2)) The mean is not interesting, i.e. it does not matter if the first nonzero observation happens in the 2. or the 40. month of observation. So all that matters is: They should start sometime, the hits per month increase, at some point they decrease and then they more or less disappear. Short Example (hits at consecutive months (Dates omitted)): 1. series: 0 0 0 2 5 8 20 42 30 19 6 1 0 0 0- Good 2. series: 0 3 8 9 20 6 0 3 25 67 7 1 0 4 60 20 10 0 4 - Bad Series 1 would be an ideal case of what I am looking for. Graphical inspection would be easy but is not an option due to the huge amount of series. Does function turnpoints)= in package pastecs help_ Kjetil Questions: 1. Which (if at all) of the many packages that handle time series is appropriate for my problem? 2. Which general approach seems to be the most straightforward and best supported by R? - Is there a way to test the time series directly (preferably)? - Or do I need to type-cast them as some kind of histogram data and then test against the pdf of e.g. a normal distribution (but how)? - Or something totally different? Thank you for your time, Andreas Neumann Data Examples (id1 is good, id2 is bad): id1 dates hits 1 2004-12-01 3 2 2005-01-01 4 3 2005-02-0110 4 2005-03-01 6 5 2005-04-0135 6 2005-05-0114 7 2005-06-0133 8 2005-07-0113 9 2005-08-01 3 10 2005-09-01 9 11 2005-10-01 8 12 2005-11-01 4 13 2005-12-01 3 id2 dates hits 1 2001-01-01 6 2 2001-02-01 5 3 2001-03-01 5 4 2001-04-01 6 5 2001-05-01 2 6 2001-06-01 5 7 2001-07-01 1 8 2001-08
Re: [R] which.minimums not which.min
Fred J. wrote:
Philippe Grosjean [EMAIL PROTECTED] wrote: What Fred is looking for is
local minima/maxima, also known as turning
points, or pits/peaks in a series. You can look at ?turnpoints in
pastecs library.
x - c(1:4,0:5, 4, 11)
x
[1] 1 2 3 4 0 1 2 3 4 5 4 11
tp - turnpoints(x)
summary(tp)
Turning points for: x
nbr observations : 12
nbr ex-aequos : 0
nbr turning points: 4 (first point is a peak)
E(p) = 6.67 Var(p) = 1.81 (theoretical)
point type proba info
1 4 peak 0.1 3.3219281
2 5 pit 0.002380952 8.7142455
310 peak 0.005952381 7.3923174
411 pit 0.7 0.5849625
plot(tp) # Only useful for a longer and more complex series!
# Get the position of peaks
(1:length(x))[extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE)]
[1] 4 10
Warning message:
arguments after the first two are ignored in: UseMethod(extract, e, n,
...)
(1:length(x))[extract(tp, no.tp = FALSE, peak = FALSE, pit = TRUE)]
[1] 5 11
Warning message:
arguments after the first two are ignored in: UseMethod(extract, e, n,
...)
# By the way, there are warnings although it works well (I ask on R-Help)
Now, you can easily code your which.minima() function using turnpoints:
x - c(1:4,0:5, 4, 11)
x
tp - turnpoints(x)
summary(tp)
plot(tp) # Only useful for a longer and more complex series!
# Get the position of peaks
(1:length(x))[extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE)]
(1:length(x))[extract(tp, no.tp = FALSE, peak = FALSE, pit = TRUE)]
# By the way, there are warnings although it works well (I ask on R-Help)
which.minima - function(x) {
if (!require(pastecs)) stop(pastecs library is required!)
x - as.vector(x)
(1:length(x))[extract(turnpoints(x), no.tp = FALSE, peak = FALSE, pit =
TRUE)]
}
which.minima(x)
Of course, you could optimize this code. This is just a rough solution!
Best,
Philippe Grosjean
..�}))
) ) ) ) )
( ( ( ( (Prof. Philippe Grosjean
) ) ) ) )
( ( ( ( (Numerical Ecology of Aquatic Systems
) ) ) ) ) Mons-Hainaut University, Pentagone (3D08)
( ( ( ( (Academie Universitaire Wallonie-Bruxelles
) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium
( ( ( ( (
) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54
( ( ( ( (email: [EMAIL PROTECTED]
) ) ) ) )
( ( ( ( (web: http://www.umh.ac.be/~econum
) ) ) ) ) http://www.sciviews.org
( ( ( ( (
..
Is there a limit as far as the data input to the function turnpoints? It
seams to be unable to process a vector with 15000 records with number in the
form of 734.2983, the data is known to have picks and pits
The steps:
Where pp is the vector with data of the above-mentioned style.
tp - turnpoints(rev(pp))
mx_id_rev - (1:length(pp))[extract(tp, no.tp = FALSE, peak = TRUE, pit =
FALSE)]
tp
Turning points for: rev(pp)
nbr observations : 11745
nbr ex-aequos : 10273
nbr turning points: 1231 (first point is a pit)
E(p) = 7828.667 Var(p) = 2087.678 (theoretical)
mx_id_rev
numeric(0)
Regards,
There is certainly a limit, but not that low. My test gives (R under Win
XP with 1Gb RAM):
x - rnorm(15000)
library(pastecs)
Loading required package: boot
tp -turnpoints(rev(x))
tp
Turning points for: rev(x)
nbr observations : 15000
nbr ex-aequos : 0
nbr turning points: 10079 (first point is a peak)
E(p) = 9998.667 Var(p) = 2666.344 (theoretical)
res - (length(x):1)[extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE)]
length(res)
[1] 6250
res - (length(x):1)[extract(tp, n= 15000, no.tp = FALSE, peak = TRUE, pit =
FALSE)]
length(res)
[1] 6250
[1] 5040
plot(x[1:500], type = l)
points(res, x[res], col = 2)
That seems to work. So, there is a bug when you don't specify 'n'. I
work on a patch for that and upload the new version of pastecs package
soon. Thanks for pointing me this bug.
Best,
Philippe Grosjean
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Re: [R] Platform independent dialogs menus?
Keith Chamberlain wrote:
Dear list mates,
Are {utils} dialog box functions, and winMenuAdd... functions used to change
(e.g. Console) menus, platform dependent?
Yes, Windows-only as the 'win' prefix suggests it.
I'm writing a script loaded with .First that provides first time users in a
lab course with the ability to select, load, and change between what I
called a 'session' (more specific save that focuses on the session object I
defined rather than the whole workspace, intended to run many different
sessions through the course of what would be one workspace).
See also the 'session' package on CRAN for that.
I'm using winMenuAdd() calls to generate their 'Session' menu at startup,
the menus call functions sourced in for the menu actions. In the menu
actions, I call routines that use select.list() and file.choose() calls to
interact with users.
I do not work with Macs often, and from what I've gathered today in posts
about cross-platform difficulties, my sense of being intimidated seems
well placed to me (then again, breaks some sleep would probably help). I
have not had the chance to test routines on a Mac yet, so I have no idea
what to expect. Is this tract I took with winMenuAdd() related [{utils}
windows build] an appropriate route to take wrt the Mac build of R, or would
I be better off using another package?
For a platform-independent way of defining menus (you will have a
floating window with your menu), look at ?MenuAdd in package svWidgets
(SciViews bundle). With these functions, you even have more control on
the menus (define shortcuts, trigger the menus through R code, for
instance), and you can define your menu in one R instruction and a
simple text file to describe the menu structure, like this:
# Create a Tk window then add a menu to it
$MyTkWindow
|$MenuTest
||Objects ~~ ls()
||-
||Path ~~ search()
# Add menus to the RGui console (Windows only)
$ConsoleMain
|$Testit
||One ~~ cat(One triggered!\n)
||-
||Two ~~ cat(Two triggered!\n) ~~ state = disable
||$SubMenu
|||Three ~~ cat(Three triggered!\n)
|||Four ~~ cat(Four triggered!\n)
||Five~~ cat(Five triggered!\n)
# Add menu to the RGui console popup (Windows only)
$ConsolePopup
|$TestitPopup
||Six ~~ cat(Six triggered!\n)
If the preceeding menu definition is in a file named Menus.txt in the
/gui subdirectory of your MyPackage package, you can do:
library(svWidgets)
tkWinAdd(MyTkWindow, title = Menu window, pos =-40+20)
MenuReadPackage(MyPackage)
... and you got all your menus configured at once (for MyTkWindows +
RGui console + RGui console popup menu
Best,
Philippe Grosjean
Please advise,
KeithC.
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Re: [R] Platform independent dialogs menus?
Keith Chamberlain wrote:
Dear Philippe, ( list)
I am not sure what is meant by 'floating window' but thank you for
clarifying the 'win' prefix. I had been considering different possible
senses of that prefix: win as in 'ts' window windowing functions (clearly
not), a generic 'win'dow function (abbreviated) for some GUI, or ms windows
GUI windowing function in particular. I'm noticing that the description in
{utils:winMenuAdd} indicates 'for windows', and it's quite clear (now,
anyway) that it is to be taken as ms windows. But cool, I WAS barking down
the wrong tree can now refocus efforts. Curious how the correct meaning
did not pop out at me.
I was not aware of the {Session} package. What I've merely glanced at
suggests the package is exactly (or really, really darn close) to what I had
in mind. I appreciate the suggestion.
You're welcome. You will often notice that it worth doing a search on
CRAN -well, as simple as looking at a couple of well-choosen keywords
with RSiteSearch()-, before programming something new. Often, the
functionnality already exists somewhere, or at least, a good starting
point for your own development. Note that I am also working on possible
improvements of 'session'. If you like, I can send you my code.
I downloaded SciViews Tinn-R 2 days ago, and LOVE Tinn-R so far; syntax
highlighting, oh yes! My rudimentary understanding, however, was that
SciViews was only compiled for MS Windows so far. Can I run SciViews
natively on a Mac now, or is the cross-platform part specific to some of the
routines?
Well, it is moving vey slowly to a platform-independent (and
graphical widgets-independent) solution with the SciViews bundle on
CRAN. This move is slow because, as a Windows user, I am satisfied by
the current SciViews-R + R Commander + Tinn-R implementation for
Windows, and I also have many priority tasks over this one.
Also for Tinn-R, Jose-Claudio Faria and myself consider to reimplement
it in a platform-independent editor (using jEdit or Eclipse as a
starting basis), but we still haven't time to start doing it. There are
still many improvements to be done on the actual Tinn-R. For instance,
Jose-Claudio is currently working on nice Sweave extensions for Tinn-R.
Best,
Philippe Grosjean
Respecftully,
KeithC.
-Original Message-
From: Philippe Grosjean [mailto:[EMAIL PROTECTED]
Sent: Monday, March 20, 2006 6:18 AM
To: Keith Chamberlain
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Platform independent dialogs menus?
Keith Chamberlain wrote:
Dear list mates,
Are {utils} dialog box functions, and winMenuAdd... functions used to
change (e.g. Console) menus, platform dependent?
Yes, Windows-only as the 'win' prefix suggests it.
I'm writing a script loaded with .First that provides first time users in
a lab course with the ability to select, load, and change between what I
called a 'session' (more specific save that focuses on the session object
I defined rather than the whole workspace, intended to run many
different sessions through the course of what would be one workspace).
See also the 'session' package on CRAN for that.
I'm using winMenuAdd() calls to generate their 'Session' menu at startup,
the menus call functions sourced in for the menu actions. In the menu
actions, I call routines that use select.list() and file.choose() calls to
interact with users.
I do not work with Macs often, and from what I've gathered today in posts
about cross-platform difficulties, my sense of being intimidated seems
well placed to me (then again, breaks some sleep would probably help). I
have not had the chance to test routines on a Mac yet, so I have no idea
what to expect. Is this tract I took with winMenuAdd() related [{utils}
windows build] an appropriate route to take wrt the Mac build of R, or
would
I be better off using another package?
For a platform-independent way of defining menus (you will have a
floating window with your menu), look at ?MenuAdd in package svWidgets
(SciViews bundle). With these functions, you even have more control on
the menus (define shortcuts, trigger the menus through R code, for
instance), and you can define your menu in one R instruction and a
simple text file to describe the menu structure, like this:
# Create a Tk window then add a menu to it
$MyTkWindow
|$MenuTest
||Objects ~~ ls()
||-
||Path ~~ search()
# Add menus to the RGui console (Windows only)
$ConsoleMain
|$Testit
||One ~~ cat(One triggered!\n)
||-
||Two ~~ cat(Two triggered!\n) ~~ state = disable
||$SubMenu
|||Three ~~ cat(Three triggered!\n)
|||Four ~~ cat(Four triggered!\n)
||Five ~~ cat(Five triggered!\n)
# Add menu to the RGui console popup (Windows only)
$ConsolePopup
|$TestitPopup
||Six ~~ cat(Six triggered!\n)
If the preceeding menu definition is in a file named Menus.txt in the
/gui subdirectory of your MyPackage
Re: [R] cat(), Rgui, and support for carriage return \r...
How did you look in the archives? It is already a dozen times that I answer:
library(svMisc) # SciViews bundle
?progress
on this list for a similar question.
If you do:
RSiteSearch(progress)
you have hundreds of results, with several items in the first page that
point to this function.
(actually, this function repeatedly uses \b which works on all system
tested (Linux console, RTerm, RGui, SciViews-R).
Best,
Philippe Grosjean
Duncan Murdoch wrote:
On 3/17/2006 9:44 AM, Jeffrey Racine wrote:
Hi, and thanks in advance for your time.
Background - I am working on a package and wish to have a routine's
progress reported. The routine can take some time, and I would like to
inform the user about the routine's progress. I have scoured the
archives but to no avail, so would like to solicit input from this list.
I am successfully using
cat(\rBootstrap replication , i, of , boot.num,)
flush.console() # To flush stdout on windows systems
which works as expected on *NIX systems and using Rterm under windows.
However, under Rgui the carriage return \r is ignored, and I certainly
don't want to use the newline escape sequence \n. Under Rgui it appears
as
Bootstrap replication 1 of 399Bootstrap replication 2 of 399Bootstrap...
but I want it to function properly if at all possible.
My question is simply whether there is a portable way to implement this
so that it works regardless of the R platform the user may be working
on?
Many thanks for any/all suggestions.
I've just been looking at the source code for this. I think it will be
relatively easy to make \r in Rgui do a destructive CR (i.e. it will
return to the start of the line, but clear any existing characters).
I'll play around a bit and then do that for R-devel.
In the meantime, \b does a destructive backspace, so you can get the
effect you want with something like this:
msg -
for (i in 1:1000) {
cat(rep(\b, nchar(msg)), sep=)
msg - paste(Message , i)
cat(msg)
flush.console()
}
This seems to work in Rgui, Rterm, (and R on Unix, if you get rid of the
flush.console call).
Duncan Murdoch
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Re: [R] Additional arguments in S3 method produces a warning
I totally agree with these considerations. However, there is another
point to consider: any existing definition of a generic function.
At the time I programmed this in pastecs (first under S-PLUS), I found
an already defined extract(e, n, ...) generic function. So, I decided to
stick with the original definition, even if 'e' or 'n' did not mean
anything special for my own use.
Ironically, doing a quick search on R, it appears that extract() is
defined only in pastecs library...
Best,
Philippe Grosjean
Martin Maechler wrote:
HenrikB == Henrik Bengtsson [EMAIL PROTECTED]
on Thu, 16 Mar 2006 07:48:49 +0100 writes:
HenrikB It is even better/more generic(!) to have:
HenrikB extract - function(...) UseMethod(extract)
HenrikB Specifying the object argument or the method
HenrikB arguments of a generic function will restrict any
HenrikB other methods with the same name to have the same
HenrikB argument. By also excluding the object argument,
HenrikB default functions such as search() will also be
HenrikB called if the generic function is called without
HenrikB any arguments.
HenrikB [http://www.maths.lth.se/help/R/RCC/]
HenrikB /Henrik
Hmm, sorry, but that is Henrik's own ``style sheet'' which
contains some views that I (and AFAIK other R-core members)
do not share.
The grain of truth in Henrik's statement is that for a generic
function, S3 or S4, one should carefully consider which
arguments should be shared by all methods and which not.
But having at least one `` non-... '' argument should be the
rule, and is even a necessity for S4.
Hence I'd strongly discourage defining generic functions with
only a (...) argument list.
HenrikB On 3/15/06, Gabor Grothendieck
HenrikB [EMAIL PROTECTED] wrote:
Define extract like this:
extract - function(e, n, ...) UseMethod(extract)
# test -- no warning
extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE)
yes, I agree with Gabor
Martin Maechler,
ETH Zurich
On 3/15/06, Philippe Grosjean [EMAIL PROTECTED] wrote:
Hello,
I just notice this:
x - c(1:4,0:5, 4, 11)
library(pastecs)
Loading required package: boot
tp - turnpoints(x)
extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE)
[1] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE
FALSE
Warning message:
arguments after the first two are ignored in: UseMethod(extract, e, n,
...)
extract(tp)
[1] 0 0 0 1 -1 0 0 0 0 1 -1 0
Warning message:
arguments after the first two are ignored in: UseMethod(extract, e, n,
...)
My extract.turnpoints() function produces warnings. I can easily spot
the origin of this warning:
extract
function (e, n, ...)
UseMethod(extract, e, n, ...)
extract.turnpoints
function (e, n, no.tp = 0, peak = 1, pit = -1, ...)
{
if (missing(n))
n - length(e)
res - rep(no.tp, length.out = e$n)
res[e$pos[e$peaks]] - peak
res[e$pos[e$pits]] - pit
if (n length(res) n 0)
res - res[1:n]
res
}
This is because my extract.turnpoints() method defines more arguments
than 'e' and 'n' in the generic function. However,
1) I though that the '...' argument in S3 generic function was there to
allow defining/passing additional arguments in/to S3 methods. Is this
correct? If yes, why the warning?
2) Despite the warning says arguments after the first two are ignored,
this appears not to be the case: in this example, 'no.tp', 'peak' and
'pit' arguments are taken into account, as you can see (different
behaviour if you give other values to them).
I am a little bit lost. Could someone help me, please.
Best,
Philippe Grosjean
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Re: [R] matrix indexing
This is really elementary indexing in S language: matA[matB] Best, Philippe Grosjean tom wright wrote: Can someone please give me a pointer here. I have two matrices matA A B C 1 5 2 4 2 2 4 3 3 1 2 4 matB A B C 1 TRUEFALSE TRUE 2 FALSE TRUETRUE 3 FALSE FALSE FALSE how do I extract all the values from matA where the coresponding entry in matB == TRUE (or FALSE), perferably in vector form. Many 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 __ 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] which.minimums not which.min
What Fred is looking for is local minima/maxima, also known as turning
points, or pits/peaks in a series. You can look at ?turnpoints in
pastecs library.
x - c(1:4,0:5, 4, 11)
x
[1] 1 2 3 4 0 1 2 3 4 5 4 11
tp - turnpoints(x)
summary(tp)
Turning points for: x
nbr observations : 12
nbr ex-aequos : 0
nbr turning points: 4 (first point is a peak)
E(p) = 6.67 Var(p) = 1.81 (theoretical)
point type proba info
1 4 peak 0.1 3.3219281
2 5 pit 0.002380952 8.7142455
310 peak 0.005952381 7.3923174
411 pit 0.7 0.5849625
plot(tp) # Only useful for a longer and more complex series!
# Get the position of peaks
(1:length(x))[extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE)]
[1] 4 10
Warning message:
arguments after the first two are ignored in: UseMethod(extract, e, n,
...)
(1:length(x))[extract(tp, no.tp = FALSE, peak = FALSE, pit = TRUE)]
[1] 5 11
Warning message:
arguments after the first two are ignored in: UseMethod(extract, e, n,
...)
# By the way, there are warnings although it works well (I ask on R-Help)
Now, you can easily code your which.minima() function using turnpoints:
x - c(1:4,0:5, 4, 11)
x
tp - turnpoints(x)
summary(tp)
plot(tp) # Only useful for a longer and more complex series!
# Get the position of peaks
(1:length(x))[extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE)]
(1:length(x))[extract(tp, no.tp = FALSE, peak = FALSE, pit = TRUE)]
# By the way, there are warnings although it works well (I ask on R-Help)
which.minima - function(x) {
if (!require(pastecs)) stop(pastecs library is required!)
x - as.vector(x)
(1:length(x))[extract(turnpoints(x), no.tp = FALSE, peak = FALSE, pit =
TRUE)]
}
which.minima(x)
Of course, you could optimize this code. This is just a rough solution!
Best,
Philippe Grosjean
..°}))
) ) ) ) )
( ( ( ( (Prof. Philippe Grosjean
) ) ) ) )
( ( ( ( (Numerical Ecology of Aquatic Systems
) ) ) ) ) Mons-Hainaut University, Pentagone (3D08)
( ( ( ( (Academie Universitaire Wallonie-Bruxelles
) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium
( ( ( ( (
) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54
( ( ( ( (email: [EMAIL PROTECTED]
) ) ) ) )
( ( ( ( (web: http://www.umh.ac.be/~econum
) ) ) ) ) http://www.sciviews.org
( ( ( ( (
..
Marc Schwartz (via MN) wrote:
On Wed, 2006-03-15 at 11:32 -0800, Fred J. wrote:
Hi
Is there a function which determines the location, i.e., index of
the all minimums or maximums of a numeric vector.
Which.min(x) only finds the (first) of such.
x - c(1:4,0:5, 4, 11)
x
[1] 1 2 3 4 0 1 2 3 4 5 4 11
which.min(x)
[1] 5
which.max(x)
[1] 11
but I need
which.min(x) to be 5 11
which.max(x) to be 4 10
thanks
There is something wrong with your example code versus data here, since:
x
[1] 1 2 3 4 0 1 2 3 4 5 4 11
which.min(x)
[1] 5
which.max(x)
[1] 12
There is one one minimum value of 0 in that vector and only one maximum
value of 11.
If you had a vector 'x':
x - c(1:4, 0:5, 4, 0, 5)
x
[1] 1 2 3 4 0 1 2 3 4 5 4 0 5
You could then do the following to get the indices of the multiple
min/max values:
which(x == min(x))
[1] 5 12
which(x == max(x))
[1] 10 13
The only other thing that I can think you might be considering would be
local minima/maxima in the vector and if that is what you want using:
RSiteSearch(local minima)
or
RSiteSearch(peaks)
should lead you to some solutions that have been discussed previously.
HTH,
Marc Schwartz
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[R] Additional arguments in S3 method produces a warning
Hello,
I just notice this:
x - c(1:4,0:5, 4, 11)
library(pastecs)
Loading required package: boot
tp - turnpoints(x)
extract(tp, no.tp = FALSE, peak = TRUE, pit = FALSE)
[1] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE
FALSE
Warning message:
arguments after the first two are ignored in: UseMethod(extract, e, n,
...)
extract(tp)
[1] 0 0 0 1 -1 0 0 0 0 1 -1 0
Warning message:
arguments after the first two are ignored in: UseMethod(extract, e, n,
...)
My extract.turnpoints() function produces warnings. I can easily spot
the origin of this warning:
extract
function (e, n, ...)
UseMethod(extract, e, n, ...)
extract.turnpoints
function (e, n, no.tp = 0, peak = 1, pit = -1, ...)
{
if (missing(n))
n - length(e)
res - rep(no.tp, length.out = e$n)
res[e$pos[e$peaks]] - peak
res[e$pos[e$pits]] - pit
if (n length(res) n 0)
res - res[1:n]
res
}
This is because my extract.turnpoints() method defines more arguments
than 'e' and 'n' in the generic function. However,
1) I though that the '...' argument in S3 generic function was there to
allow defining/passing additional arguments in/to S3 methods. Is this
correct? If yes, why the warning?
2) Despite the warning says arguments after the first two are ignored,
this appears not to be the case: in this example, 'no.tp', 'peak' and
'pit' arguments are taken into account, as you can see (different
behaviour if you give other values to them).
I am a little bit lost. Could someone help me, please.
Best,
Philippe Grosjean
--
..°}))
) ) ) ) )
( ( ( ( (Prof. Philippe Grosjean
) ) ) ) )
( ( ( ( (Numerical Ecology of Aquatic Systems
) ) ) ) ) Mons-Hainaut University, Pentagone (3D08)
( ( ( ( (Academie Universitaire Wallonie-Bruxelles
) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium
( ( ( ( (
) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54
( ( ( ( (email: [EMAIL PROTECTED]
) ) ) ) )
( ( ( ( (web: http://www.umh.ac.be/~econum
) ) ) ) ) http://www.sciviews.org
( ( ( ( (
..
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Re: [R] lapply vs. for (was: Incrementing a counter in lapply)
the for() loop is very slow in S-PLUS. This is probably one of the motivation of developing the apply() family of functions (as well as the ugly For() loop) under this system. Now, for() loops are much faster in R. Also, if you look at the R code in apply(), you will realize that there is a for() loop in it! So, why would you prefer using apply() or the like? 1) If you write code to be run both in S-PLUS and R, 2) If you want more concise code (much housekeeping is done by apply() and co), 3) Because the apply() family is more in the phylosophy of vectorized calculation, that is, the favored approach in S language. Take care, however, that the optimal approach is not just to replace for() loops with apply() and co, but to *rethink* completelly your algorithm in a vectorized way. This often ends up with a very different solution! Best, Philippe Grosjean Gregor Gorjanc wrote: From: Thomas Lumley On Tue, 14 Mar 2006, John McHenry wrote: Thanks, Gabor Thomas. Apologies, but I used an example that obfuscated the question that I wanted to ask. I really wanted to know how to have extra arguments in functions that would allow, per the example code, for something like a counter to be incremented. Thomas's suggestion of using mapply (reproduced below with corrections) is probably closest. It is probably worth pointing out here that the R documentation does not specify the order in which lapply() does the computation. If you could work out how to increment a counter (and you could, with sufficient effort), it would not necessarily work, because the 'i'th evaluation would not necessarily be of the 'i'th element. [lapply() does in fact start at the beginning, go on until it gets to the end, and then stop, but this isn't documented. Suppose R became multithreaded, for example] The corollary, it seems to me, is that sometimes it's better to leave the good old for loop alone. It's not always profitable to turn for loops into some *apply construct. The trick is learning to know when to do it and when not to. Can someone share some of this tricks with me? Up to now I have always done things with for loop. Just recently I started to pay attention to *apply* constructs and I already wanted to start implementing them instead of good old for, but then a stroke of lightning came from this thread. Based on words from Thomas, lapply should not be used for tasks where order is critical. Did I get this clear enough. Additionally, I have read notes (I lost link, but was posted on R-help, I think) from Thomas on R and he mentioned that it is commonly assumed that *apply* (I do not remember which one of *apply*) is faster than loop, but that this is not true. Any additional pointers to literature? __ 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] R GUI's on a Mac?
Anyone who responds to Berton, please, CC me: I am also interested. Best, Philippe Grosjean Berton Gunter wrote: Folks: A question for R users on Macs. AFAIK, R's Tcl/TK tools allow one to build GUI interfaces to R's functionality across all platforms. My question: How well do the TK widget tools work on a Mac? More specifically, is there any extra difficulty or complication in porting such applications to a Mac? Is there any special requirement for the Mac OS or version? Any glitches that should give one pause? Please reply privately, as this is not of general interest to the list. Many thanks. -- Bert Gunter Genentech __ 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] irregular time series
One solution is to convert an irregular time series into a regular one, interpolating missing values. Obviously, it is only acceptable if the number of missing items is low. See ?regul in pastecs, for instance. Best, Philippe Grosjean alessandro carletti wrote: Hi everybody, I'm currently working with time series: do you know if there's something like stl(package stats, seasonal decomposition of time series by loess) working also with objects of class irts? Thanks Alessandro __ 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] Multi-line paste function
I am not sure I clearly understand what you want, but getting the string
returned by your multi.line.paste() function is straightforward using
gsub():
gsub(\n, ,
SELECT *
FROM estimates a, newtable b
WHERE a.Ticker=b.Ticker
AND a.Fiscal_Year=b.Fiscal_Year
AND a.EPSb.EPS
AND a.Date_Last_change-1.9b.Date_Last_change
)
If you really want a custom function for that, then, define:
multi.line.paste - function(str) gsub(\n, , str)
Best,
Philippe Grosjean
Lapointe, Pierre wrote:
Here's my contribution to R.
When R interacts with external programs (MySQL, cURL, etc.), it often
requires a pasted string that is sent to these programs. For readability
reasons, it is often preferable to have complex commands (SQL for example)
spread on several lines. However, the normal paste function requires to add
additional ' , ' at the end of each line and another ' ' at the beginning
of each new line. It becomes fastidious for long commands.
Multi-line paste function:
multi.line.paste -function (..., sep = , collapse = NULL)
{
args - list(...)
if (length(args) == 0)
if (length(collapse) == 0)
character(0)
else
else {
for (i in seq(along = args)) args[[i]] -
gsub(\n,,as.character(args[[i]]))
.Internal(paste(args, sep, collapse))
}
}
Example with a SQL command on multiple lines:
multi.line.paste(
SELECT *
FROM estimates a, newtable b
WHERE a.Ticker=b.Ticker
AND a.Fiscal_Year=b.Fiscal_Year
AND a.EPSb.EPS
AND a.Date_Last_change-1.9b.Date_Last_change
)
Regards,
Pierre
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Re: [R] Multi-line paste function
Lapointe, Pierre wrote: Hello Phillipe 1-You are right that for a simple example as the one I provided, paste and gsub give the same result. 2-For a more complex case, where let's say, I'd like to include a variable in my SQL statement, the multi.line.paste command is essential. variable -1.9 multi.line.paste( SELECT * FROM estimates3 a, newtable b WHERE a.Ticker=b.Ticker AND a.Fiscal_Year=b.Fiscal_Year AND a.EPSb.EPS AND a.Date_Last_change_or_conf-,variable,b.Date_Last_change_or_conf ,sep=) Regards, Pierre Still simpler than your function: variable - 1.9 gsub(\, , paste( SELECT * FROM estimates3 a, newtable b WHERE a.Ticker=b.Ticker AND a.Fiscal_Year=b.Fiscal_Year AND a.EPSb.EPS AND a.Date_Last_change_or_conf-,variable,b.Date_Last_change_or_conf , sep=)) Philippe Grosjean __ 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] count pixels of same color in pixmap object?
Another solution is to use external tools. It really depends on what you
have to do: if it is to count pixels of one, or a few gray levels, it
could be fine to do it in R,... but if you want to count *all* pixels,
this could be more efficient using a C program, especially if you work
with 16bit images! You can find something in ImageMagick or in Netpbm.
Here is a solution using pgmhist from Netpbm
(http://netpbm.sourceforge.net/). This implies that you first converted
your image in PGM format (the Netpbm library provides all tools required
for that conversion).
Here is the R code, assuming pgmhist or pgmhist.exe (Windows) is
installed and accessible from the path:
# Get statistics about pixel in graylevel pgm images
pixelStats - function(imagePgm, pgmhist =
if (.Platform$OS.type == windows) pgmhist.exe else pgmhist) {
# Get pixel count for each gray level
pix - system(paste(pgmhist, imagePgm),
intern = TRUE, invisible = TRUE)
if (pix[1] != value\tcount\tb%\tw%)
stop(Error when running 'pgmhist' on the image ,
imagePgm, \n\n, pix)
pix - pix[-(1:2)]
getPixCount - function(str)
as.numeric(strsplit(str, \t)[[1]][1:2])
pix2 - t(sapply(pix, getPixCount, USE.NAMES = FALSE))
colnames(pix2) - c(pixel.value, count)
return(pix2)
}
pixelStats(myimage.pgm)
Depending on the treatment you have to do, it is sometimes better to
delegate it to specialized programs (ImageMagick, Netpbm, ImageJ, etc.)
instead of using pixmap. The best is to try both and to determine which
solution is faster for your particular application. I am working with
very large images (hundreds of megabytes) for the ZooImage application
(http://www.sciviews.org/zooimage), and I delegate 100% of the work done
on these images to external programs, because R is not designed to
handle them efficiently.
Best,
Philippe Grosjean
Roger Bivand wrote:
On Thu, 9 Mar 2006, Christian Jost wrote:
Dear all,
I try to figure out how to use R to count the number of pixels of the
same color in some gray-level picture. I managed to read it in either
tiff or jpeg format, but the returned pixmap object keeps its
information out of (my) reach. Is there an easy way to tabulate the
different color/graylevel pixels and their numbers? Or should I use a
completely different (free) software?
The objects are new-style class objects, so they are documented internally
- query by getSlots() or from ?pixmap-class:
library(pixmap)
x - read.pnm(system.file(pictures/logo.ppm, package=pixmap)[1])
z - as(x, pixmapGrey)
class(z)
getSlots(class(z)) # lets you know what the slots are
greydata - slot(z, grey) # extract the slot object
summary(c(greydata)) # c() to flatten a matrix
length(unique(c(greydata)))
length((c(greydata))) # rather a lot of different values, let's round:
rgreydata - round(greydata*10)
length(unique(c(rgreydata))) # looks good
table(c(rgreydata))
I assume that you converted from tiff or jpeg to pnm outside pixmap.
Thanks for any hint, Christian.
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Re: [R] how to close all windows?
?graphics.off is for graphic windows only. You don't tell us, but I assume you are working with RGui under Windows. If you don't want many help windows, you can still change it in Edit - GUI preferences - Pager style - single window. Best, Philippe Grosjean Uwe Ligges wrote: Michael wrote: Hi all, I have 10+ graphic windows and 10+ R help window opening now... How do I close them all at once? Thanks a lot! [[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 See ?graphics.off Uwe Ligges __ 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] Transferring R results to word prosessors
The copy to clipboard feature is written (by Eric Lecoutre myself) since a couple of years. It is in the SciViews bundle, library svIO. In this library, you have: - copy() that copies an object to the clipboard in various formats (icluding HTML, by using R2HTML and LaTeX), - export() does the same, but save to a file on disk, - you have also clippaste() to paste data from the clipboard. Moreover, in the SciViews bundle, you have also svViews that provides further interesting functions for reporting: - view() allows to generate different rich-formatted views on objects, - report() sends a view to a reporting application (but see hereunder the note about SciViews-R), - reportGraph() is the same for R graphs, ... All these functions exist on CRAN since at least two years. They are programmed under Windows(), but most of them should be working on other platforms (I would gladly consider patches, of course, if required). Now, if you want a convenient point and click approach to write a report, you should use SciViews-R (http://www.sciviews.org/SciViews-R). It has a nice GUI interface on top of these functions. For instance, you can access them from the context menu of the object explorer (but see the SciViews-R manual at http://www.sciviews.org/SciViews-R/Manual.pdf). SciViews-R is Windows only, but I am gradually moving code to a platform-independent solution (lot of code, lack of time, other priorities,... so, you have to be patient!). Finally, I uploaded the latest version of SciViews this week on CRAN. Now, the svViews package has a suite of WordXXX() functions. There are intended for sending nicely formatted data to Word. The next version of SciViews-R (next week, or so) included the functionnalities in the GUI. Regarding reproducibility of results, the strategy here is to write a template in Word with bookmarks at the locations where you want to put material coming from R. Once it is done, you can control entirely the process of filling the Word document from within a R script. For instance (extracted and reworked from the example in ?WordOpen): # Install SciViews bundle from CRAN, then... library(svViews) repdir - c:/temp # Adapt this for you WordOpen(file.path(repdir, report.doc)) # Open your template # Code to create a graph in a file, for instance graphfile - file.path(repdir, figure1.emf) win.metafile(filename = graphfile, width = 7, height = 5) hist(rnorm(500)) dev.off() # Insert that graph in Word at a location named picture1: WordGoto(figure1) # Move to the picture1 bookmark WordInsertPictureFile(graphfile, TRUE) # Insert the graph # Create a view in HTML (rich-formatted) and insert it in Word # for instance, for a simple linear regression, you can do: data(trees) trees.lm - lm(Volume ~ Girth, data = trees) viewfile - view(trees.lm, type = summary, browse = FALSE) WordGoto(view1) # Go to the regression1 bookmark in your report WordInsertFile(viewfile, TRUE) # Insert the view in the report # This is done! WordActivate(async = TRUE) # Show your report in Word. # and allow to refine it (add comments according to the results) # -- or -- # WordExit() # Close word, possibly prompting to save the doc. (note that I appended a suitable myreport.doc to this email, but it will probably be eliminated on the mailing list. so, ask me if you need it). Best, Philippe Grosjean P.S.: the formatting of text and tables in the views is managed through CSS files, independently from Word styles. So, you would presumably like to make a CSS file in accordance with the style you want in your report. Gabor Grothendieck wrote: Given that this may very well be the most common use of the R2HTML package I wonder if the R2HTML package developer would be interested in providing an HTML2clip convenience wrapper as part of the R2HTML package like this: HTML2clip - function(x, file. = file(clipboard, w), append = FALSE, ...) HTML(x, file = file., append = append, ...) so that one could just write: HTML2clip(summary(lm(rating ~., attitude))) On 2/10/06, Tom Backer Johnsen [EMAIL PROTECTED] wrote: Thank you all for very useful and interesting responses. After reading the comments and after some experiments, I added the following to a text I will be handing out to the students (I would not mind comments): QUOTEThe contents of the text output from R may be very sophisticated, but the formatting of the texts is always very simple, with absolutely no frills. For instance, all formatting of columns is managed with spaces or blanks, no tabs, nothing extra apart from line feeds. This means that transferring some types of output, like the summary of the multiple regression in part 7.4 directly to MS Word or any other wordprocessor would be far from optimal. To make a decent table for presenting results in a paper in APA format, we need a table in the word processing sense, an arrangement of things in rows and columns. With output as plain as in R, a lot
Re: [R] Tranferring R results to word prosessors
I have added several convenient methods for sending data directly from R to Microsoft Word (report() function) in the svViews package (SciViews bundle). However, I still have to upload it to CRAN. I do it right now. It should be available in a couple of days. Best, Philippe Grosjean Romain Francois wrote: Le 09.02.2006 15:41, Tom Backer Johnsen a écrit : I have just started looking at R, and are getting more and more irritated at myself for not having done that before. However, one of the things I have not found in the documentation is some way of preparing output from R for convenient formatting into something like MS Word. An example: If you use summary(lm()) you get nice output. However, if you try to paste that output into the word processor, all the text elements are separated by blanks, and that is not optimal for the creation of a table (in the word processing sense). Is there an option to generate tab-separated output in R ? That would solve the problem. Tom Hi , One way could be to output in html format from R (with the R2HTML package) and then read back the html from your word processor Romain __ 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] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
Romain Francois wrote: Le 08.02.2006 04:21, Taka Matzmoto a écrit : Hi R users This looks a simple question Is there any difference between between rnorm(1000,0,1) and running rnorm(500,0,1) twice in terms of outcome ? TM Not here : R set.seed(1) R x - rnorm(1000, 0, 1) R set.seed(1) R y - rnorm(500, 0, 1) R z - rnorm(500, 0, 1) R all(x == c(y,z)) [1] TRUE Romain Indeed! The pseudo-random number generator is initialized at the same state, and thus, returns the same 1000 pseudo-random numbers in both cases. So, no differences. Best, Philippe Grosjean __ 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 simple if() statement
Norman Goodacre wrote: the following code apprantely, for some grand old reason, induces a syntax error: if (seq[i] = A) m - trans[1,] where seq is a vector and trans is a matrix. I cannot for the life of me see why this is wrong. Syntax error is: Error: syntax error in if (seq[i] = Sincerely, Norman Goodacre Please, read An Introduction to R provided with any version of R. The correct syntax for an equality condition is ==, not =, so: if (seq[i] == A) Best, Philippe Grosjean __ 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] saving a character vector
If I understand the question correctly, both Jim Holtman's and John
Fox's answers are correct solutions. However, they are not optimal ones
(that was not the question -optimize my code, please-, but one can talk
about it a little bit).
- Jim proposes (I rework a little bit his code):
generateIndex1 - function(n.item) {
Res - character(0) # initialize vector
for (i in 1:(n.item - 1)) { # John Fox's correction introduced
for (j in ((i+1):n.item)) {
# concatenate the results
Res - c(Res, paste(i, formatC(i, digits = 2, flag = 0),
., formatC(j, digits = 2, flag = 0), sep = ))
}
}
Res
}
- John Fox proposes:
generateIndex2 - function(n.item) {
result - rep(, n.item * (n.item - 1) / 2)
index - 0
for (i in 1:(n.item - 1)) {
for (j in ((i + 1):n.item)) {
index - index + 1
result[index] - paste(i,
formatC(i, digits = 2, flag = 0), .,
formatC(j, digits = 2, flag = 0), sep = )
}
}
result
}
The difference is that Jim creates an empty character vector and
concatenate to it (simplest code), and John creates a vector of empty
characters of the correct size [result - rep(, n.item * (n.item - 1)
/ 2)]. The second solution is supposed to be better, because result is
supposed to be of the right size, limiting useless memory pagination
inside each loop iteration. However:
system.time(generateIndex1(100))
[1] 4.86 0.00 4.86 NA NA
system.time(generateIndex2(100))
[1] 4.68 0.00 4.68 NA NA
There is not much difference (well, indeed, the loops and what's
calculated repreatedly inside takes much more time in this case).
However, I wonder what happens if I allocate a vector of the right size
with strings having also the right size:
generateIndex3 - function(n.item) {
result - rep(i000.000, n.item * (n.item - 1) / 2)
index - 0
for (i in 1:(n.item - 1)) {
for (j in ((i + 1):n.item)) {
index - index + 1
result[index] - paste(i,
formatC(i, digits = 2, flag = 0), .,
formatC(j, digits = 2, flag = 0), sep = )
}
}
result
}
system.time(generateIndex3(100))
[1] 4.63 0.02 4.66 NA NA
... About the same. **Could someone explain me here, please?**
Now, where is the bottleneck?
Rprof()
res - generateIndex3(100)
Rprof(NULL)
?summaryRprof
summaryRprof()
$by.self
self.time self.pct total.time total.pct
formatC 0.48 10.5 4.30 93.9
paste 0.46 10.0 4.54 99.1
pmax0.44 9.6 0.66 14.4
as.integer 0.30 6.6 0.34 7.4
as.logical 0.24 5.2 0.34 7.4
names 0.20 4.4 0.24 5.2
...
Gosh! For sure: Why do I call FormatC() every time twice in the loop? I
can increase speed by formatting my character strings only once!
generateIndex4 - function(n.item) {
result - rep(i000.000, n.item * (n.item - 1) / 2)
index - 0
id - formatC(1:n.item, digits = 2, flag = 0)
for (i in 1:(n.item - 1)) {
for (j in ((i + 1):n.item)) {
index - index + 1
result[index] - paste(i, id[i], ., id[j], sep = )
}
}
result
}
system.time(generateIndex4(100))
[1] 0.33 0.00 0.33 NA NA
Yes! That's much better.
Now, recall that it is better to use a vectorized algorithm than loops,
could I get rid of these two ugly loops? Here is something using outer()
and lower.tri():
generateIndex5 - function(n.item) {
idx - function(x, y) paste(i, x, ., y, sep = )
id - formatC(1:n.item, digits = 2, flag = 0)
allidx - t(outer(id, id, idx))
allidx[lower.tri(allidx)]
}
system.time(generateIndex5(100))
[1] 0.02 0.00 0.02 NA NA
Indeed! That code is much, much faster!
Now, let's compare generateIndex1() with generateIndex5().
- generateIndex5() is optimized for speed (4.86/0.02, about 250 times
faster!)
- generateIndex5() is more concise code: 4 lines, no loops, compared to
8 lines with two loops.
- but... generateIndex1() is the code that comes to mind more easily
(except, perhaps for some R experts (?) because thinking with vectors is
their second nature).
- but... generateIndex1() is much easier to understand, when someone
else read the code (for the same reason).
Final conclusion:
generateIndex5() is a better R code (I am sure one can do even better!),
but it is a little bit more intellectual work to arrive to this result
(i.e., rethink the problem using matrix calculation). However, the
result is worth the effort.
(note: this will be introduced in the future R Wiki. This is the reson
why this email is so long: I took a good occasion to speak about code
optimization).
Best,
Philippe Grosjean
Re: [R] R socket communication
See package svSocket in the SciViews bundle. It uses a socket server
written in tcltk and it is not blocking the command line.
Philippe Grosjean
pau carre wrote:
Hello, I tried to code a R socket server but I did not succeed.
The problem is that once the R socket server is created,
I call the readLines function and then R gets blocked.
The client seems to work fine since I tested it with a PERL server.
I tried many combination of params in the socketConnection but
none of them worked.
I have seen some examples where the server sends something to a
client but I need the opposite example.
Thanks,
Pau.
The R server
FSsocket() - function(){
print(Creating server on localhost)
conn - socketConnection(server = TRUE, port = 7890, open = r+)
print(Reading data)
aa - readLines(conn)
print(end reading lines)
close(conn)
pirnt(Connection closed)
}
Note: I receive a Creating server on localhost and a Reading data
in the R console, but nothing else.
The PERL client
#! /usr/bin/perl
use strict;
use Socket;
# initialize host and port
my $host = shift || 'localhost';
my $port = shift || 7890;
my $proto = getprotobyname('tcp');
my $iaddr = inet_aton($host);
my $paddr = sockaddr_in($port, $iaddr);
socket(SOCKET, PF_INET, SOCK_STREAM, $proto) or die socket: $!;
connect(SOCKET, $paddr) or die connect: $!;
print SOCKET Hello \n;
close SOCKET or die close: $!;
The PERL server
#! /usr/bin/perl -w
use strict;
use Socket;
my $port = shift || 7890;
my $proto = getprotobyname('tcp');
socket(SERVER, PF_INET, SOCK_STREAM, $proto) or die socket: $!;
setsockopt(SERVER, SOL_SOCKET, SO_REUSEADDR, 1) or die setsock: $!;
my $paddr = sockaddr_in($port, INADDR_ANY);
bind(SERVER, $paddr) or die bind: $!;
listen(SERVER, SOMAXCONN) or die listen: $!;
print SERVER started on port $port ;
my $client_addr;
while ($client_addr = accept(CLIENT, SERVER))
{
my ($client_port, $client_ip) = sockaddr_in($client_addr);
my $client_ipnum = inet_ntoa($client_ip);
my $client_host = gethostbyaddr($client_ip, AF_INET);
print Connection from: $client_host,[$client_ipnum] ;
while(CLIENT){
print $_;
}
close CLIENT;
}
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Re: [R] R command line: need intelligent command history recall?
Michael wrote: Hi all, I am not sure if this feature exists in the R-console command line prompt: In Matlab, if I want to enter a command which is similar to what I have entered before, I can enter a few prefix, then press -, the previous command that matches with this prefix will then appear on this command line, and it saves a lot of our time. For example: abline(lm(new~old)) cor(new, old) ... ... ... many lines entered ... ... now I want to reuse abline(lm(new~old)), R-console provides - functionality to recall old commands, but it trace back one by one, it is slow if abline is way back, say 50 lines above my current command line... it is too slow. In Matlab, I just need to enter ab, then press -, if there is no other ab** between the abline and my current command line, then the console will intelligently recall abline back to me... Very convinient. Does this feature exist in R? Any other good Integrated Developement Environment for R? Perhaps R users are mathematicians and statisticians; but as a software engineer myself, I found a Visual C++-like integrated developement environment is really efficient and time-saving. It and Borland C++ Builder basically sets standard for modern UI design for programming IDEs. To be a good IDE, it really needs to have an embedded inline debugger. I've asked a statistician, he said he never debugged using a break-point, line-by-line execution debugger -- I cannot imagine this. Where is the productivity? I've used Tinn-R. Frankly it is quite creative. It solved the line-by-line execution problem by copying the line and pasted it to R-console automatically. But a lot of times clipboard generates error. And often times the copy and paste within Tinn editor itself are problemetic. For example, I have been never able to select a portion of a line. When I paste a paragraph, it always erases the current line and the following lines, instead of inserting, ... and if I want to select one line, it always select two lines for me... etc. Anyway, I hope there is IDEs that are better than Tinn-R. Thanks a lot! Please, submit a bug report to Tinn-R authors, if you want to see it improved. Best, Philippe Grosjean __ 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] matlab-like constant matrix initialization?
Sorry Michael, but I don't understand your question. If you want to intialize a constant matrix (there is not such thing in R, just create a numerical matrix and use it without changing its values), you just use matrix(). For help and arguments of the function, type: ?matrix Best, Philippe Grosjean Michael wrote: Hi all, Suppose I have the following matrix which is a constant matrix I've copied from some other document: 1.2 3.4 1.4 ... 2.3 3.7 2.6 ... ... How do I make it into a matrix or array in R? What is the fastest way of initializing a constant matrix with this copy/pasted values? Thanks a lot! [[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] yet another vectorization question
Hello,
Not exactly the same. By the way, why do you use do.call()? Couldn't you
do simply:
expand.grid(split(t(replicate(3, c(0, 1, NA))), 1:3))
Best,
Philippe Grosjean
Jacques VESLOT wrote:
this looks similar:
do.call(expand.grid,split(t(replicate(3,c(0,1,NA))),1:3))
Adrian DUSA a écrit :
Dear R-helpers,
I'm trying to develop a function which specifies all possible expressions
that
can be formed using a certain number of variables. For example, with three
variables A, B and C we can have
- presence/absence of A; B and C
- presence/absence of combinations of two of them
- presence/absence of all three
A B C
1 0
2 1
3 0
4 1
5 0
6 1
7 0 0
8 0 1
9 1 0
10 1 1
11 0 0
12 0 1
13 1 0
14 1 1
15 0 0
16 0 1
17 1 0
18 1 1
19 0 0 0
20 0 0 1
21 0 1 0
22 0 1 1
23 1 0 0
24 1 0 1
25 1 1 0
26 1 1 1
My function (pasted below) while producing the desired result, still needs
some more vectorizing; in particular, I can't figure out how could one modify
the element of a matrix using apply on a different matrix...
To produce the above outcome, I use:
all.expr(LETTERS[1:3])
all.expr -
function(column.names) {
ncolumns - length(column.names)
return.matrix - matrix(NA, nrow=(3^ncolumns - 1), ncol=ncolumns)
colnames(return.matrix) - column.names
rownames(return.matrix) - 1:nrow(return.matrix)
start.row - 1
all.combn - sapply(1:ncolumns, function(idx) {
as.matrix(combn(ncolumns, idx))
}, simplify=FALSE)
for (j in 1:length(all.combn)) {
idk - all.combn[[j]]
tt - matrix(NA, ncol=nrow(idk), nrow=2^nrow(idk))
for (i in 1:nrow(idk)) {
tt[,i] - c(rep(0, 2^(nrow(idk) - i)), rep(1, 2^(nrow(idk) - i)))
}
## This is _slow_ part, where I don't know how to vectorize:
for (k in 1:ncol(idk)) {
end.row - start.row + nrow(tt) - 1
return.matrix[start.row:end.row, idk[ , k]] - tt
start.row - end.row + 1
}
## How can one modify return.matrix using apply on idk?
}
return.matrix[is.na(return.matrix)] -
return.matrix
}
}
Thank you in advance,
Adrian
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Re: [R] Help with R: functions
# Here it is (using the formula interface):
dats - data.frame(visual24 = rnorm(30, 3, 5),
visual52 = rt(30, 7))
st - function(formula, data, ...) {
# Just use the formula to specify which variables to use
rcc - coef(lm(formula, data))
# Make sure to keep only variable used in the data frame
plot(data[ , rev(all.vars(formula))])
# Draw the line. Note the ... that allows to change
#lines features
abline(coef = rcc, ...)
# Return the coefficients invisibly
return(invisible(rcc))
}
st(visual52 ~ visual24, data = dats)
# Change style and color of the line (thanks to '...')
st(visual52 ~ visual24, data = dats, lty = 2, col = red)
Best,
Philippe Grosjean
Pryseley Assam wrote:
Hello R-users
I am new to R and trying to write some functions. I have problems writing
functions that takes a data set as an arguement and uses variables in the
data. I illustrate my problem with a small example below:
sample data #--
visual24-rnorm(30,3,5)
visual52-rt(30,7)
dats- data.frame(cbind(visual24,visual52))
remove(visual24, visual52)
# first code
#--
st -function(data,x,y){
rcc-coef(lm(y~x))
plot(x,y)
abline(rcc[1],rcc[2])
}
st(data=dats,x=dats$visual24,y=dats$visual52)
This code works fine, but with such a code the data as an arguement to the
funtion is not necessary.
However, i wish to write a function that reads the variables from the data
directly.
I tried using the function below but it does not work.
# second code
#--
st -function(data,x,y){
rcc-coef(lm(data$y~data$x))
plot(data$x,data$y)
abline(rcc[1],rcc[2])
}
st(dats,visual24,visual52)
I wish to inquire if any one has an idea of what i need to adjust in the
function so that it works.
I believe that the referencing $x or $y in the function is not doing the
correct thing.
Better still, will it be a problem if i code the functions as in the first
code above?
I mean given that they will be used to create a library
Best regards
Pryseley
-
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Re: [R] What's wrong with Rcmdr?
Michael wrote: thanks everyone, another problem is I cannot load Rcmdr at all in SCIView... what might be the problem? Not a problem, but a version incompatibility: SciViews is compiled for a given version of R and Rcmdr (the one on the Web site is for R 2.2.0 and Rcmdr 1.0-3... that is, not the latest ones). I still have to upload latest SciViews version compatible with both latest versions. Best, Philippe Grosjean On 1/26/06, John Fox [EMAIL PROTECTED] wrote: Dear Michael, To elaborate slightly: You can't load the same package twice in an R session. As mentioned, used Commander() to restart the Rcmdr GUI. I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Stefano Calza Sent: Thursday, January 26, 2006 4:23 AM To: r-help@stat.math.ethz.ch Subject: Re: [R] What's wrong with Rcmdr? Try using Commander() but, obviously, the first time. HIH, Ste On Thu, Jan 26, 2006 at 01:11:23AM -0800, Michael wrote: MichaelHi all, Michael MichaelI successfully installed Rcmdr. And I type library(Rcmdr), nothing Michaelhappened; Michael Michaelor if I select menu item load package and select Rcmdr, still nothing Michaelhappened... Michael MichaelWhy didn't Rcmdr start? Michael MichaelVery strangely, if I close the R console and restart R console, every first Michaeltime I load Rcmdr, it starts! But not second, third time... Michael MichaelWhat's wrong with it? Michael MichaelThanks a lot! Michael MichaelMichael. Michael Michael [[alternative HTML version deleted]] Michael Michael__ MichaelR-help@stat.math.ethz.ch mailing list Michaelhttps://stat.ethz.ch/mailman/listinfo/r-help MichaelPLEASE 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 [[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] [Q] extracting lower diagonal elements of a matrix
Try:
data[lower.tri(data)]
(the same as data[col(data) row(data)], but using the dedicated function).
Best,
Philippe Grosjean
Christos Hatzis wrote:
Try
s - matrix(rnorm(36,0,1),nrow=6)
s[col(s)row(s)]
Courtesy of VR.
-Christos
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Taka Matzmoto
Sent: Friday, January 27, 2006 1:13 AM
To: r-help@stat.math.ethz.ch
Subject: [R] [Q] extracting lower diagonal elements of a matrix
Hi R users
I like to extract lower diagonal elements of a matrix in such a way like,
data[1,2], data[1,3], , data[5,6] are extracted from a matrix called
'data'
This short script below is what I have written so far.
##
data - matrix(rnorm(36,0,1),nrow=6)
temp-c()
for (i in 1:(nrow(data)-1))
{
for (j in (i+1):nrow(data))
{
temp-append(temp,data[j,i])
}
}
##
Is there any function for this? or is there any elegant way to do this
task?
Thanks in advance.
TM
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Re: [R] regular expressions, sub
Hello,
Here is what I got after playing a little bit with your problem:
# First of all, if you prefer 'ln' instead of 'log', why not to define:
ln - function(x) log(x)
ln2 - function(x) log(x)^2
ln3 - function(x) log(x)^3
ln4 - function(x) log(x)^4
# ... as many function as powers you need
# Then, your formula is now closer to what you want
# which makes the whole code easier to read for you:
Form - ln(D) ~ ln(N) + ln2(N) + ln(t) # Same as your original formula
# Here is the function to transform it in a more readable string:
formulaTransform -
function(form, as.expression = FALSE) {
if (!inherits(form, formula))
stop('form' must be a 'formula' object!)
# Transform the formula into a string (is it a better way?)
Res - paste(as.character(form)[c(2, 1, 3)], collapse = )
if (as.expression) { # Transform the formula in a nice expression
# Change '~' into '=='
Res - sub(~, %~~%, Res) # How to do '~' in an expression?
# Eliminate brackets
Res - gsub([(]([A-Za-z0-9._]*)[)], ~ \\1, Res)
# Transform powers
Res - gsub(ln([2-9]), ln^\\1, Res)
Res - eval(parse(text = Res))
} else { # Make a nicer string
# Eliminate brackets
Res - gsub([(]([A-Za-z0-9._]*)[)], \\1, Res)
# Transform powers
Res - gsub(ln([2-9]), ln^\\1, Res)
}
# Return the result
return(Res)
}
# Here is a nicer presentation as a string
formulaTransform(Form)
# Here is an even nicer presentation (creating an expression)
plot(1:3, type = n)
text(2, 2, formulaTransform(Form, TRUE))
# The later form is really interesting when you use, for instance,
# greek letters for variables, or so...
Form2 - ln(alpha) ~ ln(beta) + ln2(beta) + ln3(beta)
formulaTransform(Form2)
plot(1:3, type = n)
text(2, 2, formulaTransform(Form2, TRUE))
# ... but this could be refined even more!
Best,
Philippe Grosjean
..°}))
) ) ) ) )
( ( ( ( (Prof. Philippe Grosjean
) ) ) ) )
( ( ( ( (Numerical Ecology of Aquatic Systems
) ) ) ) ) Mons-Hainaut University, Pentagone (3D08)
( ( ( ( (
..
Christian Hoffmann wrote:
Hi,
I am trying to use sub, regexpr on expressions like
log(D) ~ log(N)+I(log(N)^2)+log(t)
being a model specification.
The aim is to produce:
ln D ~ ln N + ln^2 N + ln t
The variable names N, t may change, the number of terms too.
I succeded only partially, help on regular expressions is hard to
understand for me, examples on my case are rare. The help page on R-help
for grep etc. and regular expressions
What I am doing:
(f - log(D) ~ log(N)+I(log(N)^2)+log(t))
(ft - sub(,,f)) # creates string with parts of formula, how to do
it simpler?
(fu - paste(ft[c(2,1,3)],collapse= )) # converts to one string
Then I want to use \1 for backreferences something like
(fv - sub(log( [:alpha:] N )^ [:alpha:),ln \\1^\\2,fu))
to change log(g)^7 to ln^7 g,
and to eliminate I(): sub(I(blabla),\\1,fv) # I(xxx) - xxx
The special characters are making trouble, sub acceps (, ) only in
pairs. Code for experimentation:
trysub - function(s,t,e) {
ii-0; for (i1 in c(TRUE,FALSE)) for (i2 in c(TRUE,FALSE)) for (i3 in
c(TRUE,FALSE)) for (i4 in c(TRUE,FALSE))
print(paste(ii-ii+1,ifelse(i1, , ~),ext,ifelse(i2, ,
~),perl,ifelse(i3, , ~),fixed ,ifelse(i4, , ~),useBytes:
, try(sub(s,t,e, extended=i1, perl=i2, fixed=i3,
useBytes=i4)),sep=));invisible(0) }
trysub(I(log(N)^2),ln n^2,fu) # A: desired result for cases
5,6,13..16, the rest unsubstituted
trysub(log(,ln ,fu) # B: no substitutions; errors for
cases 1..4,7.. 12 # typical errors:
3 ext perl ~fixed useBytes: Error in sub.perl(pattern, replacement,
x, ignore.case, useBytes) : \n\tinvalid regular expression 'log('\n
trysub(log\(,ln ,fu) # C: same as A
trysub(log\\(,ln ,fu) # D: no substitutions; errors for
cases 15,16# typical errors:
15 ~ext ~perl ~fixed useBytes: Error in sub(pattern, replacement, x,
ignore.case, extended, fixed, useBytes) : \n\tinvalid regular expression
'log\\('\n
trysub(log\\(([:alpha:]+)\\),ln \1,fu) # no substitutions, no errors
# E: typical errors:
3 ext perl ~fixed useBytes: Error in sub.perl(pattern, replacement,
x, ignore.case, useBytes) : \n\tinvalid regular expression
'log\\(([:alpha:]+)\\)'\n
Thanks for help
Christian
PS. The explanations in the documents
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Re: [R] What's wrong with Rcmdr?
I am afraid that you must be a little bit more verbose on your problem. You do not provide enough information to spot your problem. Best, Philippe Grosjean Michael wrote: Hi all, I successfully installed Rcmdr. And I type library(Rcmdr), nothing happened; or if I select menu item load package and select Rcmdr, still nothing happened... Why didn't Rcmdr start? Very strangely, if I close the R console and restart R console, every first time I load Rcmdr, it starts! But not second, third time... What's wrong with it? Thanks a lot! Michael. [[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] reducing learning curves?
Michael wrote: Hi all, Are there any R addon/pluggins with the following feature: (1) command history? even stores the command history many days ago? Like Matlab does? See ?history, and also, menu entries File - Load/Save history... in Rgui (you use R under windows, isn't it?). also, if you answer Yes at the question Save workspace image? when you quit R, the history of commands is saved and resored next time you start R from the same directory. (2) online help? for example, as I see it, the Rcmdr is a good companian for a newbie like me who just touched R for 1.5 days. I can use Rcmdr to guide me to learn the commands to use for data analysis. However, Rcmdr does not have online help reference for R commands. For example, I saw the command abline and I want to know how to use it, I have to copy/type it in R-console, and do ?abline things, so that I can obtain help. But this is troublesome, does any editor offer online-help for commands, so I just need to hover my mouse on abline and then press F1 key then a help window will open automatically? Well, it is not much work to type ?abline However, if you want a button that you can click to do so, then look at http://www.sciviews.org/Tinn-R. That editor is definitely for you! Best, Philippe Grosjean Thanks a lot! On 1/25/06, Michael [EMAIL PROTECTED] wrote: Hi all, I am really new to the R language. I am a long time Matlab and C++ user and I was forced to learn R because I am taking a statistics class. I am seeking to reduce the learning curve to as smooth as possible. Are there any addon/plug-in features that can reduce the learning curve, for example, the following features can be very helpful for new learners: 1. Matlab-like command line auto-completion: Matlab has huge amount of command and nobody is able to remember them off the head. So a nice feature of Matlab command line is that I just need to type the first a few letters and then I press TAB key, there will be a list of possible commands popping up so I just need to select one. This helps a lot in terms of learning for new comers. A more advanced command auto-completion is Visual C++-like, which is implemented in program editor. It helps a lot while doing programming; 2. A good IDE editor with embedded inline debugger: can be as good as VC++, but also can be as simple as Matlab's debugger, which can breakpoint and trace line-by-line... the editor can do syntax correction, syntax check, syntax highlighting, code formatting, etc. Could you please recommend some good addon/plugins that have the above features? Could you please also suggest some tips/tools/tricks that can help me reduce the learning curve? Thank you very much! Michael. [[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] efficiency with %*%
Excellent, but... x - rnorm(100) y - rnorm(100) system.time(x%*%y) [1] 0.03 0.00 0.03 NA NA system.time(sum(x*y)) [1] 0.05 0.00 0.04 NA NA system.time(crossprod(x, y)) [1] 0 0 0 NA NA So, to paraphrase a well-known contributor on this mailing list: Excellent! So, what did you decided to do during the next 30 milliseconds you will save by using crossprod() instead of x%*%y? (joke) Best, Philippe Grosjean P.S.: Uwe, perhaps you should consider buying a faster computer, isn't it? :-() Uwe Ligges wrote: [EMAIL PROTECTED] wrote: Hi, x and y are (numeric) vectors. I wonder if one of the following is more efficient than the other: x%*%y or sum(x*y) ? I'd try x - rnorm(100) y - rnorm(100) system.time(x%*%y) system.time(sum(x*y)) and finally (hint, hint!): system.time(crossprod(x, y)) Uwe Ligges Thanks, Dimitri Szerman __ 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
Re: [R] reducing learning curves?
Hello, If you work under Windows, you can find a lot of useful tools in SciViews-R (http://www.sciviews.org/SciViews-R) and Tinn-R (http://www.sciviews.org/Tinn-R). For instance, you have: - syntax coloring, - code completion, - calltips (tips displaying the syntax of a function as you type it), - object explorer with lots of useful shortcuts in the object's context menu, - electronic reference cards, - viewing and reproting features, - etc... For a nice, graphical, debugger, look at debug package (you have to install it from CRAN and load it using: library(debug) Then, try: ?mtrace Best, Philippe Grosjean Michael wrote: Hi all, I am really new to the R language. I am a long time Matlab and C++ user and I was forced to learn R because I am taking a statistics class. I am seeking to reduce the learning curve to as smooth as possible. Are there any addon/plug-in features that can reduce the learning curve, for example, the following features can be very helpful for new learners: 1. Matlab-like command line auto-completion: Matlab has huge amount of command and nobody is able to remember them off the head. So a nice feature of Matlab command line is that I just need to type the first a few letters and then I press TAB key, there will be a list of possible commands popping up so I just need to select one. This helps a lot in terms of learning for new comers. A more advanced command auto-completion is Visual C++-like, which is implemented in program editor. It helps a lot while doing programming; 2. A good IDE editor with embedded inline debugger: can be as good as VC++, but also can be as simple as Matlab's debugger, which can breakpoint and trace line-by-line... the editor can do syntax correction, syntax check, syntax highlighting, code formatting, etc. Could you please recommend some good addon/plugins that have the above features? Could you please also suggest some tips/tools/tricks that can help me reduce the learning curve? Thank you very much! Michael. [[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] read.table problem
Hello,
Well... the error message is explicit enough: number of items read is
not a multiple of the number of columns means that you do not have the
right number of items around line 11975 (not the same number as in the
11974 previous lines)! This is an error in you file.
Best,
Philippe Grosjean
Andrej Kastrin wrote:
Dear R useRs,
I have big (23000 rows), vertical bar delimited file:
e.g.
A1|Text a,Text b, Text c|345
A2|Text bla|456
...
..
.
Try using
A - read.table('filename.txt', header=FALSE,sep='\|')
process stop at line 11975 with warning message:
number of items read is not a multiple of the number of columns
I have no problems with processing similar file, which is only 1
rows long?
Any suggestion what's the problem here. Thank's in advance.
Cheers, Andrej
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Re: [R] paste - eliminate spaces?
Just read more carefully the online help for paste (?paste). You have: sep: a character string to separate the terms. and the default value for sep is (a space). So, just use: paste(test, 1, sep = ) Best, Philippe Grosjean r user wrote: I am trying to combine the value of a variable and text. e.g. I want “test1”, with no spaces. I try: h=1 paste(‘test’,1) But get: [1] test 1 (i.e. there is a space between “test’“ and “1”) Is there a way to eliminate the space? __ 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] Can R handle medium and large size data sets?
Hello, This is not true that R cannot handle matrices of 100 000's observations... but: - Importation (typically using read.table() and the like) saturates much faster. Solution: use scan() and fill a preallocated matrix, or better, use a database. - Data frames are very nice objects, but if you handle only numeric data, do prefer matrices: they consume less memory. Also, avoid using row/column names for very large matrices/data frames. - Finally, of course, your mileage varies greatly depending on the calculation you do on your data. In general, the relatively widely admitted idea that R cannot handle large datasets originates from: using read.table() / data frames / non optimized code. As an example, I can create a matrix of 150 000 observations (you don't tell us how many variables, so, I took 20 columns) filled with random numbers, and calculate the mean for each variable very easily. Here it is: gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 168994 4.6 35 9.4 35 9.4 Vcells 62415 0.5 786432 6.0 290343 2.3 system.time(a - matrix(runif(15 * 20), ncol = 20)) [1] 0.48 0.05 0.55 NA NA # Just a little bit more than half a second to create a table of # 3 millions entries filled with random numbers (P IV, 3Ghz, Win XP) dim(a) [1] 15 20 system.time(print(colMeans(a))) [1] 0.4998859 0.5004760 0.4994155 0.5000711 0.5005029 [6] 0.4999672 0.5003233 0.5000419 0.4997827 0.5004858 [11] 0.5004905 0.4993428 0.4991187 0.5000143 0.5016212 [16] 0.4988943 0.4990586 0.5009718 0.4997235 0.5001220 [1] 0.03 0.00 0.03 NA NA # 30 milliseconds to calculate the mean of all 20 # variables over 150 000 observations gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 169514 4.6 35 9.4 35 9.4 Vcells 3062785 23.49317558 71.1 9062793 69.2 # Less than 30 Mb used (with a peak at 80 Mb) Isn't it manageable? Best, Philippe Grosjean Gueorgui Kolev wrote: Dear R experts, Is it true that R generally cannot handle medium sized data sets(a couple of hundreds of thousands observations) and threrefore large date set(couple of millions of observations)? I googled and I found lots of questions regarding this issue, but curiously there were no straightforward answers what can be done to make R capable of handling data. Is there sth inherent in the structure of R that makes it impossible to work with say 100 000observations and more? If it is so, is there any hope that R can be fixed in the future? My experience is rather limited---I tried to load a Stata data set of about 15observations(which Stata handles instantly) using the library foreign. After half an hour R was still thinking so I stopped the attempts. Thank you in advance, Gueorgui Kolev Department of Economics and Business Universitat Pompeu Fabra __ 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] Image Processing packages
Hello, There are a couple of things for image processing in R (look at pixmap and Rimage, for instance). However, R is *not* a good software for processing images (nor is Matlab, Octave, IDL: they use to have specific packages for image processing and analysis, but resulting applications are way to slow in comparison to dedicated software). A good approach is to mix ImageJ and R, if you are looking for an Open Source solution. You could look at ZooImage for an example application using these two software (analysis of digital zooplankton images, see: http://www.sciviews.org/zooimage). Best, Philippe Grosjean Thomas Kaliwe wrote: Hi, I've been looking for Image Processing packages. Thresholding, Edge Filters, Dct, Segmentation, Restoration. I'm aware, that Octave, Matlab etc. would be a good address but then I'm missing the statistical power of R. Does anybody know of packages, projects etc. Comments on wether the use of R for such matters is useful are welcome. Greetings Thomas Kaliwe [[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] Image Processing packages
[EMAIL PROTECTED] wrote: Philippe, I am trying to get there but I keep on receiving a blank file after 5 minutes, is there something wrong with the site? H.Ghezzo McGill University Montreal - Canada Well, I am trying myself. Indded, it seems that my server is down, or very busy. I will look at this tomorrow. Best, Philippe Grosjean Quoting Philippe Grosjean [EMAIL PROTECTED]: Hello, There are a couple of things for image processing in R (look at pixmap and Rimage, for instance). However, R is *not* a good software for processing images (nor is Matlab, Octave, IDL: they use to have specific packages for image processing and analysis, but resulting applications are way to slow in comparison to dedicated software). A good approach is to mix ImageJ and R, if you are looking for an Open Source solution. You could look at ZooImage for an example application using these two software (analysis of digital zooplankton images, see: http://www.sciviews.org/zooimage). Best, Philippe Grosjean Thomas Kaliwe wrote: Hi, I've been looking for Image Processing packages. Thresholding, Edge Filters, Dct, Segmentation, Restoration. I'm aware, that Octave, Matlab etc. would be a good address but then I'm missing the statistical power of R. Does anybody know of packages, projects etc. Comments on wether the use of R for such matters is useful are welcome. Greetings Thomas Kaliwe [[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 __ 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] In which application areas is R used?
You could probably add: - Fisheries modelling - Oceanography Although there is still resistance of other software there, R is gaining more and more users in these fields. Best, Philippe Grosjean P.S.: if you need actual examples, just ask... ;-) John Maindonald wrote: If anyone has a list of application areas where there is extensive use of R, I'd like to hear of it. My current short list is: Bioinformatics Epidemiology Geophysics Agriculture and crop science John Maindonald Mathematical Sciences Institute, Australian National University. [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-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] Easy, Robust and Stable GUI???
Yes, Rcmdr is certainly the closest match. Note, however, that there are good reasons not to replicate SPSS style of GUI. This is because driving an analysis using scripts has three major advantages: - flexibility: a good, high-level programming language allows to do much more than even the best GUI. This is because, as soon as you have programmed a dialog box, you restrict possibilities to the couple of choices that you hardcoded in that dialog box. With R, the only limit is your imagination (if something does not exist, you can program it by yourself). - traceability: with a GUI, how do you remember all the mouse clicks that led you to a given analysis? On the contrary, a script is an accurate record of all steps. - comprehension: to construct a R script, you must understand the analysis. R forces to learn the logic behind *before* you can run that analysis. With a menu/dialog box interface, you can click everywhere and get results by chance. Statistical packages with intuitive GUIs tend to stimulate lazyness: here, come! Look like I am a sexy GUI! Look, I am sooo easy to use! And I can deliver you plenty of results, ... No, no, don't be afraid, you don't need to understand what you're doing. Just click me!. So, all GUIs proposed for R are just ways to learn in an easier way how to write R scripts. Even R Commander tries hard to stimulate use of R scripts... and you should consider a lack of a good GUI for R as a sign of quality and nothing else. Best, Philippe Grosjean Achim Zeileis wrote: On Mon, 23 Jan 2006 12:44:49 -0800 (PST) pat_primate (sent by Nabble.com) wrote: I know that this isn't really a R help question, but I am a psychology student at TRU (tru.ca) and my psych department is going to be switching statistical software in the near future. I thought this might be a good oppertunity to advocate for open source if an acceptable option is available. I have looked around a bit and R seems to be the most stable and mature (not to mention powerful) open source statistical program going. The only downfall is that the school has been using spss for years and would demand a similarly user friendly GUI based statistical program to replace it. I have looked at a few of the R guis and most of them look like they are just command line interfaces in pretty desktop windows and not really a gui like spss. If anyone knows of any stable, userfriendly and robust guis for R that would be similar to using spss please let me know, as I would love for my school to start embracing open source software. Have you looked at John Fox's Rcmdr package? See http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/ and John Fox (2005). The R Commander: A Basic-Statistics Graphical User Interface to R, Journal of Statistical Software, 14(9). URL http://www.jstatsoft.org/ Also look at http://www.sciviews.org/_rgui/ for an overview of other GUI projects. Best, Z Thanks Pat -- View this message in context: http://www.nabble.com/Easy%2C-Robust-and-Stable-GUI--t982193.html#a2543480 Sent from the R help forum at Nabble.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 __ 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] function for rowMedian?
Prof Brian Ripley wrote: Interchange 1 and 2 (see ?apply: Andy was answering the subject line, not that in the body). However, Max asked also for column medians of a data frame, for which use sapply(DF, median) By the way, what is the preferred code for column-wise calculation on *all numeric* data in a data frame? sapply(DF, median) which considers the list and then simplifies the results down to a vector or matrix,... or apply(DF, 2, median) which first convert into a matrix and then do the calculation on it? Best, Philippe Grosjean I didn't understand the question, and it seems I was not alone :) On Fri, 20 Jan 2006, Philippe Grosjean wrote: Note that there is a confusion here: 1st dimension is row, 2nd dimension is column for matrix data.frame. And the dim arg to apply is the one you want the answer to have. A - matrix(runif(6), 2, 3) apply(A, 1, median) # row medians apply(A, 2, median) # col medians So, if the question is about rowMedian, you have: rowMedian - function(x, na.rm = FALSE) apply(x, 2, median, na.rm = na.rm) Now, you ask for the median for specified columns, which should be as Andy proposes you, or, if you really want a colMedian function: colMedian - function(x, na.rm = FALSE) apply(x, 1, median, na.rm = na.rm) Best, Philippe Grosjean Liaw, Andy wrote: apply(x, 1, median) should do it. If not, you need to explain why. Andy -Original Message- From: Max Kauer Sent: Friday, January 20, 2006 10:24 AM To: r-help@stat.math.ethz.ch Subject: [R] function for rowMedian? Hi is anybody aware of a function to calculate a the median for specified columns in a dataframe or matrix - so analogous to rowMeans? Thanks Max __ 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 for rowMedian?
Note that there is a confusion here: 1st dimension is row, 2nd dimension is column for matrix data.frame. So, if the question is about rowMedian, you have: rowMedian - function(x, na.rm = FALSE) apply(x, 2, median, na.rm = na.rm) Now, you ask for the median for specified columns, which should be as Andy proposes you, or, if you really want a colMedian function: colMedian - function(x, na.rm = FALSE) apply(x, 1, median, na.rm = na.rm) Best, Philippe Grosjean Liaw, Andy wrote: apply(x, 1, median) should do it. If not, you need to explain why. Andy -Original Message- From: Max Kauer Sent: Friday, January 20, 2006 10:24 AM To: r-help@stat.math.ethz.ch Subject: [R] function for rowMedian? Hi is anybody aware of a function to calculate a the median for specified columns in a dataframe or matrix - so analogous to rowMeans? Thanks Max -- __ 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
[R] R Wiki and R-sig-wikii
Hello all, This is to announce the creation of R-sig-wiki, a new R SIG (Special Interest Group) mailing list dedicated to the elaboration and maintenance of a R Wiki. You can subscribe at: https://stat.ethz.ch/mailman/listinfo/r-sig-wiki. There is currently a prototype for a new R Wiki at http://www.sciviews.org/_rgui/wiki (temporary address). The main idea is to offer a site where users could collaborate in writting various kind of documentation for R. It mainly targets R beginners, but is left open for more advanced sections. Any R user interested in the setting up of this Wiki is warmly welcome to participate and to subscribe to R-sig-wiki. For the others, we will send an announcement for the final R Wiki on this list when it will be ready. Hereunder is a (rather long) summary of the discussion we had so far on this topic. Best, Philippe Grosjean == There is a proposition to create a R Wiki, stimulated essentially by two facts: 1) The traffic in R-Help is very high, with many trivial questions asked repeatedly. Obviously, searching in R-Help archives is not so obvious for some R users. Perhaps another presentation, like plain HTML pages would be fine. Since the building of these HTML pages should be a collaborative work, a Wiki seems to be a possible solution (recall that a Wiki is essentially a simple way to collaborate on writting Web pages; see Wikipedia definition at http://en.wikipedia.org/wiki/Wiki). 2) Some threads in R-Help are very long and difficult to follow in the form of a succession of emails. Again, a more structured presentation, allowed by HTML / Wiki pages is suggested as a possible solution. There is already one attempt to build a Wiki by Detlef Steuer at: http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl. Despite not much effort was put in this wiki, several people collaborated to it with time, but it appears that it was below the minimum required to make it fly as it should. Being unaware of that Wiki, I proposed recently (beginning of January 2006) a prototype of another R Wiki, just to explore if and how it could answer those two problems on R-Help. The prototype is at http://www.sciviews.org/_rgui/wiki (temporary address). There is a couple of other Wikis dedicated to R floating around, like: http://www.okada.jp.org/RWiki/ (in Japanese) and http://learnserver.csd.univie.ac.at/rcomwiki dedicated to R(D)COM and RExcel essentially. After a discussion, the R-Core Team decided to give support to one or several intiatives to make a R Wiki, with a big concern about the quality of information in the Wiki and how to keep it in phase with the rapid development of R. Here is the mail send by Martin Maechler: Martin Maechler wrote: We've had a small review time within R-core on this topic, amd would like to state the following: The R-core team welcomes proposals to develop an R-wiki. - We would consider linking a very small number of Wikis (ideally one) from www.r-project.org and offering an address in the r-project.org domain (such as 'wiki.r-project.org'). - The core team has no support time to offer, and would be looking for a medium-term commitment from a maintainer team for the Wiki(s). - Suggestions for the R documentation would best be filtered through the Wiki maintainers, who could e.g. supply suggested patches during the alpha phase of an R release. -- Our main concerns have been about ensuring the quality of such extra documentation projects, hence the 2nd point above. Several of our more general, not mainly R, experiences have been of outdated web pages which are continued to be used as reference when their advice has long been superseded. I think it's very important to try ensuring that this won't happen with an R Wiki. === After that announcement, several people started to discuss the structure and content of the Wiki (Tony Plate and Ben Bolker took the initiative to propose one structure on the experimental R Wiki at: http://www.sciviews.org/_rgui/wiki/doku.php?id=varia:organization_discussion, and I propose to leave it open until the end of February. At that time, we will implement the proposed structure as a proof-of-concept. Another topic is about how to allow discussion on the R documentation in the Wiki. This topic was fed by Frank Harrell Jr, Gabor Grothendieck and others and it leads to a trial on: http://www.sciviews.org/_rgui/wiki/doku.php?id=varia:test_include. Basically, all CRAN and Bioconductor .Rd files would be converted automatically to read-only Wiki pages (regularly updated) that are themselves included in fully
Re: [R] A comment about R:
David Forrest wrote: [...] Any volunteers? Yes, me (well, partly...)! Here is what I propose: this is a very lengthy thread in R-Help, with many interesting ideas and suggestions. I fear that, as it happens too often, those nice ideas will be lost because of the support used: email! By nature, emails are read and then deleted (well, there is the R-Help archive, but anyway, threads in a mailing list is not at all the best tool to make collaborative documents like those tutorials and co). I just cooked a little Wiki *dedicated to R beginners* (meaning they can contribute too, and are very welcome to discuss their problems -possibly trivial for others-). It is available at http://www.sciviews.org/_rgui/wiki. For the moment, everyone can edit and add pages, but I will restrict rights in the future to logged users only (with everybody allowed to log in at any time). So that we will be able to track who made changes (authorship). For those who do not know the Wiki concept, it is a very simple way of working together in the same documents. The concept has proven very powerful with a good example being Wikipedia, that is becoming one of the largest encyclopedia in the world... and also as accurate as Encyclopedia Britannica (but read this: http://www.nature.com/news/2005/051212/full/438900a.html). Here is the introduction of the R (GUI) Wiki: This Wiki is mainly dedicated to deal with R beginners problems. Although we would like to emphasize using R GUIs (Graphical User Interfaces), this Wiki is not restricted to those GUIs: one can also deal with command-line approaches. The main idea is thus to have material contributed by both beginners, and by more advanced R users, that will help novices or casual users of R (http://www.r-project.org). Overview * The various documents in the [[wiki section]] explain how to use DokuWiki to edit documents in this site. * The [[beginners section]] is dedicated to... beginners (share experience, expose problems and difficulties useful to share with other beginners, or to get help from more advanced people). * The [[tutorials section]] is the place where you can put various R session examples, or short tutorials on either general or specific use of R. * The [[easier section]] aims to collect together various pieces of R code that simplifies various tasks (especially for beginners) and that will ultimately be compiled in a “easieR” R packages on CRAN. * The [[varia section]] is for any material that does not fit in the previous sections. Final note: working with Wikis requires some learning... So, I am not sure at all that many R beginners will contribute to this wiki, but, of course, I hope so. Just let's pretend that it is a small experiment to try answering requests for another Internet space than R-Help, specifically dedicated to beginners... A good starting point would be the following: all people that expressed interesting points in this thread could copy and paste their ideas to new pages in the Wiki. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Pentagone (3D08) ( ( ( ( (Academie Universitaire Wallonie-Bruxelles ) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium ( ( ( ( ( ) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54 ( ( ( ( (email: [EMAIL PROTECTED] ) ) ) ) ) ( ( ( ( (web: http://www.umh.ac.be/~econum ) ) ) ) ) http://www.sciviews.org ( ( ( ( ( .. David Forrest wrote: On Tue, 3 Jan 2006, Gabor Grothendieck wrote: ... In fact there are some things that are very easy to do in Stata and can be done in R but only with more difficulty. For example, consider this introductory session in Stata: http://www.stata.com/capabilities/session.html Looking at the first few queries, see how easy it is to take the top few in Stata whereas in R one would have a complex use of order. Its not hard in R to write a function that would make it just as easy but its not available off the top of one's head though RSiteSearch(sort.data.frame) will find one if one knew what to search for. This sort of thing points to an opportunity for documentation. Building a tutorial session in R on how one would do a similar analysis would provide another method of learning R. An Introduction to R is a good bottom-up introduction, which if you work through it does teach you how to do several things. Adapting other tutorials or extended problems, like the Stata session, to R would give additional entry points. A few end-to-end tutorials on some interesting analyses would be helpful. Any volunteers? Dave __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE
Re: [R] A comment about R:
Roland,
Yes, indeed, you are perfectly right. The problem is that R richness
means R complexity: many different data types, sub-languages like
regexp or the formula interface, S3/S4 objects, classical versus lattice
(versus RGL versus iplots) graphs, etc. During translation of R in
French, I was thinking of a subset of one or two hundreds of functions
that would be enough for beginners to start with, and to propose a
translation of that small subset of the online help in French. This is
still on my todo list, but I must admit it is not an easy task to decide
which function should be kept in the subset and which should not!
In fact, that idea could be, perhaps, generalized into the whole online
help. It would be sufficient to add a flag somewhere (perhaps a keyword)
telling that page is fundamental and to allow filtering index and pages
(fundamental only or full help). Even for advanced users, it
should be nice to have such a filter to display only the two or three
most important functions in a new packages that proposes perhaps hundred
online help pages...
Using R Commander is also an interesting experiment. R Commander
simplifies the use of R down to the manipulation of a single data frame
(the so-called active dataset) + optionally one or two model objects.
Just look at all you can do just with one active data frame with R
Commander, and you will realize that it is perfectly manageable to learn
R that way.
Best,
Philippe Grosjean
Rau, Roland wrote:
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Gabor
Grothendieck
Sent: Monday, January 02, 2006 4:59 PM
To: Philippe Grosjean
Cc: Kort, Eric; Kjetil Halvorsen; R-help@stat.math.ethz.ch
Subject: Re: [R] A comment about R:
Probably what is needed is for someone familiar with both Stata and R
to create a lexicon in the vein of the Octave to R lexicon
http://cran.r-project.org/doc/contrib/R-and-octave-2.txt
to make it easier for Stata users to understand R. Ditto for
SAS and SPSS.
IMO this is a very good proposal but I think that the main problem is
not the translation of one function in SPSS/Stata/SAS to the
equivalent in R.
Remembering my first contact with R after using SPSS for some years (and
having some experience with Stata and SAS) was that your mental
framework is different. You think in SPSS-terms (i.e. you expect that
data are automatically a rectangular matrix, functions operate on
columns of this matrix, you have always only one dataset available,
...). This is why jumping from SPSS to Stata is relatively easy. But
to jump from any of the three to R is much more difficult.
This mental barrier is also the main obstacle for me now when I try to
encourage the use of R to other people who have a similar background as
I had.
What can be done about it? I guess the only answer is investing time
from the user which implies that R will probably never become the
language of choice for casual users. But popularity is probably not
the main goal of the R-Project (it would be rather a nice side-effect).
Just a few thoughts ...
Best,
Roland
+
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
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Re: [R] A comment about R:
Kort, Eric wrote: Kjetil Halvorsen wrote... Readers of this list might be interested in the following commenta about R. In a recent report, by Michael N. Mitchell http://www.ats.ucla.edu/stat/technicalreports/ says about R: Perhaps the most notable exception to this discussion is R, a language for statistical computing and graphics. ---8- After reading this commentary a couple of times, I can't quite figure out if he is damning with faint praise, or praising with faint damnation. (For example, after observing how many researchers around me approach statistical analysis, I'd say discouraging casual use is a _feature_.) There are numerous reasons why people tend to consider R as too complicate for them (or even worse, say peremptively to others that R is too complicate for them!). But one must decrypt the real reasons behind what they say. Mostly, it is because R imposes to think about the analysis we are doing. As Eric says, it is a _feature_ (well, not discouraging casual use, but forcing to think about what we do, which in turn forces to learn R a little deeper to get results... which in turn may discourage casual users, as an unwanted side-effect). According to my own experience with teaching to students and to advanced scientists in different environments (academic, industry, etc.), the main basic reason why people are reluctant to use R is lazyness. People are lazy by nature. They like course where they just sit and snooze. Unfortunatelly, this is not the right way to learn R: you have to dwell on the abondant litterature about R and experiment by yourself to become a good R user. This is the kind of thing people do not like at all! Someone named Dr Brian Ripley wrote once something like: `They' did write documentation that told you [...], but `they' can't read it for you. It is already many years that I write and use tools supposed to help beginners to master R: menu/dialog boxes approach, electronic reference cards, graphical object explorer, code tips, completion lists, etc... Everytime I got the same result: either these tools are badly designed because they hide the 'horrible code' those casual users don't want to see, and they make them *happy bad R users*, or they still force them to write code and think at what they exactly do (but just help them a bit), and they make them *good R users, but unhappy, poor, tortured beginners*! So, I tend to agree now: there is probably no way to instil R into lazy and reluctant minds. That said, I think one should interpret Mitchell's paper in a different way. Obviously, he is an unconditional and happy Stata user (he even wrote a book about graphs programming in Stata). His claim in favor of Stata (versus SAS and SPSS, and also, indirectly, versus R) is to be interpreted the same way as unconditional lovers of Macintoshes or PCs would argue against the other clan. Both architectures are good and have strengths and weaknesses. Real arguments are more sentimental, and could resume in: The more I use it, the more I like it,... and the aliens are bad, ugly and stupid! Would this apply to Stata versus R? I don't know Stata at all, but I imagine it could be the case from what I read in Mitchell's paper... Best, Philippe ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Pentagone (3D08) ( ( ( ( (Academie Universitaire Wallonie-Bruxelles ) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium ( ( ( ( ( ) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54 ( ( ( ( (email: [EMAIL PROTECTED] ) ) ) ) ) ( ( ( ( (web: http://www.umh.ac.be/~econum ) ) ) ) ) http://www.sciviews.org ( ( ( ( ( .. __ 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] Age of an object?
Martin Maechler wrote:
Trevor == Trevor Hastie [EMAIL PROTECTED]
on Tue, 13 Dec 2005 12:51:34 -0800 writes:
Trevor It would be nice to have a date stamp on an object.
Trevor In S/Splus this was always available, because objects were files.
[are you sure about always available?
In any case, objects were not single files anymore for a
long time, at least for S+ on windows, and AFAIK also on
unixy versions recently ]
This topic has come up before.
IIRC, the answer was that for many of us it doesn't make sense
most of the time:
I remember it was discussed several times. I don't remember why it was
considered too difficult to do.
If you work with *.R files ('scripts') in order to ensure
reproducibility, you will rerun -- often source() -- these files,
and the age of the script file is really more interesting.
Also, I *always* use the equivalent of q(save = no) and
almost only use save() to particularly save the results of
expensive computations {often, simulations}.
OK, now let me give examples where having such an information would ease
the work greatly: you have a (graphical) view of the content of an
object (for instance, the one using the view button in R commander),
or you have a graphical object explorer that has a cache to speed up
display of information about objects in a given workspace (for instance,
the SciViews-R object explorer). What a wonderful feature it will be to
tell if an object was changed since last query. In the view, one could
have a visual clue if it is up-to-date or not. In the object explorer, I
could update information only for objects that have changed...
Trevor I have looked around, but I presume this information is not
available.
I assume you will get other answers, more useful to you, which
will be based on a class of objects which carry an
'creation-time' attribute.
Yes, but that would work only for objects designed that way, and only if
the methods that manipulate that object do the required housework to
update the 'last-changed' attribute (the question was about last access
of an object, not about its creation date, so 'last-changed' is a better
attribute here). If you access the object directly with, let's say,
[EMAIL PROTECTED] - newvalue, that attribute is not updated, isn't it?
Best,
Philippe Grosjean
Martin Maechler, ETH Zurich
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Re: [R] R for Windows server
Hello, You don't tell us much info (what processor(s) are exactly in your server?). You must know the following: 1) Windows server prioritizes client accesses over local running programs (but you say there is no other process slowing down R... is it deconnected from the network?), 2) Rgui uses only one processor (at least, if you did not customized the default installation). Take care that, for instance, with an Intel HyperThreading (HT) Pentium IV processor, the system is working as if it was a bi-processor config with a single processor... and the task manager will not report more than 50% of CPU use for RGui.exe. Thus, I can imagine that, if you have a bi-processor hyperthreading config, it could report only 25% of CPU use. Best, Philippe Grosjean ..°})) ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Pentagone (3D08) ( ( ( ( (Academie Universitaire Wallonie-Bruxelles ) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium ( ( ( ( ( ) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54 ( ( ( ( (email: [EMAIL PROTECTED] ) ) ) ) ) ( ( ( ( (web: http://www.umh.ac.be/~econum ) ) ) ) ) http://www.sciviews.org ( ( ( ( ( .. Marco Geraci wrote: Hi, I need to run a burdensome simulation. I'm using a Dell PowerEdge 2850, 3.8 Ghz CPU, 2 Gb RAM, Windows server 2003, 32 bit. The task manager indicates that Rgui.exe is using 25% of the CPU speed. There is no other process that is slowing down R. Does anyone know if it's a limitation of R? If so, can I set up the program for the CPU usage like I do for the memory usage? Is there a version of R for servers? Thank you in advance, Marco Geraci - [[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
