[Rd] script window fails to load script (PR#8564)
Full_Name: helen mills poulos Version: 2.2.1 OS: windows Submission from: (NULL) (68.9.235.48) When using the randomForest package, I have had problems when running scripts after r has been open for some time, and after running multiple iterations of random forest. After about the 4th or 5th time I run a randomForest script from the script window in r, r just runs an old script that I ran before, rather than the one I just edited. This happens regardles of whether I send the script using ctrl r from the script window or I type in the script manually. I end up having to shut down r and start over again. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] javascript device for R
Hi, Has anyone started a javascript device for R. I don't see something like that googling or at on http://www.stat.auckland.ac.nz/~paul/R/devices.html For example, using that graphics library : http://www.walterzorn.com/jsgraphics/jsgraphics_e.htm (I cc that message to the author.) ps : this is not a feature request, i will do it. But if someone has started that, let me know. Romain -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php +---+ | Romain FRANCOIS - http://francoisromain.free.fr | | Doctorant INRIA Futurs / EDF | +---+ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Citation of R packages
> On Mon, 30 Jan 2006 10:06:52 +1100 (EST), > John Maindonald (JM) wrote: > The bibtex citations provided by citation() do not > work all that well in cases where there is no printed > document to reference: That's why there is a warning at the end that they will need manual editing ... IMHO they at least save you some typing effort in many cases. > (1) A version field is needed, as the note field is > required for other purposes, currently trying to > sort out nuances that cannot be sorted out in the > author list (author, compiler, implementor of R version, > contributor, ...) and maybe giving a cross-reference > to a book or paper that is somehow relevant. Why should a reference cross-reference another reference? Could you give an example? > (2) Maybe the author field should be more nuanced, or > maybe ... author fields of bibtex entries have a strict format (names separated by "and"), what do you mean by "more nuanced"? > (3) In compiling a list of packages, name order seems > preferable, and one wants the title first (achieved by > relocating the format.title field in the manual FUNCTION > in the .bst file > (4) manual seems not an ideal name for the class, if > there is no manual. A package always has a "reference manual", the concatenated help pages certainly qualify as such and can be downloaded in PDF format from CRAN. The ISBN rules even allow to assign an ISBN number to the online help of a software package which also can serve as the ISBN number of the *software itself* (which we did for base R). > Maybe what is needed is a package or suchlike class, > and several alternative .bst files that handle the needed > listings. > I know at least one other person who is wrestling with > this, and others on this list must be wrestling with it. I am certainly open for discussions and any suggestions for improvements, but it must be within the standard bibtex entry types, we cannot write our own entry types and .bst files. Many journals require the usage of their own (or standard) bibtex styles, and the entries we produce must work with those. If R creates nonstandard bibtex entries even more manual work will be necessary in many cases. I have no definitive bibtex reference at hand, but the natbib style files (a very popular collection of bibtex styles, at least I definitely want to be compatible with those) define article book booklet conference (= alias for inproceedings) inbook incollection inproceedings manual mastersthesis misc phdthesis proceedings techreport unpublished which coincide with the choices the emacs bibtex mode offers. Out of these only "manual", "misc" and "unpublished" seem appropriate for packages, and the description suggests to use manual for citing software manuals, but the definitions of those three are very similar anyway. Maybe you could give an example what your candidate for a bibtex entry for packages should look like? Best, Fritz -- --- Friedrich Leisch Institut für Statistik Tel: (+43 1) 58801 10715 Technische Universität WienFax: (+43 1) 58801 10798 Wiedner Hauptstraße 8-10/1071 A-1040 Wien, Austria http://www.ci.tuwien.ac.at/~leisch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] What about a bib file
> On Mon, 30 Jan 2006 17:49:37 -0500 (EST), > Vincent Carey 525-2265 (VC5) wrote: > Romain Francois suggests that a central bibliographic database > (possibly in bibtex format) might be useful for reference inclusion > in R package man pages. This has been discussed by a small > group, with one proposal presented for a package-specific bibtex database > placed in a dedicated package subdirectory. Man page references would > then cite the sources enumerated in the database using their bibtex > tags. This approach could encourage better annotation and should > confer greater accuracy on package:literature referencing. > This does not rule out a central archive that might include all the > references cited in base man pages. > We are doing some work on harvesting the bibliographic citations > in man pages in an R distribution, and converting them to a regular > format. The \references section is free form, so the conversion > is not trivial, but progress has been made. > The infrastructure required to use this approach to propagate > (e.g., bibtex-formatted) bibliographic data into the man pages that > cite the sources is not yet available, but we hope to have some > prototypes in the next month. Sounds great! The "hardest" parts are probably 1) a bibtex parser in R 2) at least one function converting arbitrary bibtex entries to text, i.e., the R equivalent of a .bst file. (I'm only guessing what such a system would involve). After looking into it when writing the citation() infrastructure I decided I don't want to do it and went straight to S objects written by the package author. All those string replacements and possible LaTeX markup simply looked like too much effort for just 1-2 entries per package ;-) But it would be great to have the above functionality in R, of course, and "all references" in a package are certainly a larger set then what citation() should report, making the effort worthwhile. My only wish is that the bibtex parser returns objects compatible to class "citation" (either the same class or simple coercion). I modelled the class after bibtex entries anyway, so that shouldn't be a restriction (I hope). If we need to modify class "citation" to be accomodate your needs, please let me know. Once we can suck bibtex files into R it would be trivial to give users a choice between writing CITATION files in the current form (with the benefit of headers and footers) or mark certain entries in the PACKAGE.bib file (whatever its name may be) that they should be reported by citation(). Best, Fritz PS: Of course I volunteer to alpha-test any prototypes you have, __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Rprintf loop status does not print under windows
Hello,
I am writing a c/c++ extension package that does some mcmc sampling, and
periodically writes the sampling status to the terminal via Rprintf. So in
my sampling loop I have:
if(status == 100){
Rprintf("%i...", s);
status = 0;
}
status++;
Under linux/unix this works fine, but under windows the status is not
printed. Am I missing something?
Thanks-
Andy
--
Andrew Finley, Research Fellow
Department of Forest Resources
College of Natural Resources
University of Minnesota
305 Green Hall
1530 Cleveland Avenue N.
St. Paul, MN 55108
Ph 612-624-1714 office
http://blue.fr.umn.edu/home
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Re: [Rd] Rprintf loop status does not print under windows
On 2/4/2006 1:14 PM, Andrew Finley wrote:
> Hello,
> I am writing a c/c++ extension package that does some mcmc sampling, and
> periodically writes the sampling status to the terminal via Rprintf. So in
> my sampling loop I have:
>
> if(status == 100){
> Rprintf("%i...", s);
> status = 0;
> }
> status++;
>
> Under linux/unix this works fine, but under windows the status is not
> printed. Am I missing something?
Looks like you have buffering enabled (the default). In the Misc menu
item, uncheck "buffered output" and you should see things sooner (but
slower).
Duncan Murdoch
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Re: [Rd] Rprintf loop status does not print under windows
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of Duncan Murdoch
> Sent: Saturday, February 04, 2006 1:23 PM
> To: Andrew Finley
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] Rprintf loop status does not print under windows
>
>
> On 2/4/2006 1:14 PM, Andrew Finley wrote:
> > Hello,
> > I am writing a c/c++ extension package that does some mcmc
> sampling, and
> > periodically writes the sampling status to the terminal via
> Rprintf. So in
> > my sampling loop I have:
> >
> > if(status == 100){
> > Rprintf("%i...", s);
> > status = 0;
> > }
> > status++;
> >
> > Under linux/unix this works fine, but under windows the
> status is not
> > printed. Am I missing something?
>
> Looks like you have buffering enabled (the default). In the
> Misc menu
> item, uncheck "buffered output" and you should see things sooner (but
> slower).
... or add something like this in your C code:
#ifdef win32
R_FlushConsole();
#endif
Andy
> Duncan Murdoch
>
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>
>
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Re: [Rd] pbinom with size argument 0 (PR#8560)
(Ted Harding) wrote: > On 03-Feb-06 Peter Dalgaard wrote: > >>(Ted Harding) <[EMAIL PROTECTED]> writes: >> >> >>>On 03-Feb-06 [EMAIL PROTECTED] wrote: >>> Full_Name: Uffe Høgsbro Thygesen Version: 2.2.0 OS: linux Submission from: (NULL) (130.226.135.250) Hello all. pbinom(q=0,size=0,prob=0.5) returns the value NaN. I had expected the result 1. In fact any value for q seems to give an NaN. >>> >>>Well, "NaN" can make sense since "q=0" refers to a single sampled >>>value, and there is no value which you can sample from "size=0"; >>>i.e. sampling from "size=0" is a non-event. I think the probability >>>of a non-event should be NaN, not 1! (But maybe others might argue >>>that if you try to sample from an empty urn you necessarily get >>>zero "successes", so p should be 1; but I would counter that you >>>also necessarily get zero "failures" so q should be 1. I suppose >>>it may be a matter of whether you regard the "r" of the binomial >>>distribution as referring to the "identities" of the outcomes >>>rather than to how many you get of a particular type. Hmmm.) >>> >>> Note that dbinom(x=0,size=0,prob=0.5) returns the value 1. >>> >>>That is probably because the .Internal code for pbinom may do >>>a preliminary test for "x >= size". This also makes sense, for >>>the cumulative p for any with a finite range, >>>since the answer must then be 1 and a lot of computation would >>>be saved (likewise returning 0 when x < 0). However, it would >>>make even more sense to have a preceding test for "size<=0" >>>and return NaN in that case since, for the same reasons as >>>above, the result is the probability of a non-event. >> >>Once you get your coffee, you'll likely realize that you got >>your p's and d's mixed up... > > > You're right about the mix-up! (I must mend the pipeline.) > > >>I think Uffe is perfectly right: The result of zero experiments will >>be zero successes (and zero failures) with probability 1, so the >>cumulative distribution function is a step function with one step at >>zero ( == as.numeric(x>=0) ). > > > I'm perfectly happy with this argument so long as it leads to > dbinom(x=0,size=0,prob=p)=1 and also pbinom(q=0,size=0,prob=p)=1 > (which seems to be what you are arguing too). And I think there > are no traps if p=0 or p=1. > > >>>(But it depends on your point of view, as above ... However, >>>surely the two should be consistent with each other.) > > > Ted. I prefer a (consistent) NaN. What happens to our notion of a Binomial RV as a sequence of Bernoulli RVs if we permit n=0? I have never seen (nor contemplated, I confess) the definition of a Bernoulli RV as anything other than some dichotomous-outcome one-trial random experiment. Not n trials, where n might equal zero, but _one_ trial. I can't see what would be gained by permitting a zero-trial experiment. If we assign probability 1 to each outcome, we have a problem with the sum of the probabilities. Peter Ehlers > > > E-Mail: (Ted Harding) <[EMAIL PROTECTED]> > Fax-to-email: +44 (0)870 094 0861 > Date: 03-Feb-06 Time: 15:07:49 > -- XFMail -- > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] pbinom with size argument 0 (PR#8560)
(Ted Harding) wrote: > On 03-Feb-06 Peter Dalgaard wrote: > >>(Ted Harding) <[EMAIL PROTECTED]> writes: >> >> >>>On 03-Feb-06 [EMAIL PROTECTED] wrote: >>> Full_Name: Uffe Høgsbro Thygesen Version: 2.2.0 OS: linux Submission from: (NULL) (130.226.135.250) Hello all. pbinom(q=0,size=0,prob=0.5) returns the value NaN. I had expected the result 1. In fact any value for q seems to give an NaN. >>> >>>Well, "NaN" can make sense since "q=0" refers to a single sampled >>>value, and there is no value which you can sample from "size=0"; >>>i.e. sampling from "size=0" is a non-event. I think the probability >>>of a non-event should be NaN, not 1! (But maybe others might argue >>>that if you try to sample from an empty urn you necessarily get >>>zero "successes", so p should be 1; but I would counter that you >>>also necessarily get zero "failures" so q should be 1. I suppose >>>it may be a matter of whether you regard the "r" of the binomial >>>distribution as referring to the "identities" of the outcomes >>>rather than to how many you get of a particular type. Hmmm.) >>> >>> Note that dbinom(x=0,size=0,prob=0.5) returns the value 1. >>> >>>That is probably because the .Internal code for pbinom may do >>>a preliminary test for "x >= size". This also makes sense, for >>>the cumulative p for any with a finite range, >>>since the answer must then be 1 and a lot of computation would >>>be saved (likewise returning 0 when x < 0). However, it would >>>make even more sense to have a preceding test for "size<=0" >>>and return NaN in that case since, for the same reasons as >>>above, the result is the probability of a non-event. >> >>Once you get your coffee, you'll likely realize that you got >>your p's and d's mixed up... > > > You're right about the mix-up! (I must mend the pipeline.) > > >>I think Uffe is perfectly right: The result of zero experiments will >>be zero successes (and zero failures) with probability 1, so the >>cumulative distribution function is a step function with one step at >>zero ( == as.numeric(x>=0) ). > > > I'm perfectly happy with this argument so long as it leads to > dbinom(x=0,size=0,prob=p)=1 and also pbinom(q=0,size=0,prob=p)=1 > (which seems to be what you are arguing too). And I think there > are no traps if p=0 or p=1. > > >>>(But it depends on your point of view, as above ... However, >>>surely the two should be consistent with each other.) > > > Ted. I prefer a (consistent) NaN. What happens to our notion of a Binomial RV as a sequence of Bernoulli RVs if we permit n=0? I have never seen (nor contemplated, I confess) the definition of a Bernoulli RV as anything other than some dichotomous-outcome one-trial random experiment. Not n trials, where n might equal zero, but _one_ trial. I can't see what would be gained by permitting a zero-trial experiment. If we assign probability 1 to each outcome, we have a problem with the sum of the probabilities. Peter Ehlers > > > E-Mail: (Ted Harding) <[EMAIL PROTECTED]> > Fax-to-email: +44 (0)870 094 0861 > Date: 03-Feb-06 Time: 15:07:49 > -- XFMail -- > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Using the lazy data mechanism
Dear list members, I'm trying to use the lazy data mechanism with the car package, so far without success. The data sets are in the source package's data subdirectory in the form of compressed .rda files, and I added the directive LazyData: yes to the package's DESCRIPTION file. I suspect that the problem is that the package has no namespace, but I've been unable to find a reference in the Writing R Extensions manual (nor elsewhere) that suggests that this is necessary. Is there a place that I've missed that describes the lazy data mechanism? My system info: - snip - Version: platform = i386-pc-mingw32 arch = i386 os = mingw32 system = i386, mingw32 status = major = 2 minor = 2.1 year = 2005 month = 12 day = 20 svn rev = 36812 language = R Windows XP Professional (build 2600) Service Pack 2.0 Locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 Search Path: .GlobalEnv, package:MASS, package:car, package:methods, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, package:svIO, package:R2HTML, package:svMisc, package:svSocket, package:svIDE, package:tcltk, Autoloads, package:base - snip - Thanks, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] pbinom with size argument 0 (PR#8560)
P Ehlers <[EMAIL PROTECTED]> writes: > I prefer a (consistent) NaN. What happens to our notion of a > Binomial RV as a sequence of Bernoulli RVs if we permit n=0? > I have never seen (nor contemplated, I confess) the definition > of a Bernoulli RV as anything other than some dichotomous-outcome > one-trial random experiment. What's the problem ?? An n=0 binomial is the sum of an empty set of Bernoulli RV's, and the sum over an empty set is identically 0. > Not n trials, where n might equal zero, > but _one_ trial. I can't see what would be gained by permitting a > zero-trial experiment. If we assign probability 1 to each outcome, > we have a problem with the sum of the probabilities. Consistency is what you gain. E.g. binom(.,n=n1+n2,p) == binom(.,n=n1,p) * binom(.,n=n2,p) where * denotes convolution. This will also hold for n1=0 or n2=0 if the binomial in that case is defined as a one-point distribution at zero. Same thing as any(logical(0)) etc., really. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] a generic 'attach'?
Is there any reason why 'attach' is not generic in R? I notice that it is in another system, for example, and I can see some applications if it were so in R. Bill Venables. Bill Venables, CMIS, CSIRO Laboratories, PO Box 120, Cleveland, Qld. 4163 AUSTRALIA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
