Re: [R] ROracle connection problem
I guess the issue is the use of R-1.9.0 (2.0.1 is current). Please ask the person who provided you with a Windows binary for ROracle which version it worked with. On Thu, 18 Nov 2004, Andi Felber wrote: Hi, I found the same question in the mailing list already a few months ago - but there was no answer to it - so I'll try it again Could somebody help me to solve this following problem? I just begin to learn how to connect my Oracle database with R. library(DBI) library(ROracle) Warning message: DLL attempted to change FPU control word from 8001f to 9001f ora=dbDriver(Oracle) Error in initialize(value, ...) : Invalid names for slots of class OraDriver: Id My system is: Windows 2000, Oracle 9.2 R1.9.0 Thank you very much andi Andreas Felber Swiss Federal Institute for Snow and Avalanche Research Flüelastrasse 11 CH-7260 Davos Dorf phone ++41 81 417 02 52 email: [EMAIL PROTECTED] personal homepage: http://www.slf.ch/staff/pers-home/felber/felber-en.html web www.slf.ch __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Redirect standard input and output of R
Victor Robles wrote:
Dear R-people!
Im trying to write a C program that write to the standard input of R
and read the standard output.
I can perfectly read the R output, but Im not able of writing anything
to R.
This program really works with the cat UNIX command, but it does not
work with R. What Im doing wrong??? It is possible to do it???
Please read the manual Writing R Extensions, in particular the lines
about Rprintf.
Uwe Ligges
I want to start R once and use it thousands of times... thats why Im
trying to use this system.
pipe(fdW);
pipe(fdR);
pid = fork();
if (pid==-1)
perror(Error fork);
if (pid==0)
{
close(0);
dup(fdW[0]);
close(fdW[0]);
close(fdW[1]);
close(1);
dup(fdR[1]);
close(fdR[1]);
close(fdR[0]);
execlp(R,R,--slave,NULL);
perror(Error exec);
}
else
{
close(fdW[0]);
close(fdR[1]);
write(fdW[1], 3+7, 3);
total = 0;
while (total3)
{
leidos = read(fdR[0], k, sizeof(k));
printf(leidos son %d \n,leidos);
k[leidos]='\0';
if (leidos 0){
total = total + leidos;
printf(%s\n,k);
}
}
}
exit(0);
Best regards,
Victor
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Re: [R] Power sampling
Thomas Schönhoff wrote: Hello, after a unsuccessful search in lists maliarchive I wonder how I could estimate the power of a sample size related to an unknown population. Given the following (fake))situation: I do have a database containing about 5 millions observations over 70 variables. I would like to compute (as epidemiologists are used to) the required size of a sample to do some test on a test sample (test data), later doing some subsequent analysis of a new sample to build a prediction model. Help facilities of R show some entries regarding power, but none of them seemed to be appropriate for my purpose (maybe I am wrong, but sometimes I have some difficulties to decipher the message of those tiny hints for available packages) You have to tell us for which test you are going to calculate the power ... (and there might be nothing, since calculating the power precisely is not always that easy). Uwe Ligges I would appreciate somebody effort to point me to the right package/function to archieve this task! regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] OOP pkg compilation failure
Gorden Jemwa wrote: Hi all, I'm trying to install the OOP package (http://www.omegahat.org/OOP) but having difficulty in resolving the errors generated during compilation. Googling doesn't seem to be giving much help. Can anyone please help. Below is the transcript of what I get from my command prompt. (I'm running on rw_2.0.0 WIN XP SP2 platform). Thanks in advance ---transcript Microsoft Windows XP [Version 5.1.2600] (C) Copyright 1985-2001 Microsoft Corp. C:\...\R CMD INSTALL OOP.tar.gz -- Making package OOP adding build stamp to DESCRIPTION making DLL ... making treeApply.d from treeApply.c gcc -Ic:/R/rw2000/include -Wall -O2 -c treeApply.c -o treeApply.o ar cr OOP.a treeApply.o ranlib OOP.a windres --include-dir c:/R/rw2000/include -i OOP_res.rc -o OOP_res.o gcc --shared -s -o OOP.dll OOP.def OOP.a OOP_res.o -Lc:/R/rw2000/src/gnuwin32 -lg2c -lR ... DLL made installing DLL installing R files save image [1] TRUE Initializing OOP objects in database 1 execution of package source for 'OOP' failed make[2]: *** [c:/R/rw2000/library/OOP/R/OOP] Error 1 make[1]: *** [all] Error 2 make: *** [pkg-OOP] Error 2*** Installation of OOP failed *** Removing 'c:/R/rw2000/library/OOP' a) The package does not pass the checks under R-2.0.1 on Windows, so please contact the maintainer! b) It can be installed, I guess something is wrong with your settings or collection of tools. c) I have *temporarily* put a binary up to http://www.statistik.uni-dortmund.de/~ligges/OOP_0.5-1.zip Uwe Ligges ---end transcript __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re[2]: [R] Where has the Debian respository gone?
Hello Dirk, Monday, November 15, 2004, 1:35:27 AM, you wrote: DE On Sun, Nov 14, 2004 at 10:53:42PM +0100, Christoph Bier wrote: Hi all! Did I miss something or is it just a temporary problem? Where has the Debian respository http://cran.r-project.org woody/main Packages resp. http://cran.r-project.org/bin/linux/debian/ gone? I tried it for about the last 7 hours. DE Current R and CRAN packages are on the Debian archives; you can install DE these on testing too. To the best of my knowledge, there are no backports DE of current R and Debian CRAN packages to Debian stable. I'm a bit puzzled. I had deb http://cran.r-project.org/bin/linux/debian woody main in /etc/apt/sources.list and had hoped, perhaps rather unwisely, that this would look after the transition from 1.8.0 on my internet server (Debian stable) where it serves up some cgi-bin work. (Most of my R work is on a Win2k machine, much though I'd like to go Debian all the way, that isn't possible for my main job in near future.) Is there an easy way of upgrading R on a Debian stable machine? I don't want to move off stable as the security side of that server is too important. I also don't really want to compile it myself if I can avoid that, the server is pretty old iron and that might back up all the Email stuff it does. Advice anyone? TIA, Chris __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Chinese character
Hello R-help team, I am a R user in China. I just downloaded the latest R which is R2001 for Windows. This new version can not store Chinese character which the previous version R 1.9.1 does. Specifically when I enter x-²âÊÔ then type x, I got x [1] \262\342\312\324 . Please kindly give me a clue how to fix it. Thanks John [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R/S-related projects on Sourceforge? Trove Categorization
Hi, This are the project which I have extracted from all your mails. 1. http://sourceforge.net/projects/rpgsql/ R PostgreSQL Interface 2. http://sourceforge.net/projects/r-spatial/ R package for spatial data classes 3. http://sourceforge.net/projects/rpy/ RPy (R from Python) 4. http://sourceforge.net/projects/ep-sf/ Expression Profiler 5. http://sourceforge.net/projects/fsap fish stock assessment for R 6. http://sourceforge.net/projects/flr/ R packages for use in fisheries modelling 7. https://sourceforge.net/projects/runit/ R Unit Test Framework 8. http://sourceforge.net/projects/ep-sf/ Expression Profiler 9. http://sourceforge.net/projects/r-asp/ Analysis of Spatial Data in R 10. http://sourceforge.net/projects/r4proteomics/ R Packages for proteomics 11. http://sourceforge.net/projects/rdbi/ R Database Interface 12. http://sourceforge.net/projects/nlmeode/ R package combining nlme and odesolve 13. http://sourceforge.net/projects/rarcinfo/ RArcInfo 14. http://sourceforge.net/projects/rgdal GDAL Package for R 15. http://sourceforge.net/projects/gretl/ GNU Regression, Econometrics and Time-series Library 16. ... Sorry if I have missed any. But it is surely more than five. Thanks all of you for your numerous response and also for some more general thoughts concerning *collaboratory* development using source code repositories: https://stat.ethz.ch/pipermail/r-devel/2004-November/031398.html. If I see how R is evolving I believe that this ideas will be realized soon. Especially that there are already repositories covering some of the functionality and dedicated to R -- Bioconductor with a svn archive. Unfortunately, as I was told by Geff Gentry the costs of administering the svn, cvs servers are high, hence the number of developers must be limited. Also CRAN has some of the functionality but the svn or cvs support is missing. Luckily hosting the sources on e.g. sourceforge and the builds on CRAN or Bioconductor gives already some of the essential functionality. Therefore at this place big thanks to the Bioconductor, CRAN and sourceforge people. /E __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Fwd: Re: [R] 3d scatter plot with drop line
Hi
try this:
p3dpairs - function(x,x1,
xlim=NULL,ylim=NULL,zlim=NULL,col=par(col), pch=par(pch),
cex=par(cex), ...){
if(is.matrix(x)){
z - x[,3]
y - x[,2]
x - x[,1]
}
if(is.matrix(x1)){
z1 - x1[,3]
y1 - x1[,2]
x1 - x1[,1]
}
if(missing(zlim)) {
z.grid - matrix(range(z),2,2)
} else {
z.grid - matrix(zlim,2,2)
}
if(missing(xlim)){ xlim - range(x) }
if(missing(ylim)){ ylim - range(y) }
persp(xlim, ylim, z.grid, col = NA, border=NA, ...) - res
trans3d - function(x,y,z, pmat) {
tr - cbind(x,y,z,1) %*% pmat
list(x = tr[,1]/tr[,4], y= tr[,2]/tr[,4])
}
out - trans3d(x,y,z,pm=res)
out1 - trans3d(x1,y1,z1,pm=res)
points(out, col=col, pch=pch, cex=cex, ...)
for(i in 1:length(out$x)){
lines(c(out$x[i],out1$x[i]),c(out$y[i],out1$y[i]), col=gray, ...)
}
return(invisible(out))
}
then
a - matrix(rnorm(60),20,3)
b - a
b[,3] - 0
p3dpairs(a,b)
gives you a good approximation to what you want
HTH
rksh
This is a follow up to my question from yesterday. I want to do in R
what is called a 3d scatter plot with drop lines in S-PLUS.
Basically, it's a 3dscatterplot with lines connecting the x-y grid to
the z points.
The lines give a better perspective on the shape of the data surface.
How to?
Joel Bremson
UC Davis Statistics
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--
Robin Hankin
Uncertainty Analyst
Southampton Oceanography Centre
SO14 3ZH
tel +44(0)23-8059-7743
[EMAIL PROTECTED] (edit in obvious way; spam precaution)
--
Robin Hankin
Uncertainty Analyst
Southampton Oceanography Centre
SO14 3ZH
tel +44(0)23-8059-7743
[EMAIL PROTECTED] (edit in obvious way; spam precaution)
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RE: [R] summary.lme() vs. anova.lme()
For anyone following this thread in the future: Following Prof. Ripley's advice, I compared models fitted with ML, with and without treatment as a predictor: anova(mconc.lme1,mconc.lme2) Model df AIC BIC logLik Test L.Ratio p-value mconc.lme1 1 10 -1366.184 -1327.240 693.0919 mconc.lme2 2 16 -1363.095 -1300.785 697.5475 1 vs 2 8.91124 0.1786 I can't reject the null hypothesis of no effect of treatment. Many thanks. Dan Bebber Department of Plant Sciences University of Oxford South Parks Road Oxford OX1 3RB UK Tel. 01865 275000 -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: 17 November 2004 15:32 To: Dan Bebber Cc: [EMAIL PROTECTED] Subject: Re: [R] summary.lme() vs. anova.lme() On Wed, 17 Nov 2004, Dan Bebber wrote: I modelled changes in a variable (mconc) over time (d) for individuals (replicate) given one of three treatments (treatment) using: mconc.lme - lme(mconc~treatment*poly(d,2), random=~poly(d,2)|replicate, data=my.data) summary(mconc.lme) shows that the linear coefficient of one of the treatments is significantly different to zero, viz. Value Std.Error DF t-value p-value ... ... ... ... ... treatmentf:poly(d, 2)1 1.3058562 0.5072409 315 2.574430 0.0105 But anova(mconc.lme) gives a non-significant result for the treatment*time interaction, viz. numDF denDF F-value p-value (Intercept) 1 315 159.17267 .0001 treatment239 0.51364 0.6023 poly(d, 2) 2 315 17.43810 .0001 treatment:poly(d, 2) 4 315 2.01592 0.0920 Pinheiro Bates (2000) only discusses anova() for single arguments briefly on p.90. I would like to know whether these results indicate that the significant effect found in summary(mconc.lme) is spurious (perhaps due to multiplicity). Probably yes (but p values of 9% and 1% are not that different, and in both cases you are looking at a few p values). But since both summary.lme and anova.lme use Wald tests, I would use a LRT, using anova on two fits (and I would use ML fits to get a genuine LRT but that is perhaps being cautious). To Dimitris Rizopoulos: as this is the last term in the sequential anova, it is the correct Wald test. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Redirect standard input and output of R
On Wed, 17 Nov 2004, Victor Robles wrote: I'm trying to write a C program that write to the standard input of R and read the standard output. I can perfectly read the R output, but I'm not able of writing anything to R. [SNIP C code] Several years ago, I wrote some software that used S-plus as its back-end and Java for the front-end. I found what worked best was to add a pseudoterminal inbetween; you can use the code from UNIX Programming Environment to create one. The solution was later reused when a similar project used R for its back-end. -- SIGSIG -- signature too long (core dumped) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R-gui] RE: [R] The hidden costs of GPL software?
John W. Eaton wrote: On 17-Nov-2004, Philippe Grosjean [EMAIL PROTECTED] wrote: | - There is no possibility to make a commercial GUI for R (thanks to | the GPL), This is false. Please don't confuse commercial (Red Hat and SuSE GNU/Linux distributions are commercial software) with proprietary. jwe Ooops! Sorry, and thank you for correcting me. I mean proprietary, of course. Best, Philippe Grosjean __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Power sampling
Hello Uwe, Uwe Ligges schrieb: Thomas Schönhoff wrote: You have to tell us for which test you are going to calculate the power ... (and there might be nothing, since calculating the power precisely is not always that easy). Given my example from the first message I asked for a function which enables me to calculate a reasonable sample size. I don't know the true mean or standard deviation of the population, I only know: n= 5.000.000 observations over 70 variables determined alpha = 0.01 I want to know how to generate a sufficiently sized sample based upon above mentioned facts to make some valid predictions regarding my population. All I can hink of for now is that a two-tailed power test is required to find out if H0= random effect or H1= no random effect hypothesis is accepted/rejected. In epidemiological studies this situation is described like this: How many cases do I have to include in my sample (s) to gain some representative results from a unknown population (=true mean, std-deviation etc.)? How can I approach a situation like this in R ? Regards Thomas platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status major2 minor0.1 year 2004 month11 day 15 language R __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
On 17 Nov 2004, at 2:27 pm, Patrick Burns wrote: I think Ted Harding was on the mark when he said that it is the help system that needs enhancement. I can imagine a system that gets the user to the right function and then helps fill in the arguments; all of the time pointing them towards the command line rather than away from it. I think this is spot on. My situation is that I am a scientist turned system administrator, and R is a package which I am increasingly being asked to install for the use of scientists at this Institute. I am by no means a statistician; the statistics I learned in A-level maths almost 20 years ago were as far as I got, and most of that I have forgotten. But I like to have some understanding of the software packages I am asked to support, so I've been looking at R with a view to learning some of its more basic functions. It looks potentially very useful to me anyway for summarising activity on the supercomputing cluster that I run. So I'm a newbie to R, armed with only a very basic knowledge of statistics (I know the difference between a Normal and a Poisson distribution at least, and with a bit of prodding could probably remember a binomial distribution too). I'm an experienced programmer in several languages, and a PhD-level scientist. And yet I have still found R really quite hard to learn, and this is principally because the on-line help is a reference manual. I'm sure it's a fabulous resource if you're a statistician who uses R every day, but for me it's not very helpful. The R Intro PDF is good, but it would be nice if it were integrated better, with hyperlinks to the reference documentation, or to other parts of the introduction, for those platforms that support such things (it looks like this was intended for MacOS X, which is the version I am playing with for my own use, although the version I maintain for users is on Linux [ and would be on Alpha/Tru64 too if I could get it to pass its tests ]) but the on-line help link to the Intro on the Aqua R version brings up a blank page, so I'm using the generic PDF document instead. I think the GUI question has nothing to do with the hidden costs of the GPL, or otherwise. This is the age-old ease-of-use versus power and capability argument. I don't think a fancy GUI is necessary - the GUI aspects that have been added to R on Mac OS X are sufficient. I get the impression that the real power of R is the fact that really it's a programming language, and should probably be treated and learned as such. Quite apart from the fact that a GUI will necessarily be a somewhat restricted subset of the total functionality, and a lot slower to use once you've taken the effort to learn the software, I think there is another danger, which I have already seen in other pieces of software in the bioinformatics community. Users frequently run completely pointless analyses through the GUI wrappers we provide. The users using the command line interfaces typically do much more sensible things. If you make a piece of software trivial for a user to use without thinking about what they're doing, then the users won't think. I may not know much about statistics, but what little I do know is that understanding exactly what form of analysis or significance test is required to be meaningful is a real skill that takes a lot of experience to master. Having to perform that analysis with written commands means that your method is recorded, and could be published, and more importantly be checked and reproduced by other researchers. It also gives you ample time to think about what you're doing, rather than just bashing out a pretty graph which actually has no real meaning whatsoever. Any GUI to R could (and should) be able to store the command line equivalent to what it has just done, to satisfy the reproducible criterion above, but I suspect it could still lead to some pretty shoddy work being done by careless and lazy scientists, and we get enough of that already. Tim -- Dr Tim Cutts Informatics Systems Group, Wellcome Trust Sanger Institute GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5 860B 3CDD 3F56 E313 4233 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] changing (core) function argument defaults?
Berton Gunter [EMAIL PROTECTED] writes: Yes, I think for all practical purposes it (usually?) is. Here's an example. Suppose I wish to change the default constant argument of mad from 1.48 to 2. Then z-formals(mad) z$constant-2 mad-as.function(c(z,body(mad))) Actually, formals(mad)$constant-2 will do the same. In either case, you need to be careful to note that the environment of the function is changed to the current frame. So if you redefine median(), this will be picked up by your mad(), but not by stats::mad(). If you now attach the workspace/environment containing this newly defined mad function to the search list before the stats package (which contains the original mad()) you have effectively changed the default argument without changing the function. I hope experts will let us know when this can't be done (perhaps with .internal functions or non-exported functions in namespaces, though it isn't clear to me that one couldn't manually export them and do this here, too). I'd expect that it works whenever the function has default arguments to modify (.Primitive functions do not). The namespace mechanism only ensures that you don't overwrite the original, and that packages expecting to use the original can continue to do so. Of course, all the usual warnings about masking existing functions apply. Yes, R is not preventing users from shooting themselves in the foot, nor preventing package writers from shooting users in the foot (as a recent query involving [.factor showed). -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Lexical Scoping: eval(expr,envir=)
Hi R-listers,
I am trying to better undertand what we would call functional paradigm
use of S/R to better map my programming activities in other languages.
This little function is aimed to create an object (at the end end, it would
have it's own class):
--
myObject =function(){
list(
a=1,
foo=function(b)
{
cat(b:,b)
cat(\na:, a)
}
)
}
--
To my minds, a would be a property of the object and foo one of it's
method.
Let instantiate one version of this object:
--
tmp = myObject()
tmp
$a
[1] 1
$foo
function(b)
{
cat(b:,b)
cat(\na:, a)
}
environment: 012DDFC8
--
Now I try to invoke it's foo method (definitively not a S terminology!)
For sure, tmp$foo() wont work, as it can't know anything about a.
Reading eval() help page, It is said:
envir: the 'environment' in which 'expr' is to be evaluated. May
also be a list, a data frame, or an integer as in 'sys.call' was
so that I was thinking that
eval(tmp$foo(),envir=tmp)
Error in cat(b:, b) : Argument b is missing, with no default
would solve my problem, which is not the case.
tmp is a list, in which a is defined hand has a value.
Where is my fault?
Eric
R version 2.0.1, Windows
Eric Lecoutre
UCL / Institut de Statistique
Voie du Roman Pays, 20
1348 Louvain-la-Neuve
Belgium
tel: (+32)(0)10473050
[EMAIL PROTECTED]
http://www.stat.ucl.ac.be/ISpersonnel/lecoutre
If the statistics are boring, then you've got the wrong numbers. -Edward
Tufte
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RE: [R] AYUDA
Hi Brian You could check the R-Documentation: functions KalmanLike, KalmanRun, KalmanSmooth, KalmanForecast and makeARIMA. Leonardo Trujillo -- Leonardo Trujillo Southampton Statistical Sciences Research - S3RI University of Southampton -- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Brian pfeng Sent: 17 November 2004 20:44 To: [EMAIL PROTECTED] Subject: [R] AYUDA Hola, necesito informacion sobre como aplicar un modelo espacio estado y filtro de kalman en R. Soy nuevo en R. Gracias _ Información de Estados Unidos y América Latina, en Yahoo! Noticias. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
On 18 Nov 2004, at 10:27 am, Tim Cutts wrote: The R Intro PDF is good, but it would be nice if it were integrated better, with hyperlinks to the reference documentation, or to other parts of the introduction, for those platforms that support such things I should correct myself here, and note that there are some cross-references within the PDF document, it's not completely devoid of them. Tim -- Dr Tim Cutts Informatics Systems Group, Wellcome Trust Sanger Institute GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5 860B 3CDD 3F56 E313 4233 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
H, interesting thread and minds will not be changed but regarding GUIs...I thought S (aka R) was a PROGRAMMING LANGUAGE with a statistical and numerical slant, and not a statistics application. ;O) Certainly there is an important place for GUIs but I believe that it is very much overemphasized in modern computer culture. My experience and bias--and I started in the 1960's-- is that except for 'trivial' uses, GUIs are a detriment to any reasonably complex CREATIVE computational task. They are adequate for the simple, common task. But even then, typing a command or two is not overly taxing--- particularly when compared to navigating layer upon layer of submenus as is some times needed. If I need to, I will add a little syntactical sugaring when coding and move on. GUIs encourage a passive approach to using computers when solving problems. In addition, it is regretable that a lot of people in the 'workplace' will carry out incomplete and/or incorrect quantitative work because of the real or perceived limitations of the particular (GUI) apps they are using. There is no inclination to go beyond the menu and even then many menu items gather 'electronic dust'. Finally, there are times for many of us when work 'goes home' at the end of the day. That just comes with the territory. I (and most others) can not afford the luxury of S-plus, Statistica, SPSS, etc. at home. So in a sense there is a very real 'loss of productivity' cost associated with using commercial software. Now that does bring us around to supporting R doesn't it? (Mea culpa. And I resolve to do better!) What value does one put on the vitality of the R community? Best regards, Michael Grant, Ph.D. * The requirements for creating packages are on target, and have the desired impact on both the quality and breadth of R. --- Philippe Grosjean [EMAIL PROTECTED] wrote: Hello, In the latest 'Scientific Computing World' magazine (issue 78, p. 22), there is a review on free statistical software by Felix Grant ...2.) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
Tim Cutts schrieb: Any GUI to R could (and should) be able to store the command line equivalent to what it has just done, to satisfy the reproducible criterion above, but I suspect it could still lead to some pretty shoddy work being done by careless and lazy scientists, and we get enough of that already. In that respect you should have a look at Emacs/XEmacs/ESS package. This package combines the power of command line and reproducibility of what has been done to generate graphs or whatever you like. Its also equipped with a nice ref-card-pdf which is very helpful to learn common shortcuts to increase your productivity levels. I wouldn't call ESS necessarily a GUI in a traditional sense, though. When I started using R I was inclined to use the RCommander-GUI. After fiddling with this for a while I came to the conclusion that its possibilities are, at least for the moment, really limited. Furthermore some things increased my irritation levels, i.e. orientation to push the correct buttons to achieve a specific task. If I hit a false button I hardly wasn't able to find out what actually went wrong. Nevertheless, for me as a beginner in GNU R, who never used S before, but primarily SPSS and BMDP in early times, it is a long way to gain some control of advanced aspects of using R. This is also true despite the fact that I took statistics courses for several years and do have experiences in research projects (social sciences and epidemiology), so I'll would agree that using GNU R has some hidden costs for me! To sum up, what I am in need to is an extensive example based help-system, focused on how to do things in R. In parts this is already there, i.e. SimpleR from Verzani (contributed docs area) etc. Hopefully I can contribute to this in future, since it is seems to me invaluable to learn R by going through example-based lessons (some are found in vignette() ). These are much more comprehensible to me than those short reference like entries in the current help-system, mostly due to their very technical approach (same is to be said about the official GNU R manuals, especially The R Language, which wasn't a great help for me when I took my first look at GNU R). In this context something like the GuideMaps of Vista come to my mind! But to be as clear as possible, I think GNU R is great and I appreciate all the efforts done by the R core team and associates! Nevertheless it seems to be valuable to re-think the help-system in R with respect to those who may have a good understanding in statistics, but lacking some basic experiences in how to introduce themselves to sophisticated world of R/S languages. Regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Lexical Scoping: eval(expr,envir=)
Hello,
I'm quite new to the objet-oriented vision of life in R, but I think you are
looking for
?setClass
or other functions in the methods package.
Selon Eric Lecoutre [EMAIL PROTECTED]:
Hi R-listers,
I am trying to better undertand what we would call functional paradigm
use of S/R to better map my programming activities in other languages.
This little function is aimed to create an object (at the end end, it would
have it's own class):
--
myObject =function(){
list(
a=1,
foo=function(b)
{
cat(b:,b)
cat(\na:, a)
}
)
}
--
To my minds, a would be a property of the object and foo one of it's
method.
Let instantiate one version of this object:
--
tmp = myObject()
tmp
$a
[1] 1
$foo
function(b)
{
cat(b:,b)
cat(\na:, a)
}
environment: 012DDFC8
--
Now I try to invoke it's foo method (definitively not a S terminology!)
For sure, tmp$foo() wont work, as it can't know anything about a.
Reading eval() help page, It is said:
envir: the 'environment' in which 'expr' is to be evaluated. May
also be a list, a data frame, or an integer as in 'sys.call' was
so that I was thinking that
eval(tmp$foo(),envir=tmp)
Error in cat(b:, b) : Argument b is missing, with no default
would solve my problem, which is not the case.
tmp is a list, in which a is defined hand has a value.
Where is my fault?
Eric
R version 2.0.1, Windows
Eric Lecoutre
UCL / Institut de Statistique
Voie du Roman Pays, 20
1348 Louvain-la-Neuve
Belgium
tel: (+32)(0)10473050
[EMAIL PROTECTED]
http://www.stat.ucl.ac.be/ISpersonnel/lecoutre
If the statistics are boring, then you've got the wrong numbers. -Edward
Tufte
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Re: [R] Lexical Scoping: eval(expr,envir=)
Hi Eric,
this my novice point of view (since I'm still learning R) about what
is happening:
First, `tmp' is not an evironment. Check:
is.environment(tmp)
[1] FALSE
If you'd like to create an environment based on tmp then a simple way
could be:
e1 - new.env()
for(i in seq(along=tmp)) assign(names(tmp)[[i]], tmp[[i]], envir=e1)
Then, `tmp$foo()' is defined in the enviroment of `myObject()', thus
you could set its evironment to be e1 using:
environment(tmp$foo) - e1
now
eval(tmp$foo(2), envir=e1)
maybe is what you want.
Of course maybe someone more experienced than me has a better
solution-explanation but I hope this helps.
Best,
Dimitrs
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/396887
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: Eric Lecoutre [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Sent: Thursday, November 18, 2004 12:05 PM
Subject: [R] Lexical Scoping: eval(expr,envir=)
Hi R-listers,
I am trying to better undertand what we would call functional
paradigm use of S/R to better map my programming activities in
other languages.
This little function is aimed to create an object (at the end end,
it would have it's own class):
--
myObject =function(){
list(
a=1,
foo=function(b)
{
cat(b:,b)
cat(\na:, a)
}
)
}
--
To my minds, a would be a property of the object and foo one of
it's method.
Let instantiate one version of this object:
--
tmp = myObject()
tmp
$a
[1] 1
$foo
function(b)
{
cat(b:,b)
cat(\na:, a)
}
environment: 012DDFC8
--
Now I try to invoke it's foo method (definitively not a S
terminology!)
For sure, tmp$foo() wont work, as it can't know anything about a.
Reading eval() help page, It is said:
envir: the 'environment' in which 'expr' is to be evaluated. May
also be a list, a data frame, or an integer as in
'sys.call' was
so that I was thinking that
eval(tmp$foo(),envir=tmp)
Error in cat(b:, b) : Argument b is missing, with no default
would solve my problem, which is not the case.
tmp is a list, in which a is defined hand has a value.
Where is my fault?
Eric
R version 2.0.1, Windows
Eric Lecoutre
UCL / Institut de Statistique
Voie du Roman Pays, 20
1348 Louvain-la-Neuve
Belgium
tel: (+32)(0)10473050
[EMAIL PROTECTED]
http://www.stat.ucl.ac.be/ISpersonnel/lecoutre
If the statistics are boring, then you've got the wrong
numbers. -Edward Tufte
__
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[R] Errors checking a library
Hi I am writing an R library. The documentation for one of my functions includes an example that I *know* works - simply cut and paste into R on either Windows and Linux and it works perfectly, no errors or warnings, nothing, nyet. However, when I run R CMD check on the library, I get an error. I am running R CMD check on linux, and the offending piece of code appears to be: cox[cox$group %in% onc,] cox is a data frame, one of the columns of which is group, which contains numbers. onc is a vector of numbers. The output on Linux from R CMD check is this: # lots of code # lots of code cox[cox$group + + + # the rest of my code Error: syntax error Execution halted As can be seen, my code cox[cox$group %in% onc,] seems to have been executed incorrectly. Does R CMD check have a problem with the %in% operator? It would seem that R has somehow got mixed up and has lost the rest of my command. I'm using R 1.9.1 on Suse Linux 8.2. The example code works fine on both Windows and Linux when cut-and-pasted into an R window. Mick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Lexical Scoping: eval(expr,envir=)
Hi again,
In a sense, I have answered myself my question.
The functional paradigm is very well described in the article
lexical scope and Statistical computing by Ross Ihaka and Robert Gentleman.
And I did have read it several times...
Solution is function closure. And following code will work as I want.
Except i dont understand the help page on eval.
What about the ability to pass a list for the value of environment()? Can I
have an example of such a use?
My (now working) code:
---
### First version: function closure
myObject1 =function(){
+ # Function Closure
+ function(){
+ a=1
+ list(foo=function(b=3)
+ {
+ cat(b:,b)
+ cat(\na:, a)
+ }
+)
+ }
+ }
(tmp=myObject())
function(){
a=1
list(
foo=function(b=3){
cat(b:,b)
cat(\na:, a)
},
set.a=function(newval) a -newval
)
}
environment: 012B2CAC
tmp()$foo()
b: 3
a: 1 tmp()$foo(b=32)
b: 32
a: 1
### Second version: add a function that allows to change the property a
myObject2 =function(){
+ function(){
+ a=1
+ return(list(
+ foo=function(b=3){
+ cat(b:,b)
+ cat(\na:, a)
+ },
+set.a=function(newval) a -newval
+))
+ }
+ }
(tmp=myObject2()())
$foo
function(b=3){
cat(b:,b)
cat(\na:, a)
}
environment: 012BBF08
$set.a
function(newval) a -newval
environment: 012BBF08
tmp$foo(b=32)
b: 32
a: 1 tmp$set.a(10)
tmp$foo(b=32)
b: 32
a: 10
---
This achieves exactly the object-oriented aspect I wanted to have. And in
fact myObject()() acts as a new instantiation of my object.
Best wishes,
Eric
At 12:05 18/11/2004, Eric Lecoutre wrote:
Hi R-listers,
I am trying to better undertand what we would call functional paradigm
use of S/R to better map my programming activities in other languages.
This little function is aimed to create an object (at the end end, it
would have it's own class):
--
myObject =function(){
list(
a=1,
foo=function(b)
{
cat(b:,b)
cat(\na:, a)
}
)
}
--
To my minds, a would be a property of the object and foo one of it's
method.
Let instantiate one version of this object:
--
tmp = myObject()
tmp
$a
[1] 1
$foo
function(b)
{
cat(b:,b)
cat(\na:, a)
}
environment: 012DDFC8
--
Now I try to invoke it's foo method (definitively not a S terminology!)
For sure, tmp$foo() wont work, as it can't know anything about a.
Reading eval() help page, It is said:
envir: the 'environment' in which 'expr' is to be evaluated. May
also be a list, a data frame, or an integer as in 'sys.call' was
so that I was thinking that
eval(tmp$foo(),envir=tmp)
Error in cat(b:, b) : Argument b is missing, with no default
would solve my problem, which is not the case.
tmp is a list, in which a is defined hand has a value.
Where is my fault?
Eric
R version 2.0.1, Windows
Eric Lecoutre
UCL / Institut de Statistique
Voie du Roman Pays, 20
1348 Louvain-la-Neuve
Belgium
tel: (+32)(0)10473050
[EMAIL PROTECTED]
http://www.stat.ucl.ac.be/ISpersonnel/lecoutre
If the statistics are boring, then you've got the wrong numbers. -Edward Tufte
__
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Re: [R] Errors checking a library
michael watson (IAH-C) wrote: Hi I am writing an R library. The documentation for one of my functions includes an example that I *know* works - simply cut and paste into R on either Windows and Linux and it works perfectly, no errors or warnings, nothing, nyet. However, when I run R CMD check on the library, I get an error. I am running R CMD check on linux, and the offending piece of code appears to be: cox[cox$group %in% onc,] You need to quote %: \%. Uwe Ligges cox is a data frame, one of the columns of which is group, which contains numbers. onc is a vector of numbers. The output on Linux from R CMD check is this: # lots of code # lots of code cox[cox$group + + + # the rest of my code Error: syntax error Execution halted As can be seen, my code cox[cox$group %in% onc,] seems to have been executed incorrectly. Does R CMD check have a problem with the %in% operator? It would seem that R has somehow got mixed up and has lost the rest of my command. I'm using R 1.9.1 on Suse Linux 8.2. The example code works fine on both Windows and Linux when cut-and-pasted into an R window. Mick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Lexical Scoping: eval(expr,envir=)
On Thu, 18 Nov 2004 12:05:34 +0100, Eric Lecoutre
[EMAIL PROTECTED] wrote :
Hi R-listers,
I am trying to better undertand what we would call functional paradigm
use of S/R to better map my programming activities in other languages.
This little function is aimed to create an object (at the end end, it would
have it's own class):
--
myObject =function(){
list(
a=1,
foo=function(b)
{
cat(b:,b)
cat(\na:, a)
}
)
}
--
To my minds, a would be a property of the object and foo one of it's
method.
To work with lexical scoping, you could do it as
myObject - function(){
a - 1
list(
a=function() a,
a- = function(x, value) a - value,
foo=function(b)
{
cat(b:,b,\n)
cat(a:, a,\n)
}
)
}
Then you can access the a property pretty easily, but changing it is
really ugly:
m - myObject()
m$a()
[1] 1
m$foo()
Error in cat(b:, b, \n) : Argument b is missing, with no default
m$foo(1)
b: 1
a: 1
(m$a-)(m, 4)
m$foo(1)
b: 1
a: 4
It would be slightly nicer (but still ugly) if this worked:
(m$a)(m) - 4
Error: invalid function in complex assignment
but it doesn't.
Duncan Murdoch
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[R] JGR Tablet PC
(1) A minor point; the JGR console recognizes when the input panel (think tool bar) is docked at the top of the screen and acts appropriately. However, the editor opens under the input panel. I can close the input panel, move the editor, and open the input panel to continue work. On the other hand, it would be real nice if the editor just opened in a more appropriate place. (2) I am very impressed with JGR as it is and I have completely switched from XEmacs to JGR. Chuck Charles E. White, Senior Biostatistician, MS Walter Reed Army Institute of Research 503 Robert Grant Ave., Room 1w102 Silver Spring, MD 20910-1557 301 319-9781 Personal/Professional Site: http://users.starpower.net/cwhite571/professional/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Errors checking a library
On Thu, 18 Nov 2004, michael watson (IAH-C) wrote:
Hi
I am writing an R library. The documentation for one of my functions
includes an example that I *know* works - simply cut and paste into R on
either Windows and Linux and it works perfectly, no errors or warnings,
nothing, nyet.
However, when I run R CMD check on the library, I get an error. I am
running R CMD check on linux, and the offending piece of code appears to
be:
cox[cox$group %in% onc,]
cox is a data frame, one of the columns of which is group, which
contains numbers. onc is a vector of numbers.
The output on Linux from R CMD check is this:
# lots of code
# lots of code
cox[cox$group
+
+
+ # the rest of my code
Error: syntax error
Execution halted
As can be seen, my code cox[cox$group %in% onc,] seems to have been
executed incorrectly. Does R CMD check have a problem with the %in%
operator? It would seem that R has somehow got mixed up and has lost
the rest of my command.
I'm guessing at what you may mean, so excuse me getting it wrong. If the
code is in an example in a help file (*.Rd, \examples{} block), then the %
may be being interpreted as a comment character, and the remainder of the
line not processed - see Writing R Extensions - Writing R documentation
files - Insertions.
If that is the problem, then escaping the % by \% should fix it, that it
what is done in src/library/base/man/match.Rd anyway.
I'm using R 1.9.1 on Suse Linux 8.2. The example code works fine on
both Windows and Linux when cut-and-pasted into an R window.
Mick
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--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Breiviksveien 40, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93
e-mail: [EMAIL PROTECTED]
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[R] Informix database
We use Informix database. I was able to connect to the database with S-PLUS by using its CONNECT/Java through the JDBC driver. How can I connect to Informix with R, wither using JDBC or any other method? we run Linux so I prefer a method other than ODBC. Thankx for the help __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Errors checking a library
michael watson (IAH-C) [EMAIL PROTECTED] writes:
I am writing an R library.
A whole library? Shouldn't you try a package first?
The documentation for one of my functions
includes an example that I *know* works - simply cut and paste into R on
either Windows and Linux and it works perfectly, no errors or warnings,
nothing, nyet.
However, when I run R CMD check on the library, I get an error. I am
running R CMD check on linux, and the offending piece of code appears to
be:
cox[cox$group %in% onc,]
cox is a data frame, one of the columns of which is group, which
contains numbers. onc is a vector of numbers.
The output on Linux from R CMD check is this:
# lots of code
# lots of code
cox[cox$group
+
+
+ # the rest of my code
Error: syntax error
Execution halted
As can be seen, my code cox[cox$group %in% onc,] seems to have been
executed incorrectly. Does R CMD check have a problem with the %in%
operator? It would seem that R has somehow got mixed up and has lost
the rest of my command.
Think: What is the comment character in .Rd files?
Checking out src/library/base/man/match.Rd should be enlightening, but
since you might not have R sources installed, here are the relevant
bits:
\name{match}
\alias{match}
\alias{\%in\%}
\title{Value Matching}
\description{
\code{match} returns a vector of the positions of (first) matches of
its first argument in its second.
\code{\%in\%} is a more intuitive interface as a binary operator,
which returns a logical vector indicating if there is a match or not
for its left operand.
}
\usage{
match(x, table, nomatch = NA, incomparables = FALSE)
x \%in\% table
}
\examples{
## The intersection of two sets :
intersect - function(x, y) y[match(x, y, nomatch = 0)]
intersect(1:10,7:20)
1:10 \%in\% c(1,3,5,9)
sstr - c(c,ab,B,bba,c,@,bla,a,Ba,\%)
sstr[sstr \%in\% c(letters,LETTERS)]
\%w/o\% - function(x,y) x[!x \%in\% y] #-- x without y
(1:10) \%w/o\% c(3,7,12)
}
\keyword{manip}
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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[R] how to rewrite this without a loop ?
Dear Rexperts,
First of all let me say that R is a wonderful and useful piece of
software.
The only thing is that sometimes it takes me a long time to find out how
something can be done, especially when aiming to write compact (and
efficient) code.
For instance, I have the following function (very rudimentary) which
takes a (very specific) data frame as input and for certain subsets
calculates the rank correlation between two corresponding columns.
The aim is to add all the rank correlations.
code
add.fun - function(perf.data) {
ss - 0
for (i in 0:29) {
ss - ss + cor(subset(perf.data, dataset == i)[3],
subset(perf.data, dataset == i)[7], method = kendall)
}
ss
}
/code
As one can see this function uses a for-loop. Now chapter 9 of 'An
introduction to R' tells us that we should avoid for-loops as much as
possible.
Is there an obvious way to avoid this for-loop is this case ?
I would like to see something in the lines of
(maple style)
code
add( seq(FUN(i), i = 0..29) )
/code
Greetings
Stijn.
--
==
Dept. of Applied Mathematics and Computer Science, University of Ghent
Krijgslaan 281 - S9, B - 9000 Ghent, Belgium
Phone: +32-9-264.48.91, Fax: +32-9-264.49.95
E-mail: [EMAIL PROTECTED], URL: http://allserv.ugent.be/~slievens/
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[R] Re: Informix database
Hi, see DBI: R/S-Plus Database Interface, maybe it could help you: http://stat.bell-labs.com/RS-DBI http://www.ci.tuwien.ac.at/Conferences/DSC-2001/Proceedings/HothornJamesRipley.pdf I found: Other Database Connections from S-Plus Depending on the platform it's running, S-Plus provides access to some DBMS through the importData/exportData functions. Under Microsoft Windows you may import/export data through ODBC; under Solaris (and only Solaris) you may import data from Informix, Oracle, and Sybase. See also the function executeSQL. Best regards Vito You wrote: We use Informix database. I was able to connect to the database with S-PLUS by using its CONNECT/Java through the JDBC driver. How can I connect to Informix with R, wither using JDBC or any other method? we run Linux so I prefer a method other than ODBC. Thankx for the help = Diventare costruttori di soluzioni Became solutions' constructors The business of the statistician is to catalyze the scientific learning process. George E. P. Box Visitate il portale http://www.modugno.it/ e in particolare la sezione su Palese http://www.modugno.it/archivio/palese/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Lexical Scoping: eval(expr,envir=)
Eric Lecoutre lecoutre at stat.ucl.ac.be writes:
:
: Hi R-listers,
:
: I am trying to better undertand what we would call functional paradigm
: use of S/R to better map my programming activities in other languages.
:
: This little function is aimed to create an object (at the end end, it would
: have it's own class):
:
: --
:myObject =function(){
: list(
:a=1,
:foo=function(b)
:{
:cat(b:,b)
:cat(\na:, a)
:}
: )
:}
: --
: To my minds, a would be a property of the object and foo one of it's
: method.
:
: Let instantiate one version of this object:
:
: --
: tmp = myObject()
: tmp
: $a
: [1] 1
:
: $foo
: function(b)
:{
:cat(b:,b)
:cat(\na:, a)
:}
: environment: 012DDFC8
: --
:
: Now I try to invoke it's foo method (definitively not a S terminology!)
: For sure, tmp$foo() wont work, as it can't know anything about a.
:
: Reading eval() help page, It is said:
:
: envir: the 'environment' in which 'expr' is to be evaluated. May
:also be a list, a data frame, or an integer as in 'sys.call' was
:
: so that I was thinking that
:
: eval(tmp$foo(),envir=tmp)
: Error in cat(b:, b) : Argument b is missing, with no default
:
: would solve my problem, which is not the case.
: tmp is a list, in which a is defined hand has a value.
:
: Where is my fault?
:
: Eric
:
: R version 2.0.1, Windows
An example of lexical scoping lose to yours
is found by issuing the R command:
demo(scoping)
However, you probably want to use the builtin
facilities, namely the S3 or S4 object oriented
system or possibly the more conventional oo system
defined in the R.oo package of the R.classes bundle
found at:
http://www.maths.lth.se/help/R/R.classes/
In S3 your problem is done like this:
# use S3 to define 2 objects of class myObject and a method
tmp - list(a=1); class(tmp) - myObject
tmp2 - list(a=2); class(tmp2) - myObject
foo - function(obj, b) UseMethod(foo)
foo.myObject - function(obj, b) cat(b, b, \a, obj$a, \n)
# try out the method
foo(tmp, 3)
foo(tmp2, 5)
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[R] Re: Informix database
There is no DBI implementation for Informix. I would appreciate some pointers to R's Java extension, if exists. I already have a solution for S-PLUS. I am interested in finding one for R to compare the two, otherwise my company will go with S-PLUS. On Thu, 18 Nov 2004 15:45:25 +0100 (CET), Vito Ricci [EMAIL PROTECTED] wrote: Hi, see DBI: R/S-Plus Database Interface, maybe it could help you: http://stat.bell-labs.com/RS-DBI http://www.ci.tuwien.ac.at/Conferences/DSC-2001/Proceedings/HothornJamesRipley.pdf I found: Other Database Connections from S-Plus Depending on the platform it's running, S-Plus provides access to some DBMS through the importData/exportData functions. Under Microsoft Windows you may import/export data through ODBC; under Solaris (and only Solaris) you may import data from Informix, Oracle, and Sybase. See also the function executeSQL. Best regards Vito You wrote: We use Informix database. I was able to connect to the database with S-PLUS by using its CONNECT/Java through the JDBC driver. How can I connect to Informix with R, wither using JDBC or any other method? we run Linux so I prefer a method other than ODBC. Thankx for the help = Diventare costruttori di soluzioni Became solutions' constructors The business of the statistician is to catalyze the scientific learning process. George E. P. Box Visitate il portale http://www.modugno.it/ e in particolare la sezione su Palese http://www.modugno.it/archivio/palese/ ___ Nuovo Yahoo! Messenger: E' molto pi divertente: Audibles, Avatar, Webcam, Giochi, Rubrica Scaricalo ora! http://it.messenger.yahoo.it __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
At 11/18/2004 07:01 AM Thursday, Thomas Schönhoff wrote: To sum up, what I am in need to is an extensive example based help-system, focused on how to do things in R. In parts this is already there, i.e. SimpleR from Verzani (contributed docs area) etc. Hopefully I can contribute to this in future, since it is seems to me invaluable to learn R by going through example-based lessons (some are found in vignette() ). These are much more comprehensible to me than those short reference like entries in the current help-system, mostly due to their very technical approach (same is to be said about the official GNU R manuals, especially The R Language, which wasn't a great help for me when I took my first look at GNU R). In this context something like the GuideMaps of Vista come to my mind! But to be as clear as possible, I think GNU R is great and I appreciate all the efforts done by the R core team and associates! Nevertheless it seems to be valuable to re-think the help-system in R with respect to those who may have a good understanding in statistics, but lacking some basic experiences in how to introduce themselves to sophisticated world of R/S languages. (I posted similar material before, but it was moved to R-devel, and I wanted to express a bit of it here.) I have frequently felt, like Thomas, that what could make R easier to use is not a GUI, but a help system more focused on tasks and examples, rather than on functions and packages. This has obvious and large costs of development, and I am unlikely to contribute much myself, for reasons of time and ability. Yet, I mention it for the sake of this discussion. Such a help system could be a tree (or key) structure in which through making choices, the user's description of the desired task is gradually narrowed. At the end of each twig of the tree would be a list of suggested functions for solving the problem, hyperlinked into the existing help system (which in many ways is outstanding and has evolved just as fast as R itself). This could be coupled with the continued expansion of the number of examples in the help system. Now I must express appreciation for what exists already that helps in this regard: MASS (in its many editions), Introductory Statistics with R, Simple R, and the other free documentation that so many authors have generously provided. Not to mention the superlative contribution of R itself, and the work of the R development team. It is beyond my understanding how something so valuable and well thought out has been created by people with so many other responsibilities. Mike -- Michael Prager, Ph.D. Population Dynamics Team, NMFS SE Fisheries Science Center NOAA Center for Coastal Fisheries and Habitat Research Beaufort, North Carolina 28516 http://shrimp.ccfhrb.noaa.gov/~mprager/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Chinese character
On Thu, 18 Nov 2004, john zhao wrote: Hello R-help team, I am a R user in China. I just downloaded the latest R which is R2001 for Windows. This new version can not store Chinese character which the previous version R 1.9.1 does. Specifically when I enter The previous version was 2.0.0. x-²âÊÔ then type x, I got x [1] \262\342\312\324 . That is because your locale is saying those are non-printable characters. It's an OS issue, not an R issue (and has been discussed before for R 2.0.0). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Where has the Debian respository gone?
On Thu, Nov 18, 2004 at 08:52:38AM +, stats wrote: Hello Dirk, Monday, November 15, 2004, 1:35:27 AM, you wrote: DE On Sun, Nov 14, 2004 at 10:53:42PM +0100, Christoph Bier wrote: Hi all! Did I miss something or is it just a temporary problem? Where has the Debian respository http://cran.r-project.org woody/main Packages resp. http://cran.r-project.org/bin/linux/debian/ gone? I tried it for about the last 7 hours. DE Current R and CRAN packages are on the Debian archives; you can install DE these on testing too. To the best of my knowledge, there are no backports DE of current R and Debian CRAN packages to Debian stable. I'm a bit puzzled. I had deb http://cran.r-project.org/bin/linux/debian woody main in /etc/apt/sources.list and had hoped, perhaps rather unwisely, that this would look after the transition from 1.8.0 on my internet server (Debian stable) where it serves up some cgi-bin work. (Most of my R work is on a Win2k machine, much though I'd like to go Debian all the way, that isn't possible for my main job in near future.) Is there an easy way of upgrading R on a Debian stable machine? I don't want to move off stable as the security side of that server is too important. I also don't really want to compile it myself if I can avoid that, the server is pretty old iron and that might back up all the Email stuff it does. Advice anyone? More than advice, we need a volunteer to backport the current R package(s) for Debian to the Debian stable distribution. As I said, testing and unstable are taken care of (and yes, testing is still lagging because of the now much more formal interdependence of packages; R 2.0.* will appears once all dependent packages are available on all architectures) Dirk -- If your hair is standing up, then you are in extreme danger. -- http://www.usafa.af.mil/dfp/cockpit-phys/fp1ex3.htm __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Informix database
On Thu, 18 Nov 2004, Yasser El-Zein wrote: We use Informix database. I was able to connect to the database with S-PLUS by using its CONNECT/Java through the JDBC driver. How can I connect to Informix with R, wither using JDBC or any other method? we run Linux so I prefer a method other than ODBC. ODBC runs perfectly well under Linux. There is an Informix driver, see http://www.unixodbc.org/doc/informix.html R does not have a JDBC driver, and trying to use one under RSJava is likely to be *far* more work that using ODBC. Vito Ricci mentioned DBI, but I am unaware of any Informix backend for DBI, which is not of itself a DBMS interface, more a meta-driver (as ODBC is). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R-gui] Re: [R] The hidden costs of GPL software?
Hello, I appreciate many comments and the various points of view, especially because there are a couple of clear explanations why several people do not need (or even do not want) a GUI for R! Another part of the discussion seems to switch to the never-ending question of what kind of GUI... which will never be answered, because there is not one best GUI, and it also depends on the use (both the application and the user). It's a long time I hesitate to propose in R-SIG-GUI + the R GUI projects web site to place a description for one or several prototype GUI(s) we would like for R, with the intention to include all the good ideas everybody has in this list. I never did that, because I am pretty sure it is useless! Now, I feel that one guy, with a clear view of what he wants, a lot of free time, a lot of energy, and some decent skills in programming, is actually required to make real what he has in his head! Indeed, it is such a huge work that several people are required! Here are the topics currently developed (sorry if I don't cite Bioconductor stuff: I don't know it): - Most of the low-level work is done, I think, like interface with graphical toolkits: tcltk by Peter Dalgaard, of course, but many others (Gtk, wxPython, ...), a better control of Rgui under Windows (ongoing, Duncan Murdoch), ESS, ... All this is already available, even if one could always argue that it is not optimal in some respects. - A better console (multiple-lines editing, syntax coloring, code tip presenting the syntax of a function when you type it, contextual completion list, ...). This is ongoing project in both JGR and SciViews-R. - A better table editor: RKward team. - A classical menus/dialog box approach: John Fox's R commander, - An object explorer: JGR, RKward, SciViews-R, experimental functions in R, - A plug-in approach, that is, a piece of code that brings a GUI for a targeted analysis and builds R code for you: RKward team, but also some functions in svDialogs (part of the SciViews bundle, R GUI API), - Interactive documents mixing formatted text, graphs, etc... with R input/output: Rpad, Sweave (not interactive), and some other, - Rich-formatted output of R objects (in/out, views, reporting,...): Eric Lecoutre's R2HTML + SciViews-R, - Code editor with interaction with R: Tinn-R, WinEdt, Emacs, and many others, - IDE (humm, some code editors are not so far away from an IDE, but there is still some lack here), - A R GUI API: SciViews. I hope all these projects will continue, will mature, and their developers will ultimately realize that they provide complementary pieces of a giant puzzle and start to work together. This is when it will become most exciting! I hope also that it will result in an original GUI that keeps most of the spirit of R, that is, not a simplified pointclick UI, leading to meaningless analyses by lazy people, but a real tool whose goal is to make R easier and faster to learn for beginner, and pretty usable for occasional users. May be, I am just a dreamer, but all I read in this discussion reinforce my conviction that an **innovative** GUI would be a good addition to R: most criticisms clearly relate to the kind of inflexible GUI, with a forest of menus and submenus, and other bad things one could find. I never, and will never advocate for such a GUI! For sure, the alternate GUI will only support you in writing R code, and will deliver plenty of help to achieve this goal. I think it is possible... with enough people collaborating in a common project! I think the later point is really the problem: not enough people, too many projects! Is it a consequence of the way R is developed (GPL)? Well, I think so, but only partly. It is also the consequence of ego (everybody wants to be the leader of his own project), and a lack of communication (R-SIG-GUI is not what one would call an active list!) Or, may be, a good GUI for R is a fuzzy target and it is not possible to cristallize enough power around a common goal: to reach it! Anyway, despite R GUI projects are progressing very slowly, I think only when we would have a good GUI available for R, we would be able to evaluate if there are really hidden costs in R, as Felix Grant suggests in his paper. Best regards and thank you all for your comments and suggestions. Philippe Grosjean __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Informix database
The Informix linux ODBC driver is not free, isn't it? Shoudl I be worried of ODBC performance on linux? On Thu, 18 Nov 2004 15:22:56 + (GMT), Prof Brian Ripley [EMAIL PROTECTED] wrote: On Thu, 18 Nov 2004, Yasser El-Zein wrote: We use Informix database. I was able to connect to the database with S-PLUS by using its CONNECT/Java through the JDBC driver. How can I connect to Informix with R, wither using JDBC or any other method? we run Linux so I prefer a method other than ODBC. ODBC runs perfectly well under Linux. There is an Informix driver, see http://www.unixodbc.org/doc/informix.html R does not have a JDBC driver, and trying to use one under RSJava is likely to be *far* more work that using ODBC. Vito Ricci mentioned DBI, but I am unaware of any Informix backend for DBI, which is not of itself a DBMS interface, more a meta-driver (as ODBC is). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to rewrite this without a loop ?
Stijn Lievens wrote:
Dear Rexperts,
First of all let me say that R is a wonderful and useful piece of software.
The only thing is that sometimes it takes me a long time to find out how
something can be done, especially when aiming to write compact (and
efficient) code.
For instance, I have the following function (very rudimentary) which
takes a (very specific) data frame as input and for certain subsets
calculates the rank correlation between two corresponding columns.
The aim is to add all the rank correlations.
code
add.fun - function(perf.data) {
ss - 0
for (i in 0:29) {
ss - ss + cor(subset(perf.data, dataset == i)[3],
subset(perf.data, dataset == i)[7], method = kendall)
}
ss
}
/code
As one can see this function uses a for-loop. Now chapter 9 of 'An
introduction to R' tells us that we should avoid for-loops as much as
possible.
Is there an obvious way to avoid this for-loop is this case ?
Using the lapply function in the e-mail of James, I came up with the
following.
code
sum (as.numeric( lapply( split(perf.data, perf.data$dataset),
function(x) cor(x[3],x[7],method=kendall) ) ))
/code
So, first I split the dataframe into a list of dataframes using split,
and using lapply I get a list of correlations, which I convert to
numeric and finally sum up.
I definitely avoided the for-loop in this way, although I am not sure
whether this is more efficient or not.
Cheers,
Stijn.
I would like to see something in the lines of
(maple style)
code
add( seq(FUN(i), i = 0..29) )
/code
Greetings
Stijn.
--
==
Dept. of Applied Mathematics and Computer Science, University of Ghent
Krijgslaan 281 - S9, B - 9000 Ghent, Belgium
Phone: +32-9-264.48.91, Fax: +32-9-264.49.95
E-mail: [EMAIL PROTECTED], URL: http://allserv.ugent.be/~slievens/
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RE: [R-gui] RE: [R] The hidden costs of GPL software?
On Thu, 18 Nov 2004, Philippe Grosjean wrote: John W. Eaton wrote: On 17-Nov-2004, Philippe Grosjean [EMAIL PROTECTED] wrote: | - There is no possibility to make a commercial GUI for R (thanks to | the GPL), This is false. Please don't confuse commercial (Red Hat and SuSE GNU/Linux distributions are commercial software) with proprietary. jwe Ooops! Sorry, and thank you for correcting me. I mean proprietary, of course. Best, And it isn't obvious that it is true even if you mean proprietary. A GUI that ran R just by sending commands to stdin and getting results from stdout could clearly be proprietary without violating the GPL. The question of exactly what level of closer integration is allowed would get complicated and I won't speculate. -thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
On Thu, 2004-11-18 at 03:24 -0800, Michael Grant wrote: H, interesting thread and minds will not be changed but regarding GUIs...I thought S (aka R) was a PROGRAMMING LANGUAGE with a statistical and numerical slant, and not a statistics application. ;O) From the R web site: R is a language and environment for statistical computing and graphics. I think that this is a critical point and that there is, to my mind, a false predicate at play here. That predicate is that somehow one should be able to rapidly learn R (or any programming language for that matter) solely via the available online reference help or via the freely provided documentation (whether via R Core or via Contributors). How many people here have learned to use C, FORTRAN, SAS, VBA, Perl or any other language strictly by using built-in reference help systems. If any, it will be a very small proportion. Sure, SAS comes with documentation that can be measured in hernia inducing tonnage, but at a substantial annual cost, which I have referenced here and elsewhere previously. R is free. Is there anyone who has learned to code in C that does not have a copy of KR someplace on their shelf, probably along with copies of other both general and application specific C references published by Prentice-Hall, Addison-Wesley, McGraw-Hill or Hayden? It has been years since I actively coded in C, but I have almost 3 shelves filled with C reference books. I have books dating back to the early 80's for 80x86 Assembly, MS-DOS/BIOS interrupts and Windows API technical references and other such books that I used to use on a daily basis in a former life. For Linux, I have two shelves filled with various O'Reilly and other references running the gambit from general Linux stuff to Perl, Procmail, Postfix, Bash, Regex, Emacs, Admin, Firewalls and others. For R, I have most of a shelf filled with multiple references, including three of the four editions of MASS (somehow I missed the 2nd edition). I have a copy of Peter's ISwR (because on occasion I have an acute attack of cerebral flatulence and have to go back to basics) along with copies of Pinheiro Bates, Fox, Maindonald Braun, Krause Olson, Everitt Rabe-Hesketh and VR's S Programming. I have copies of the White Book and the Green Book and I have copies of Harrell and Therneau Grambsch for specific applications of R. There are a fair number of already published books on R/S with more coming by Faraway, Heiberger Holland, Verzani and others including a new series from Springer. My point being that the old philosophy of No Pain, No Gain is a component of the learning curve with R. R is not going to be for everybody. That's why there are other point and click statistical _applications_ like JMP (albeit not cheap). They are relatively easy, but at the same time, they are self-limiting. No single math/statistical product is going to meet the needs of the entire spectrum of the potential user space. As I have mentioned previously, I am a firm believer in Pareto's 80/20 Rule. In this case, you develop a product to meet the needs of 80% of your target user space, because you will go bankrupt meeting the needs of the other 20%. Said differently, meeting the needs of the other 20% will consume 80% of your development resources, restricting your ability to meet the needs of the larger audience. Having spent 12 years previously with a commercial medical software company, I will also suggest that typically 20% of your user base will consume 80% of your support resources. I will also note that having been on both sides of that equation, the support provided here within this community is superb and has no peer in the commercial arena. In R's case, the 80% of the user space has perhaps been extended by the kind offerings of those who have made specialty packages available via CRAN, BioC and others. It takes a certain level of commitment and time with R to become effective with it. That commitment includes, in my mind, supplementing the available _free_ documentation that has kindly been provided by R Core and others, with other available resources. That does not mean that everyone needs to get on Amazon.com and spend hundreds of $YOUR_MONETARY_UNIT on books. Many are available via libraries and/or other resources, especially for those here in academic environments. This is a community effort folks and not everything is going to be provided to you free of charge, with that notion being either in actual financial cost or time. It appears that, since this is not the first time this subject has come up, there is strong interest in building a c(new, different, better, ...) documentation/help system for R. That's fine. For those that have interest in pursuing this, perhaps the time has come for a group to form a new r-sig-doc list and move forward with the development of a framework for a new system that can be developed and implemented by that same group and then provided back to the community.
Re: [R] Re: Informix database
Yasser El-Zein [EMAIL PROTECTED] writes: There is no DBI implementation for Informix. I would appreciate some pointers to R's Java extension, if exists. I already have a solution for S-PLUS. I am interested in finding one for R to compare the two, otherwise my company will go with S-PLUS. unixODBC works fine for me using MySQL with R and there appears to be an Informix driver that works: The driver from informix works fine, but you need to have a look at the doc in the manuals section of the this site http://www.unixodbc.org/drivers.html I haven't tried it, but it looks in principle like you should be able to access the Informix database from R via unixODBC. Dave -- David Whiting University of Newcastle upon Tyne, UK __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to rewrite this without a loop ?
On Thu, 18 Nov 2004, Stijn Lievens wrote:
code
add.fun - function(perf.data) {
ss - 0
for (i in 0:29) {
ss - ss + cor(subset(perf.data, dataset == i)[3], subset(perf.data,
dataset == i)[7], method = kendall)
}
ss }
/code
As one can see this function uses a for-loop. Now chapter 9 of 'An
introduction to R' tells us that we should avoid for-loops as much as
possible.
You don't say whether `dataset' is the name of a column in `perf.data'.
Assuming it is, and assuming that 0:29 are all the values of `dataset'
sum(by(perf.data, list(perf.data$dataset),
function(d) cor(d[,3],d[,7], method=kendall)))
would work. If this is faster it will be because you don't call subset()
twice per iteration, rather than because you are avoiding a loop. However
it has other benefits: it doesn't have the variable `i', it doesn't have
to change the value of `ss', and it doesn't have the range of `dataset'
hard-coded into it. These are all clarity optimisations.
-thomas
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[R] hashing using named lists
hi all, I am trying to use named list to hash a bunch of vector by name, for instance: test = list() test$name = c(1,2,3) the problem is that when i try to get the values back by using the name, the matching isn't done in an exact way, so test$na is not NULL. is there a way around this? Why by default all.equal.list doesnt require an exact match? How can I do hashing in R? thanks. ulas. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: The hidden costs of GPL software?
My background: I am a biologist coming to R via Bioconductor. I have no computer background in computer sciences and only basic undergraduate training level in statistics. I have used R with great pleasure and great pains. The most difficult thing is to know what functions to use - sometimes I know that one function is most likely available, but there's really no easy way to get it (yes, even going to the archives and reading the help files). I feel that more examples in the help files would definitely be a good way to fully understand the potencial of the functions. I know how difficult this is to do and how much of a time sink it must be. One thing I defeinitely think would be a great improvement is to have a beefed up Object Explorer as Splus does. I think it's the great advantage of Splus when compared to R is to have much easier access to what type of object, col names, classes and so on there are. And how much easier it is to change all these attributes in Splus. I think R 2.0 in Mac did a lot to improve this, but I think that for someone that very frequently needs to know whether the object created turned out to be a vector or a list, the easy access to objects is very, very, very important and would be a great improvement in the ease of use of R. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
On Wed, 17 Nov 2004, Mike Prager wrote: ... Using CLI software, an infrequent user has trouble remembering the known functions needed and trouble finding new ones (especially as that user gets older). What might help is an added help facility more oriented towards tasks, rather than structured around functions or packages. ... Another good (non-GUI) tool for the CLI is keyword completion. R in ESS does this, giving you lists of possible functions, variables and objects, or feedback if there isn't any. R's CLI completes, but only with filenames in the current directory. Dave -- Dave Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
On 17-Nov-04 Patrick Burns wrote: [...] Perhaps an overly harsh summary of some of Ted Harding's statements is: You can make a truck easier to get into by taking off the wheels, but that doesn't make it more useful. Yes, perhaps overly harsh ... but if you had said instead by deflating the tyres then I think I'd agree that you were spot on! Otherwise I agree with your other comments. All best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 [NB: New number!] Date: 18-Nov-04 Time: 16:57:20 -- XFMail -- __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] hashing using named lists
You could try using environments: e - new.env(hash = TRUE) e$new - 1:4 ls(e) [1] new e$new [1] 1 2 3 4 e$ne NULL -roger ulas karaoz wrote: hi all, I am trying to use named list to hash a bunch of vector by name, for instance: test = list() test$name = c(1,2,3) the problem is that when i try to get the values back by using the name, the matching isn't done in an exact way, so test$na is not NULL. is there a way around this? Why by default all.equal.list doesnt require an exact match? How can I do hashing in R? thanks. ulas. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Roger D. Peng http://www.biostat.jhsph.edu/~rpeng/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] hashing using named lists
On Thu, 18 Nov 2004, ulas karaoz wrote: hi all, I am trying to use named list to hash a bunch of vector by name, for instance: test = list() test$name = c(1,2,3) the problem is that when i try to get the values back by using the name, the matching isn't done in an exact way, so test$na is not NULL. is there a way around this? ?match on the names Why by default all.equal.list doesnt require an exact match? What do you mean by that? It (by default or not) tests all the attributes, including the names: test - list(name=1:3) test2 - list(na=1:3) all.equal(test, test2) [1] Names: 1 string mismatches Now, all.equal does not require an exact match, deliberately: that is what identical() is for: identical(test, test2) [1] FALSE How can I do hashing in R? ?match -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Re: The hidden costs of GPL software?
[...] I am a biologist coming to R via Bioconductor. I have no computer background in computer sciences and only basic undergraduate training level in statistics. I have used R with great pleasure and great pains. The most difficult thing is to know what functions to use - sometimes I know that one function is most likely available, but there's really no easy way to get it (yes, even going to the archives and reading the help files). I feel that more examples in the help files would definitely be a good way to fully understand the potencial of the functions. I know how difficult this is to do and how much of a time sink it must be. Yes, I' often have the same problem when it comes to programming in R (data manipulation, formatting etc ...). When thinking about a solution, I often come up with something slow and complicated. A positng to this list usually reveals a very simple solution thanks to a function that I didn't find when exploring help, help.search and the archives (and thanks to those who give me the hint ;-). However, I don't know how to improve this, i.e. how to implement a more sophisticated help.search. Maybe the keywords in the help files or some kind of free text mining would help - well, maybe this is a bit over the top. On the other hand, when it comes to the statistics (I'm a not a statistician) and it's minimal formatting of data etc , I think that developing an understanding of the stats itself is the main probelm and a GUI doesn't help very much in for this. Once the basic understanding is there (which one needs anyway, even with a GUI), the rest is not too difficult. In addition I usually need to script the calculations for many different datasets, and again most GUIs are bad in repeating tasks systematically. I've spent quite some time with learing R (and I haven't stoped yet ;-), but it's devinitely worth it. As a scientists I appreciate it, and since it is a tool that use often, I would not exchange the command-line for any GUI. This list and the many books and manuals (mentioned in the other postings here) do a pretty good job in teaching R! kind regards, Arne [...] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] hashing using named lists
ulas karaoz wrote: is there a way around this? yes... Why by default all.equal.list doesnt require an exact match? because we're lazy? :) How can I do hashing in R? you can explicitly test the names for equality, eg with this 2-element list: x $name [1] 1 2 3 $n [1] 3 2 1 You can do: x[names(x)=='name'] $name [1] 1 2 3 x[names(x)=='na'] list() x[names(x)=='n'] $n [1] 3 2 1 Of course, the right way would be to create a new class, 'hash' perhaps, that did all this in its '$' or '[' methods. Baz __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R/S-related projects on Sourceforge? Trove Categorization - GDAL
Dirk == Dirk Eddelbuettel [EMAIL PROTECTED] on Wed, 17 Nov 2004 12:25:16 -0600 writes: Dirk On Wed, Nov 17, 2004 at 11:52:57AM -0500, Dirk [EMAIL PROTECTED] wrote: Gretl, RPad and RMetrics, plus Ernesto's FLR and fsap make five. Dirk Isn't RMetrics at rmetrics.org at the ETH in Zuerich, CH? that's definitely correct. There might have been oral plans to change the development process, but I'm not even sure about that. Martin Maechler (at ETH, but not connected to Rmetrics in any ways). __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] hashing using named lists
Use match() for exact matching, i.e., test[[match(name, names(test))]] Yes, it is more cumbersome. This partial matching is considered by some to be a design fault, but changing it would break too many programs that depend upon it. I don't understand your question about all.equal.list() -- it does seem to require exact matches on names, e.g.: all.equal(list(a=1:3), list(aa=1:3)) [1] Names: 1 string mismatches all.equal(list(aa=1:3), list(a=1:3)) [1] Names: 1 string mismatches (the above run in R 2.0.0) -- Tony Plate (BTW, in R this operation is generally called indexing or subscripting or extraction, but not hashing. Hashing is a specific technique for managing and looking up indices, which is why some other programming languages refer to list-like objects that are indexed by character strings as hashes. I don't think hashing is used for list names in R, but someone please correct me if I'm wrong! ) At Thursday 09:29 AM 11/18/2004, ulas karaoz wrote: hi all, I am trying to use named list to hash a bunch of vector by name, for instance: test = list() test$name = c(1,2,3) the problem is that when i try to get the values back by using the name, the matching isn't done in an exact way, so test$na is not NULL. is there a way around this? Why by default all.equal.list doesnt require an exact match? How can I do hashing in R? thanks. ulas. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] hashing using named lists
It seems that that behavior is hard-coded in the subscript code, but I bet you could fix it easily by changing the call to get1index offset = get1index(CAR(subs), getAttrib(x, R_NamesSymbol), length(x), /*partial ok*/TRUE, i); in src/main/subset.c (line 762 I think, R-2.0.0) to supply FALSE in place of TRUE and recompiling... I haven't tried yet though so maybe I'm quite badly wrong. Reid Huntsinger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of ulas karaoz Sent: Thursday, November 18, 2004 11:30 AM To: [EMAIL PROTECTED] Subject: [R] hashing using named lists hi all, I am trying to use named list to hash a bunch of vector by name, for instance: test = list() test$name = c(1,2,3) the problem is that when i try to get the values back by using the name, the matching isn't done in an exact way, so test$na is not NULL. is there a way around this? Why by default all.equal.list doesnt require an exact match? How can I do hashing in R? thanks. ulas. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
Mike Prager wrote: At 11/18/2004 07:01 AM Thursday, Thomas Schönhoff wrote: To sum up, what I am in need to is an extensive example based help-system, focused on how to do things in R. In parts this is already there, i.e. SimpleR from Verzani (contributed docs area) etc. Hopefully I can contribute to this in future, since it is seems to me invaluable to learn R by going through example-based lessons (some are found in vignette() ). These are much more comprehensible to me than those short reference like entries in the current help-system, mostly due to their very technical approach (same is to be said about the official GNU R manuals, especially The R Language, which wasn't a great help for me when I took my first look at GNU R). In this context something like the GuideMaps of Vista come to my mind! But to be as clear as possible, I think GNU R is great and I appreciate all the efforts done by the R core team and associates! Nevertheless it seems to be valuable to re-think the help-system in R with respect to those who may have a good understanding in statistics, but lacking some basic experiences in how to introduce themselves to sophisticated world of R/S languages. (I posted similar material before, but it was moved to R-devel, and I wanted to express a bit of it here.) I have frequently felt, like Thomas, that what could make R easier to use is not a GUI, but a help system more focused on tasks and examples, rather than on functions and packages. This has obvious and large costs of development, and I am unlikely to contribute much myself, for reasons of time and ability. Yet, I mention it for the sake of this discussion. Such a help system could be a tree (or key) structure in which through making choices, the user's description of the desired task is gradually narrowed. At the end of each twig of the tree would be a list of suggested functions for solving the problem, hyperlinked into the existing help system (which in many ways is outstanding and has evolved just as fast as R itself). This could be coupled with the continued expansion of the number of examples in the help system. Now I must express appreciation for what exists already that helps in this regard: MASS (in its many editions), Introductory Statistics with R, Simple R, and the other free documentation that so many authors have generously provided. Not to mention the superlative contribution of R itself, and the work of the R development team. It is beyond my understanding how something so valuable and well thought out has been created by people with so many other responsibilities. Mike ... I second all of that. What you are describing Mike could be done with a community-maintained wiki, with easy to add hyperlinks to other sites. Just think what a great value it would be to the statistical community to have an ever-growing set of examples with all code and output, taking a cue from the BUGS examples guides. The content could be broken down by major areas (data import examples, data manipulation examples, many analysis topics, many graphics topics, etc.). Ultimately the more elaborate case studies could be peer-reviewied (a la the Journal of Statistical Software) and updated. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: The hidden costs of R?
Thomas == Thomas Schönhoff [EMAIL PROTECTED] writes: To sum up, what I am in need to is an extensive example based help-system, focused on how to do things in R. In parts this is already there, i.e. SimpleR from Verzani (contributed docs area) etc. I have a nice set of extensive help with documentation sitting on my shelf: - Peter Dalgaard. Introductory Statistics with R. Springer, 2002. ISBN 0-387-9 - William N. Venables and Brian D. Ripley. Modern Applied Statistics with S. Fourth Edition. Springer, 2002. ISBN 0-387-95457-0. - Jose C. Pinheiro and Douglas M. Bates. Mixed-Effects Models in S and S-Plus. Springer, 2000. ISBN 0-387-98957-0. I suspect that I would have spent the money on these books even if I'd started by spending money for S-plus, instead of R. But I've never seen the S-plus help system, so I may be wrong. See http://www.r-project.org/doc/bib/R-publications.html and http://www.r-project.org/doc/bib/R_bib.html for yet more. Mike -- Michael A. Miller [EMAIL PROTECTED] Imaging Sciences, Department of Radiology, IU School of Medicine __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] gibbs sampling for mixture of normals
hi i'm looking for a gibbs sampling algorithm for R for the case of mixture of K normals, and in particular for the case of bivariate normals. i'd be grateful if anyone could send its own R-routine, at least for the univariate case. thank you in advance matteo __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] SJava
I failed to build SJava dure to teh error below. Any ideas? # R CMD INSTALL -c SJava_0.68-0.tar.gz * Installing *source* package 'SJava' ... checking for java... /opt/j2sdk1.4.2_06//bin/java Java VM /opt/j2sdk1.4.2_06//bin/java checking for javah... /opt/j2sdk1.4.2_06//bin/javah Looking in /opt/j2sdk1.4.2_06/include Looking in /opt/j2sdk1.4.2_06/include/linux checking for g++... no checking for c++... no checking for gpp... gpp checking for C++ compiler default output... b.out checking whether the C++ compiler works... configure: error: cannot run C++ compiled programs. If you meant to cross compile, use `--host'. See `config.log' for more details. ERROR: configuration failed for package 'SJava' __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] The hidden costs of GPL software?
On Thu, 18 Nov 2004, Frank E Harrell Jr wrote:
...
...
I second all of that. What you are describing Mike could be done with
a community-maintained wiki, with easy to add hyperlinks to other sites.
There is a wiki at http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl but it
doesn't seem to get much use.
Last time I was hunting for help on R, I made the page
http://fawn.unibw-hamburg.de/cgi-bin/Rwiki.pl?SearchFunctions
and in particular:
help.search.archive-function(string){
RURL=http://www.google.com/u/newcastlemaths;
RSearchURL=paste(RURL,?q=,string,sep='')
browseURL(RSearchURL)
return(invisible(0))
}
help.search.archive('wiki') # example
Dave
--
Dave Forrest
[EMAIL PROTECTED](804)684-7900w
[EMAIL PROTECTED] (804)642-0662h
http://maplepark.com/~drf5n/
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] hashing using named lists
On Thu, 18 Nov 2004, Huntsinger, Reid wrote: It seems that that behavior is hard-coded in the subscript code, the behaviour being partial matching? but I bet you could fix it easily by changing the call to get1index offset = get1index(CAR(subs), getAttrib(x, R_NamesSymbol), length(x), /*partial ok*/TRUE, i); in src/main/subset.c (line 762 I think, R-2.0.0) to supply FALSE in place of TRUE and recompiling... I haven't tried yet though so maybe I'm quite badly wrong. That is the [[ ]] code. The $ code is at about line 968. And if you did that a lot of R code may break, so please don't even think about it. Partial matching is a long-standing feature. There have been proposals from time to time for [ ] and [[ ]] to have an exact=TRUE argument for character indices. That seems a good idea, except that they are generic and there are now many methods out there which would ignore the argument. Reid Huntsinger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of ulas karaoz Sent: Thursday, November 18, 2004 11:30 AM To: [EMAIL PROTECTED] Subject: [R] hashing using named lists hi all, I am trying to use named list to hash a bunch of vector by name, for instance: test = list() test$name = c(1,2,3) the problem is that when i try to get the values back by using the name, the matching isn't done in an exact way, so test$na is not NULL. is there a way around this? Why by default all.equal.list doesnt require an exact match? How can I do hashing in R? thanks. ulas. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] SJava
Seem pretty straightforward to me: either gpp is not a C++ compiler or it does not work (possibly because LD_LIBRARY_PATH does not contain its run-time libraries). On Thu, 18 Nov 2004, Yasser El-Zein wrote: I failed to build SJava dure to teh error below. Any ideas? # R CMD INSTALL -c SJava_0.68-0.tar.gz * Installing *source* package 'SJava' ... checking for java... /opt/j2sdk1.4.2_06//bin/java Java VM /opt/j2sdk1.4.2_06//bin/java checking for javah... /opt/j2sdk1.4.2_06//bin/javah Looking in /opt/j2sdk1.4.2_06/include Looking in /opt/j2sdk1.4.2_06/include/linux checking for g++... no checking for c++... no checking for gpp... gpp checking for C++ compiler default output... b.out checking whether the C++ compiler works... configure: error: cannot run C++ compiled programs. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] SJava
Thank you Prof Ripley for your guidance. I re-installed gpp and SJava installed correctly. I am now running into this problem: When I load the SJava library I get: library(SJava) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library /usr/local/lib/R/site-library/SJava/libs/SJava.so: libRSNativeJava.so: cannot open shared object file: No such file or directory Error in library(SJava) : .First.lib failed for 'SJava' The file does exit: $ ls -la /usr/local/lib/R/site-library/SJava/libs/SJava.so -rwxr-xr-x 1 root staff 283388 Nov 18 13:27 /usr/local/lib/R/site-library/SJava/libs/SJava.so I then ran: $ R CMD ldd /usr/local/lib/R/site-library/SJava/libs/SJava.so libRSNativeJava.so = not found libjvm.so = not found libR.so = /usr/lib/R/lib/libR.so (0x40014000) libc.so.6 = /lib/tls/libc.so.6 (0x401df000) libblas.so.3 = /usr/lib/atlas/libblas.so.3 (0x4031a000) libg2c.so.0 = /usr/lib/libg2c.so.0 (0x40663000) libm.so.6 = /lib/tls/libm.so.6 (0x40681000) libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x406a5000) libpcre.so.3 = /usr/lib/libpcre.so.3 (0x406ae000) libbz2.so.1.0 = /usr/lib/libbz2.so.1.0 (0x406be000) libz.so.1 = /usr/lib/libz.so.1 (0x406ce000) libreadline.so.4 = /lib/libreadline.so.4 (0x406df000) libdl.so.2 = /lib/tls/libdl.so.2 (0x4070b000) libncurses.so.5 = /lib/libncurses.so.5 (0x4070f000) /lib/ld-linux.so.2 = /lib/ld-linux.so.2 (0x8000) libjvm.so does exist in 4 locations in my intel box running debian: /opt/splus/java/jre/lib/i386/client/libjvm.so /opt/splus/java/jre/lib/i386/server/libjvm.so /opt/j2sdk1.4.2_06/jre/lib/i386/server/libjvm.so /opt/j2sdk1.4.2_06/jre/lib/i386/client/libjvm.so I have JAVA_HOME defined as: $ echo $JAVA_HOME /opt/j2sdk1.4.2_06/ Your further help is greatly appreciated. On Thu, 18 Nov 2004 19:27:53 + (GMT), Prof Brian Ripley [EMAIL PROTECTED] wrote: Seem pretty straightforward to me: either gpp is not a C++ compiler or it does not work (possibly because LD_LIBRARY_PATH does not contain its run-time libraries). On Thu, 18 Nov 2004, Yasser El-Zein wrote: I failed to build SJava dure to teh error below. Any ideas? # R CMD INSTALL -c SJava_0.68-0.tar.gz * Installing *source* package 'SJava' ... checking for java... /opt/j2sdk1.4.2_06//bin/java Java VM /opt/j2sdk1.4.2_06//bin/java checking for javah... /opt/j2sdk1.4.2_06//bin/javah Looking in /opt/j2sdk1.4.2_06/include Looking in /opt/j2sdk1.4.2_06/include/linux checking for g++... no checking for c++... no checking for gpp... gpp checking for C++ compiler default output... b.out checking whether the C++ compiler works... configure: error: cannot run C++ compiled programs. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] The hidden costs of GPL software?
From: David Forrest On Wed, 17 Nov 2004, Mike Prager wrote: ... Using CLI software, an infrequent user has trouble remembering the known functions needed and trouble finding new ones (especially as that user gets older). What might help is an added help facility more oriented towards tasks, rather than structured around functions or packages. ... Another good (non-GUI) tool for the CLI is keyword completion. R in ESS does this, giving you lists of possible functions, variables and objects, or feedback if there isn't any. R's CLI completes, but only with filenames in the current directory. That works only if R was compiled with readline. Thus it doesn't work that way on Windows, for example. Completion still works on Windows under ESS though. Andy Dave -- Dave Forrest [EMAIL PROTECTED](804)684-7900w [EMAIL PROTECTED] (804)642-0662h http://maplepark.com/~drf5n/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Advanced R programming course in North Carolina (RTP area) ?
Anyone knows of an upcomming Advanced R programming course in NC? Would like to take this class before my project ends in December. Thanks, Paul __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] SJava
You need to ensure that libRSNativeJava.so is in your LD_LIBRARY_PATH: last time I looked SJava came with scripts to achieve this, and I suspect you need to read the documentation about them. As a further note, these are programming questions about a non-R product, and R-help is _really not_ the appropriate forum. Do please consult the posting guide. On Thu, 18 Nov 2004, Yasser El-Zein wrote: Thank you Prof Ripley for your guidance. I re-installed gpp and SJava installed correctly. I am now running into this problem: When I load the SJava library I get: library(SJava) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library /usr/local/lib/R/site-library/SJava/libs/SJava.so: libRSNativeJava.so: cannot open shared object file: No such file or directory Error in library(SJava) : .First.lib failed for 'SJava' The file does exit: $ ls -la /usr/local/lib/R/site-library/SJava/libs/SJava.so -rwxr-xr-x 1 root staff 283388 Nov 18 13:27 /usr/local/lib/R/site-library/SJava/libs/SJava.so I then ran: $ R CMD ldd /usr/local/lib/R/site-library/SJava/libs/SJava.so libRSNativeJava.so = not found libjvm.so = not found libR.so = /usr/lib/R/lib/libR.so (0x40014000) libc.so.6 = /lib/tls/libc.so.6 (0x401df000) libblas.so.3 = /usr/lib/atlas/libblas.so.3 (0x4031a000) libg2c.so.0 = /usr/lib/libg2c.so.0 (0x40663000) libm.so.6 = /lib/tls/libm.so.6 (0x40681000) libgcc_s.so.1 = /lib/libgcc_s.so.1 (0x406a5000) libpcre.so.3 = /usr/lib/libpcre.so.3 (0x406ae000) libbz2.so.1.0 = /usr/lib/libbz2.so.1.0 (0x406be000) libz.so.1 = /usr/lib/libz.so.1 (0x406ce000) libreadline.so.4 = /lib/libreadline.so.4 (0x406df000) libdl.so.2 = /lib/tls/libdl.so.2 (0x4070b000) libncurses.so.5 = /lib/libncurses.so.5 (0x4070f000) /lib/ld-linux.so.2 = /lib/ld-linux.so.2 (0x8000) libjvm.so does exist in 4 locations in my intel box running debian: /opt/splus/java/jre/lib/i386/client/libjvm.so /opt/splus/java/jre/lib/i386/server/libjvm.so /opt/j2sdk1.4.2_06/jre/lib/i386/server/libjvm.so /opt/j2sdk1.4.2_06/jre/lib/i386/client/libjvm.so I have JAVA_HOME defined as: $ echo $JAVA_HOME /opt/j2sdk1.4.2_06/ Your further help is greatly appreciated. On Thu, 18 Nov 2004 19:27:53 + (GMT), Prof Brian Ripley [EMAIL PROTECTED] wrote: Seem pretty straightforward to me: either gpp is not a C++ compiler or it does not work (possibly because LD_LIBRARY_PATH does not contain its run-time libraries). On Thu, 18 Nov 2004, Yasser El-Zein wrote: I failed to build SJava dure to teh error below. Any ideas? # R CMD INSTALL -c SJava_0.68-0.tar.gz * Installing *source* package 'SJava' ... checking for java... /opt/j2sdk1.4.2_06//bin/java Java VM /opt/j2sdk1.4.2_06//bin/java checking for javah... /opt/j2sdk1.4.2_06//bin/javah Looking in /opt/j2sdk1.4.2_06/include Looking in /opt/j2sdk1.4.2_06/include/linux checking for g++... no checking for c++... no checking for gpp... gpp checking for C++ compiler default output... b.out checking whether the C++ compiler works... configure: error: cannot run C++ compiled programs. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Off Topic: GSL installation for Windows
Hi R People! Has anyone installed the Gnu Scientific Library on a Windows system, please? I'm having a dreadful time with that. Any advance would be much appreciated. Sincerely, Laura Holt mailto: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Enormous Datasets
Dear List, I have some projects where I use enormous datasets. For instance, the 5% PUMS microdata from the Census Bureau. After deleting cases I may have a dataset with 7 million+ rows and 50+ columns. Will R handle a datafile of this size? If so, how? Thank you in advance, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re[2]: [R] Where has the Debian respository gone?
Hello Dirk, Thursday, November 18, 2004, 3:18:40 PM, you wrote: DE On Thu, Nov 18, 2004 at 08:52:38AM +, stats wrote: I'm a bit puzzled. I had deb http://cran.r-project.org/bin/linux/debian woody main in /etc/apt/sources.list and had hoped, perhaps rather unwisely, that this would look after the transition from 1.8.0 on my internet server (Debian stable) where it serves up some cgi-bin work. (Most of my R work is on a Win2k machine, much though I'd like to go Debian all the way, that isn't possible for my main job in near future.) Is there an easy way of upgrading R on a Debian stable machine? I don't want to move off stable as the security side of that server is too important. I also don't really want to compile it myself if I can avoid that, the server is pretty old iron and that might back up all the Email stuff it does. Advice anyone? DE More than advice, we need a volunteer to backport the current R package(s) DE for Debian to the Debian stable distribution. As I said, testing and DE unstable are taken care of (and yes, testing is still lagging because of the DE now much more formal interdependence of packages; R 2.0.* will appears once DE all dependent packages are available on all architectures) I'm sure this is in itself proof that I'm not the person to do it but can you say a bit more about what's involved Dirk? I run a pretty low powered Debian stable server on i386 hardware (an athlon if I remember rightly) with pretty much the standard packages, GCC, perl etc. and I'm not completely stupid. However, debugging compiler and make complaints is really not my area of competence and I do wonder about the likely load on the machine and on my time. In the not too distant future this machine should be replaced with a much more powerful one and a somewhat more powerful backup machine so hardware may not be a long term problem. Any chance I can be useful? Could I team up with someone who really knows what s/he is doing but doesn't use Debian stable and work this together? Let me know, I'd love to put something very direct back into the R project. Chris __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to calculate the stratified means in a data frame?
Dear R people, I have a simple question to ask. Suppose I have a data.frame with two variables: one factor (x) and one numeric (y), I want to calculate the mean of y for each value of x. Although it's easy to do it within a for a loop, I believe there may be a concise way by using some kinds of apply functions. Could anyone tell me how to do that? Thank you. Frank __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Time series plot orientation
Hello, I am trying to rotate by 90 degrees a time series plot. So I need the time axis to be the vertical one. Is there an easy way? I couldn't guess anything from the help pages. Apologies for a silly question. Regards, Costas -- = This e-mail contains information intended for the addressee only. It may be confidential and may be the subject of legal and/or professional Privilege. Any dissemination, distribution, copyright or use of this communication without prior permission of the addressee is strictly prohibited. - Dr. Costas Vorlow | Tel: +44 (0)191 33 45727 Durham Business School | Fax: +44 (0)191 33 45201 Room(324), University of Durham | email: K.E.Vorloou(at)durham.ac.uk Mill Hill Lane, | or : costas(at)vorlow.org Durham DH1 3LB, UK. | http://www.vorlow.org - Fingerprint: B010 577A 9EC3 9185 08AE 8F22 1A48 B4E7 9FA6 C31A __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Off Topic: GSL installation for Windows
See the ReadMe (which should be the first place to look) at http://cran.r-project.org/bin/windows/contrib/2.0/@ReadMe It's easy once you have gsl-1.5 built (the gnuwin32 project's version is too old), but getting gsl-1.5 built is not straightforward. On Thu, 18 Nov 2004, Laura Holt wrote: Has anyone installed the Gnu Scientific Library on a Windows system, please? I'm having a dreadful time with that. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to calculate the stratified means in a data frame?
On Thu, 18 Nov 2004, Frank Duan wrote: I have a simple question to ask. Suppose I have a data.frame with two variables: one factor (x) and one numeric (y), I want to calculate the mean of y for each value of x. Although it's easy to do it within a for a loop, I believe there may be a concise way by using some kinds of apply functions. Could anyone tell me how to do that? Thank you. tapply(y, x, mean) # which _is_ in `An Introduction to R', BTW ?by ?aggregate for more sophisticated packaging of such ideas. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Enormous Datasets
Thomas W Volscho [EMAIL PROTECTED] writes: Dear List, I have some projects where I use enormous datasets. For instance, the 5% PUMS microdata from the Census Bureau. After deleting cases I may have a dataset with 7 million+ rows and 50+ columns. Will R handle a datafile of this size? If so, how? With a big machine... If that is numeric, non-integer data, you are looking at something like 7e6*50*8 [1] 2.8e+09 i.e. roughly 3 GB of data for one copy of the data set. You easily find yourself with multiple copies, so I suppose a machine with 16GB RAM would cut it. These days that basically suggests x86_64 architecture running Linux (e.g. multiprocessor Opterons), but there are also 64 bit Unix big iron solutions (Sun, IBM, HP,...). If you can avoid dealing with the whole dataset at once, smaller machines might get you there. Notice that 1 column is only 56MB, and you may be able to work with aggregated data from some step onwards. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Enormous Datasets
Very unlikely R will be able to handle this. The problems are: * the data set may simply not fit into the memory * it will take forever to read from the ASCII file * any meaningful analysis of a dataset in R typically require 5 - 10 times more memory than the size of the dataset (unless you are a real insider and know all the knobs) Your best strategy is probably to partition the file in meaningful sub-categories and work with them. To save time on conversion from ASCII you can read the sub-files into a data frame and then save the data frame in .rda file using save(). Subsequent loading .rda files is much faster than reading ASCII Another strategy which is often advocated on the list is to put the data into a data base and draw random samples of manageable size from the database. I have no experience with this approach HTH, Vadim -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Thomas W Volscho Sent: Thursday, November 18, 2004 12:11 PM To: [EMAIL PROTECTED] Subject: [R] Enormous Datasets Dear List, I have some projects where I use enormous datasets. For instance, the 5% PUMS microdata from the Census Bureau. After deleting cases I may have a dataset with 7 million+ rows and 50+ columns. Will R handle a datafile of this size? If so, how? Thank you in advance, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to calculate the stratified means in a data frame?
Frank Duan [EMAIL PROTECTED] writes: Dear R people, I have a simple question to ask. Suppose I have a data.frame with two variables: one factor (x) and one numeric (y), I want to calculate the mean of y for each value of x. Although it's easy to do it within a for a loop, I believe there may be a concise way by using some kinds of apply functions. Could anyone tell me how to do that? Thank you. tapply() will do that. (help(tapply), look at the presidents example). -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to calculate the stratified means in a data frame?
Got it. Many thanks. On Thu, 18 Nov 2004 13:10:53 -0800, Jeff Laake [EMAIL PROTECTED] wrote: look at by Frank Duan wrote: Dear R people, I have a simple question to ask. Suppose I have a data.frame with two variables: one factor (x) and one numeric (y), I want to calculate the mean of y for each value of x. Although it's easy to do it within a for a loop, I believe there may be a concise way by using some kinds of apply functions. Could anyone tell me how to do that? Thank you. Frank __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to calculate the stratified means in a data frame?
On Thu, 2004-11-18 at 15:34 -0500, Frank Duan wrote: Dear R people, I have a simple question to ask. Suppose I have a data.frame with two variables: one factor (x) and one numeric (y), I want to calculate the mean of y for each value of x. Although it's easy to do it within a for a loop, I believe there may be a concise way by using some kinds of apply functions. Could anyone tell me how to do that? Thank you. Frank One way is to use by(). Using the 'iris' dataset to get the means for Sepal.Length by Species: with(iris, by(Sepal.Length, Species, mean)) INDICES: setosa [1] 5.006 -- INDICES: versicolor [1] 5.936 -- INDICES: virginica [1] 6.588 See ?by, also ?tapply and ?aggregate. Note also the use of with() as a wrapper, in lieu of attach() here. HTH, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] How to calculate the stratified means in a data frame?
See ?tapply or ?by. Andy From: Frank Duan Dear R people, I have a simple question to ask. Suppose I have a data.frame with two variables: one factor (x) and one numeric (y), I want to calculate the mean of y for each value of x. Although it's easy to do it within a for a loop, I believe there may be a concise way by using some kinds of apply functions. Could anyone tell me how to do that? Thank you. Frank __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] adjusting the map of France to 1830
I'm doing some analyses of historical data from France in 1830 on 'moral
statistics' that I'd like to
show on a map. I've done most of my analyses in SAS, but a few things
would work better in R.
To do this, I have to adjust the modern map,
library(maps)
map('france')
to adjust for changes in departments (86 in 1830, to 97 now). I've read
the documentation
for the maps and maptools package, but there seems to be no functions to
allow this, and
I can't find information on the exact structure of map datasets, but I
understand them to
be delimited lists of polygon coordinates.
In SAS, all maps have (one or more) ID variables representing the
geographical region,
and there is also a proc gremove that can remove internal boundaries
inside the polygons
for regions with the same ID. Is there some way I can do this in R?
Here's what I did in SAS:
*-- Fix the map of France to conform to Guerry:
- adjust the 97 current departments to correspond to the 86 in 1830
- delete those not part of France then
;
data gfrtemp;
set maps.france;
/* Corse was one dept - merge these to one area, new ID */
if id in (201, 202)then dept=200;
/* Seine et Oise (78) was cut into
Essonne (91), Val d'Oise (95) and Yvelines (78) */
else if id in (91, 95)then dept=78;
/* Seine (75) now split into
Hauts-de-Seine (92), Seine-Saint-Denis (93) et Val-de-Marne (94)*/
else if id in (92, 93, 94)then dept=75;
/* departments not part of France in 1830 */
else if id in (
6, /* Alpes-Maritimes */
73,74, /* Savoie, Haute-Savoie */
90)/* Territore-de-Belfort */
then delete;
else dept=id;
run;
*-- remove internal boundaries based on merged DEPT;
proc sort data=gfrtemp;
by dept;
proc gremove data=gfrtemp out=gfrance;
by dept;
id id;
run;
--
Michael Friendly Email: [EMAIL PROTECTED]
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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RE: [R] Enormous Datasets
It depends on what you want to do with that data in R. If you want to play with the whole data, just storing it in R will require more than 2.6GB of memory (assuming all data are numeric and are stored as doubles): 7e6 * 50 * 8 / 1024^2 [1] 2670.288 That's not impossible, but you'll need to be on a computer with quite a bit more memory than that, and running on an OS that supports it. If that's not feasible, you need to re-think what you want to do with that data in R (e.g., read in and process a small chunk at a time, or read in a random sample, etc.). Andy From: Thomas W Volscho Dear List, I have some projects where I use enormous datasets. For instance, the 5% PUMS microdata from the Census Bureau. After deleting cases I may have a dataset with 7 million+ rows and 50+ columns. Will R handle a datafile of this size? If so, how? Thank you in advance, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: R package installation
Dear Prof. Johnson, sorry for posting the reply so late. I am already using FINK. But you were right, R was looking for g77 and the gcc libraries under the MacOs distributions. Rather than creating symbolic links I updated FLIBS in /Library/Frameworks/R.framework/Resources/etc/Makeconf so that it searches in the right path /sw/lib/gcc/powerpc-apple-darwin7.2.0/ For g77 I made instead the link you suggest under /usr/bin/. I removed and reinstalled the package and everything run fine, in spite of my versions of libraries and compilers (g77 was already up-date from FINK). Thank you all for the help, Marco Dear Marco, I was given an excerpt with your problem about installing package on a MAC, such as Hmisc. I had the same problems and found a work around. I have not had any trouble loading in source packages since, include Hmisc and Design, acepack and vgam. First, I downloaded and installed the g77 compiler. I use a progam named FINK to find, download and intall g77 (so first I installed FINK then from within FINK I downloaded/installed the g77 compiler.) Do a Google search for FINK, it is easy to find and install. After g77 was installed I had to make a symbolic link so R could find it: ln -s \sw\bin\g77 \usr\bin\g77 (I think I had to make a link to my gcc compiler also) \n -s \sw\bin\gcc \usr\bin\g77 It looks like you already have the g77 compiler from the message. the next mesage you can also remedy by symbolic links. Try ln -s /sw/lib/gcc /usr/local/lib/gcc ln -s /sw/lib/gcc/powerpc-apple-darwin7.5.0 \usr\local\lib\gcc\powerpc-apple-darwin6.8 ln -s /sw/lib/gcc/powerpc-apple-darwin7.5.0/3.4.1 \usr\local\lib\gcc\powerpc-apple-darwin6.8\3.4.2 The first directory path in each of the above may be specific to your configuration for gcc. But this did work for me, and if you find the correct location for gcc/ powerpc-apple-darwinX.Y.Z/U.V.W, you should have no trouble either. Good luck. Sincerely Tim Johnson Adjunct Asst. Professor University of Michigan --- Marco Chiarandini, Fachgebiet Intellektik, Fachbereich Informatik, Technische Universität Darmstadt, Hochschulstraße 10, D-64289 Darmstadt - Germany, Office: S2/02 Raum E317 Tel: +49.(0)6151.166802 Fax: +49.(0)6151.165326 email: [EMAIL PROTECTED] web page: http://www.intellektik.informatik.tu-darmstadt.de/~machud __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] The hidden costs of GPL software?
The author of the article says nothing about the large number of hours and weeks that he surely spent learning S-plus! There should be attention to the costs that arise from a wrong or inappropriate analysis, perhaps because the software that is in use makes it difficult to do anything better, perhaps because of statistical skill limitations, often with these two factors working together. Analyses that misrepresent the science, or designs and analyses that conspire together to this end, have serious and costly implications for research. I've refereed several papers recently, in broadly ecological fields of endeavour, with seemingly quite reasonable data, where the mix of author skill and abilities of the package was clearly not up to the task in hand. Relative to getting on top of the statistical issues (for which they will probably end up getting, as they need to, statistical help), the GUI/noGUI issue will be a minor consideration, and hours or weeks spent learning R will be at most a modest consideration. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Bioinformation Science, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. On 17 Nov 2004, at 10:27 PM, [EMAIL PROTECTED] wrote: From: Philippe Grosjean [EMAIL PROTECTED] Date: 17 November 2004 8:53:28 PM To: [EMAIL PROTECTED], [EMAIL PROTECTED] Cc: Subject: Hello, In the latest 'Scientific Computing World' magazine (issue 78, p. 22), there is a review on free statistical software by Felix Grant (doesn't have to pay good money to obtain good statistics software). As far as I know, this is the first time that R is even mentioned in this magazine, given that it usually discuss commercial products. In this article, the analysis of R is interesting. It is admitted that R is a great software with lots of potentials, but: All in all, R was a good lesson in the price that may have to be paid for free software: I spent many hours relearning some quite basic things taken for granted in the commercial package. Those basic things are releated with data import, obtention of basic plots, etc... with a claim for a missing more intuitive GUI in order to smooth a little bit the learning curve. There are several R GUI projects ongoing, but these are progressing very slowly. The main reason is, I believe, that a relatively low number of programmers working on R are interested by this field. Most people wanting such a GUI are basic user that do not (cannot) contribute... And if they eventually become more knowledgeable, they tend to have other interests. So, is this analysis correct: are there hidden costs for free software like R in the time required to learn it? At least currently, for the people I know (biologists, ecologists, oceanographers, ...), this is perfectly true. This is even an insurmountable barrier for many of them I know, and they have given up (they come back to Statistica, Systat, or S-PLUS using exclusively functions they can reach through menus/dialog boxes). Of course, the solution is to have a decent GUI for R, but this is a lot of work, and I wonder if the intrinsic mechanism of GPL is not working against such a development (leading to a very low pool of programmers actively involved in the elaboration of such a GUI, in comparison to the very large pool of competent developers working on R itself). Do not misunderstand me: I don't give up with my GUI project, I am just wondering if there is a general, ineluctable mechanism that leads to the current R / R GUI situation as it stands,... and consequently to a general rule that there are indeed most of the time hidden costs in free software, due to the larger time required to learn it. I am sure there are counter-examples, however, my feeling is that, for Linux, Apache, etc... the GUI (if there is one) is often a way back in comparison to the potentials in the software, leading to a steep learning curve in order to use all these features. I would be interested by your impressions and ideas on this topic. Best regards, Philippe Grosjean __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: Re: [R] 3d scatter plot with drop line
Very nice!
I noticed that you wrote the function to drop points to any surface.
Is it possible to add the surface to the plot as a translucent surface,
so the points and drop lines still show?
David L. Reiner
-Original Message-
From: Robin Hankin [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 18, 2004 3:39 AM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: Fwd: Re: [R] 3d scatter plot with drop line
Hi
try this:
p3dpairs - function(x,x1,
xlim=NULL,ylim=NULL,zlim=NULL,col=par(col), pch=par(pch),
cex=par(cex), ...){
if(is.matrix(x)){
z - x[,3]
y - x[,2]
x - x[,1]
}
if(is.matrix(x1)){
z1 - x1[,3]
y1 - x1[,2]
x1 - x1[,1]
}
if(missing(zlim)) {
z.grid - matrix(range(z),2,2)
} else {
z.grid - matrix(zlim,2,2)
}
if(missing(xlim)){ xlim - range(x) }
if(missing(ylim)){ ylim - range(y) }
persp(xlim, ylim, z.grid, col = NA, border=NA, ...) - res
trans3d - function(x,y,z, pmat) {
tr - cbind(x,y,z,1) %*% pmat
list(x = tr[,1]/tr[,4], y= tr[,2]/tr[,4])
}
out - trans3d(x,y,z,pm=res)
out1 - trans3d(x1,y1,z1,pm=res)
points(out, col=col, pch=pch, cex=cex, ...)
for(i in 1:length(out$x)){
lines(c(out$x[i],out1$x[i]),c(out$y[i],out1$y[i]), col=gray, ...)
}
return(invisible(out))
}
then
a - matrix(rnorm(60),20,3)
b - a
b[,3] - 0
p3dpairs(a,b)
gives you a good approximation to what you want
HTH
rksh
This is a follow up to my question from yesterday. I want to do in R
what is called a 3d scatter plot with drop lines in S-PLUS.
Basically, it's a 3dscatterplot with lines connecting the x-y grid to
the z points.
The lines give a better perspective on the shape of the data surface.
How to?
Joel Bremson
UC Davis Statistics
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tel +44(0)23-8059-7743
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[R] Memory problems...leaky?
Hi list folks,
I have been trying to figure out how I can run the script that I have
included below. I have 1.2 gigs of memory on the computer, but this is
not enough, given the size of the input datasets. The input matrix
('input') is a little under 2400 x 2900 cells, and is about 60 megs when
stored on hard drive...what is R doing, that this (small) size of file
takes up so much memory? The script uses three variables of this size,
but I don't see why that would add up to over 1.2 gigs...Is the way
that I call variables in the for-loops causing this problem, with some
sort of leakiness? I had heard of leaky memory problems with version
1.5.1, but I am using 1.9.1. Alternatively, I had wondered if it was
just the way memory works in R, as I had read a post earlier today that
suggested that R requires 5-10 times more memory than the input to
meaninfully calculate anything...
Thanks...Sam
bflow - 2
pie - 3.141592654
input - read.table (xxx.txt, sep=, header=FALSE, na.strings = -)
rowsize - dim(input)[1]
colsize - dim(input)[2]
result - matrix (NA, rowsize, colsize)
for (i in 1:rowsize)
for (j in 1:colsize)
if (is.na (input [i,j]) == FALSE) {
probability - matrix (NA, rowsize, colsize)
for (p in 1:rowsize) {
or (q in 1:colsize){
distance - sqrt ((p - i)^2 + (q - j)^2)
probability [p,q] - (2 / (bflow * pie * (1 + (distance /
bflow)^2)))
}
}
kernsum - sum ((probability * input / input), na =
TRUE)
intmean - sum (input * probability, na = TRUE) /
kernsum
result [i,j] - sum (((input - intmean)^2 * probability), na =
TRUE) / kernsum
}
}
}
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Re: [R] Where has the Debian respository gone?
Chris, On Thu, Nov 18, 2004 at 08:21:04PM +, Chris Evans wrote: DE More than advice, we need a volunteer to backport the current R package(s) DE for Debian to the Debian stable distribution. As I said, testing and DE unstable are taken care of (and yes, testing is still lagging because of the DE now much more formal interdependence of packages; R 2.0.* will appears once DE all dependent packages are available on all architectures) I'm sure this is in itself proof that I'm not the person to do it but can you say a bit more about what's involved Dirk? I run a pretty low [..] Any chance I can be useful? Could I team up with someone who really knows what s/he is doing but doesn't use Debian stable and work this together? Let me know, I'd love to put something very direct back into the R project. Thanks a bunch -- I'll follow up off-list! Dirk -- If your hair is standing up, then you are in extreme danger. -- http://www.usafa.af.mil/dfp/cockpit-phys/fp1ex3.htm __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] implementing a loop using by(x,x$factor,FUN)
Hi,
I'm writing some R code that requires a massive amount of looping and would
ideally like to write it so that it avoid the use of for loop ... however I'm
having some trouble.
Very briefly, the basic idea is to implement a binary partitioning algorithm to
determine the optimal cutpoint based on deviance measures obtained from
likelihood estiamtes. This is in the geo-spatial context so I'm actually using
the geoRglm package to obtain this likelihood fit. I initially use the variog
function to help specify the initial parameter values passed to likfit to
ensure convergence.
Although not the most elegant solution, the code works ... I just want to
re-code it to avoid using the for loop.
Any help would be greatly appreciated.
This is what I've got
RootDev - 600
splits - NULL
for (cutpoint in cutpoints) {
LRGdata - split(gdata, gdata[,4] = cutpoint)
vgrmL - variog(as.geodata(LRGdata$TRUE), covar.col=covcol))
vgrmR - variog(as.geodata(LRGdata$FALSE), covar.col=covcol))
mlL- likfit(as.geodata(LRGdata$TRUE),
ini=expand.grid(seq(0, max(vgrmL$v), l=10), seq(0,max(vgrmL$u), l=10)))
mlR- likfit(as.geodata(LRGdata$FALSE),
ini=expand.grid(seq(0, max(vgrmR$v), l=10), seq(0,max(vgrmR$u), l=10)))
LeftDev - summary(mlL)[[8]]$log.L
RightDev - summary(mlR)[[8]]$log.L
LeftN - dim(LRGdata$TRUE)[1]
RightN - dim(LRGdata$FALSE)[1]
splits - rbind(splits, c(paste(=,cutpoint),paste(,cutpoint),
LeftN, RightN, RootDev, LeftDev, RightDev,
-2*(RootDev-(LeftDev+RightDev
}
- Mohamed
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Re: [R] adjusting the map of France to 1830
Hello. I do not know if you can merge polygons, but you can select easily:
departements=map('france',namesonly=T) # returns a vector of names of
regions
map('france',regions=departements[1:20],namesonly=T) # use what you need
with regions argument
Hope this helps,
At 16:29 18/11/2004, Michael Friendly wrote:
I'm doing some analyses of historical data from France in 1830 on 'moral
statistics' that I'd like to
show on a map. I've done most of my analyses in SAS, but a few things
would work better in R.
To do this, I have to adjust the modern map,
library(maps)
map('france')
to adjust for changes in departments (86 in 1830, to 97 now). I've read
the documentation
for the maps and maptools package, but there seems to be no functions to
allow this, and
I can't find information on the exact structure of map datasets, but I
understand them to
be delimited lists of polygon coordinates.
In SAS, all maps have (one or more) ID variables representing the
geographical region,
and there is also a proc gremove that can remove internal boundaries
inside the polygons
for regions with the same ID. Is there some way I can do this in R?
Here's what I did in SAS:
*-- Fix the map of France to conform to Guerry:
- adjust the 97 current departments to correspond to the 86 in 1830
- delete those not part of France then
;
data gfrtemp;
set maps.france;
/* Corse was one dept - merge these to one area, new ID */
if id in (201, 202)then dept=200;
/* Seine et Oise (78) was cut into
Essonne (91), Val d'Oise (95) and Yvelines (78) */
else if id in (91, 95)then dept=78;
/* Seine (75) now split into
Hauts-de-Seine (92), Seine-Saint-Denis (93) et Val-de-Marne (94)*/
else if id in (92, 93, 94)then dept=75;
/* departments not part of France in 1830 */
else if id in (
6, /* Alpes-Maritimes */
73,74, /* Savoie, Haute-Savoie */
90)/* Territore-de-Belfort */
then delete;
else dept=id;
run;
*-- remove internal boundaries based on merged DEPT;
proc sort data=gfrtemp;
by dept;
proc gremove data=gfrtemp out=gfrance;
by dept;
id id;
run;
--
Michael Friendly Email: [EMAIL PROTECTED] Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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Université de Montréal, C.P. 6128, succursale centre-ville
Montréal, Québec H3C 3J7, Canada
Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293
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Re: [R] adjusting the map of France to 1830
At 16:29 18/11/2004, Michael Friendly wrote:
I'm doing some analyses of historical data from France in 1830 on 'moral
statistics' that I'd like to
show on a map. I've done most of my analyses in SAS, but a few things
would work better in R.
To do this, I have to adjust the modern map,
library(maps)
map('france')
to adjust for changes in departments (86 in 1830, to 97 now). I've read
the documentation
for the maps and maptools package, but there seems to be no functions to
allow this, and
I can't find information on the exact structure of map datasets, but I
understand them to
be delimited lists of polygon coordinates.
In SAS, all maps have (one or more) ID variables representing the
geographical region,
and there is also a proc gremove that can remove internal boundaries
inside the polygons
for regions with the same ID. Is there some way I can do this in R?
Unfortunately not with the current implementation of several of the
'extra' databases in the mapdata package. The map() function does have
the interior=FALSE option, which would normally do what you want, but
only when the data has been manipulated to allow it. Currently this
option is only useful with the world and usa maps (and their
derivatives, such as world2 and state).
Currently every department is a complete polygon, and so every interior
line segment occurs twice in the data. What has to happen to the data
is for it to be split up into non-overlapping line segments, and each
polygon reconstructed from a list of these line segments (with
direction being important).
If you are prepared to perform this somewhat tedious process, I am
happy to assist you with further details.
However even with the interior= option functioning, it would still not
be easy to produce the map you would require, since you would have to
build it up from many components (namely each of the 'combined'
departments, plus 'all the rest').
HTH,
Ray Brownrigg
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[R] Date time Differences
Greetings from an R newbie Table imported with 4 columns containing Dates and Times, I desire to determine the differences between said columns Have loaded the base and chron packages for R commander. Have tried to use format but without success. Have tried the Postix commands but error states unused argument (s) (...), even though some of the examples do not use (...) at the end of the command Example: Table is named GvY1 Operation.Time.End Operation.Time.Dictated Operation.Time.Verfiy 7/10/2004 10:10:12 7/12/2004 9:18:03 7/28/2004 05:00:02 Information is mm/dd/year hh:mm:ss (time of day, e.g. the first column is July 10th 2004 10:10 AM at 12 seconds) What is the best way to get the difference between any of the 2 columns? And eventually test statistics on the columns (eg. P values, if needed, but not a priority at this time) Thanks in advance Platform WinXP IBM T40p R v 1.8.1 R commander -- Mark R Laflamme,MD Regenstrief Institute 1050 Wishard Blvd RG5 Indianapolis, IN 46202 317 630-7833 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Date Time differences
Greetings from an R newbie Table imported with 4 columns containing Dates and Times, I desire to determine the differences between said columns Have loaded the base and chron packages for R commander. Have tried to use format but without success. Have tried the Postix commands but error states unused argument (s) (...), even though some of the examples do not use (...) at the end of the command Example: Table is named GvY1 Operation.Time.End Operation.Time.Dictated Operation.Time.Verfiy 7/10/2004 10:10:12 7/12/2004 9:18:03 7/28/2004 05:00:02 Information is mm/dd/year hh:mm:ss (time of day, e.g. the first column is July 10th 2004 10:10 AM at 12 seconds) What is the best way to get the difference between any of the 2 columns? And eventually test statistics on the columns (eg. P values, if needed, but not a priority at this time) Thanks in advance Platform WinXP IBM T40p R v 1.8.1 R commander -- Mark R Laflamme,MD Regenstrief Institute 1050 Wishard Blvd RG5 Indianapolis, IN 46202 317 630-7833 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] adjusting the map of France to 1830
At 19:07 18/11/2004, Ray Brownrigg wrote:
At 16:29 18/11/2004, Michael Friendly wrote:
I'm doing some analyses of historical data from France in 1830 on 'moral
statistics' that I'd like to
show on a map. I've done most of my analyses in SAS, but a few things
would work better in R.
To do this, I have to adjust the modern map,
library(maps)
map('france')
to adjust for changes in departments (86 in 1830, to 97 now). I've read
the documentation
for the maps and maptools package, but there seems to be no functions to
allow this, and
I can't find information on the exact structure of map datasets, but I
understand them to
be delimited lists of polygon coordinates.
In SAS, all maps have (one or more) ID variables representing the
geographical region,
and there is also a proc gremove that can remove internal boundaries
inside the polygons
for regions with the same ID. Is there some way I can do this in R?
Unfortunately not with the current implementation of several of the
'extra' databases in the mapdata package. The map() function does have
the interior=FALSE option, which would normally do what you want, but
only when the data has been manipulated to allow it. Currently this
option is only useful with the world and usa maps (and their
derivatives, such as world2 and state).
Currently every department is a complete polygon, and so every interior
line segment occurs twice in the data. What has to happen to the data
is for it to be split up into non-overlapping line segments, and each
polygon reconstructed from a list of these line segments (with
direction being important).
There is the gpclib package which computes intersection, union... of
polygons. I have try to play with its union function and the france data,
but the results are good but a little bit complicate:
# i merge the two firts polygons:
departements=map('france')
which(is.na(departements$x))[1:2]
[1] 66 122
gpcA - as(cbind(departements$x[1:65],departements$y[1:65]),gpc.poly)
gpcB - as(cbind(departements$x[67:121],departements$y[67:121]),gpc.poly)
union(gpcA,gpcB)
GPC Polygon
Num. Contours: 1
Num. Vertices: 74
BBox (X): 1.563161 -- 4.225965
BBox (Y): 49.97212 -- 51.09752
gpcAB-union(gpcA,gpcB)
departements$x=c(attr(gpcAB,pts)[[1]]$x,attr(gpcAB,pts)[[1]]$x[1],departements$x[-(1:121)])
departements$y=c(attr(gpcAB,pts)[[1]]$y,,attr(gpcAB,pts)[[1]]$y[1],departements$y[-(1:121)])
map(departements)
Another solution is to do the job in a GIS and to import the new map with
maptools.
The package gpclib is very intersting and I think that it can be used to
develop some basic GIS tools. I have write a functions to compute
intersections for objects of class polys easily.
The only thing is to know for which class of spatial objects these
functions must be developed !
Stéphane DRAY
--
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Université de Montréal, C.P. 6128, succursale centre-ville
Montréal, Québec H3C 3J7, Canada
Tel : (514) 343-6111 poste 1233 Fax : (514) 343-2293
E-mail : [EMAIL PROTECTED]
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[R] Creating logical value from the difference of two absolute values
Hi, Using R 2.0.1 on Mac g5 running Mac OS X 10.3.6. I would expect that abs(.7 - .5) = abs(.3 - .5) should be returned TRUE. Instead www - abs(.7 - .5) = abs(.3 - .5) www [1] FALSE Is this a result of floating point or the implementation of abs or something else? In a function I need to compare two absolute values - each being of the form |variable - constant|. Any suggestions for implementing this correctly? Nathan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Creating logical value from the difference of two absolut e values
It's imprecision of floating point representation of real numbers: print(abs(.7 - .5) - abs(.3 - .5), digit=20) [1] -5.551115123125783e-17 one of the first things to learn about programming: be extremely careful testing for equality of floating point numbers. Andy From: Nathan Leon Pace, MD, MStat Hi, Using R 2.0.1 on Mac g5 running Mac OS X 10.3.6. I would expect that abs(.7 - .5) = abs(.3 - .5) should be returned TRUE. Instead www - abs(.7 - .5) = abs(.3 - .5) www [1] FALSE Is this a result of floating point or the implementation of abs or something else? In a function I need to compare two absolute values - each being of the form |variable - constant|. Any suggestions for implementing this correctly? Nathan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] how to get to interesting part of pattern match
Hi, I am looking for a way to extract an interesting part of the match to a regular expression. For example the pattern [./](*.) matches a substring that begins with either . or / followed by anything. I am interested in this anything w/o the . or / prefix. If say I match the pattern against abc/foo I want to get foo, not /foo. In Perl one can simply wrap the interesting part in () and get it out of the match. Is it possible to do a similar thing in R? There seems to be a way to refer to the match, see below, but I couldn't figure out how to make gsub return it. gsub([./](*.), \\1, abc/foo) [1] abcfoo Thanks, Vadim __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] NLME plottting and Confidence Intervals
All, I have been learning about mixed models and have been able to successfully use lme( ) and nlme( ) to fit some simple linear and 4PL logistic models. As a relative newbie I am at a loss as to how I can do the following: (1) Import a SAS dataset with DATE9. formatted time values and get them converted into a convenient time variable for use with the nlme package. In particular, I would like to use the lattice package to produce panel plots for diagnostic and exploratory purposes. (2) Plot the fitted model(s) along with appropriate 95% confidence bounds for the model (3) Obtain prediction intervals for given individuals in the datasets. Sorry for what must be trivial questions! I very much appreciate any insight. Thanks, Greg __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to get to interesting part of pattern match
sub(.*/, , abc/foo) [1] foo Jean On Thu, 18 Nov 2004, Vadim Ogranovich wrote: Hi, I am looking for a way to extract an interesting part of the match to a regular expression. For example the pattern [./](*.) matches a substring that begins with either . or / followed by anything. I am interested in this anything w/o the . or / prefix. If say I match the pattern against abc/foo I want to get foo, not /foo. In Perl one can simply wrap the interesting part in () and get it out of the match. Is it possible to do a similar thing in R? There seems to be a way to refer to the match, see below, but I couldn't figure out how to make gsub return it. gsub([./](*.), \\1, abc/foo) [1] abcfoo Thanks, Vadim __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] The hidden costs of GPL software?
Dear list members, This has been a stimulating discussion, now spread over three lists. Although I'd like to address issues that have been raised on all three lists, I expect that more or less everyone reads r-help, so I'm just posting these comments there. (1) As everyone else, I've had experience with a number of other statistical packages and programming environments in addition to R (including, more years ago than I care to say, the mainframe predecessor of the MicrOsiris package mentioned positively in the SCW article cited by Philippe in his original message). I don't believe that extensive point-and-click GUIs for broad statistical packages/programming environments such as Stata, R, S-PLUS, or SAS are very helpful: They tend to be labyrinths that are difficult to navigate. Some of the suggestions for other kinds of GUIs (e.g., aids to command specification) seem to me more promising. Moreover, I don't think that one should expect to learn an extensive system such as R or SAS without doing some reading. My own experience is that S (i.e., encompassing R and S-PLUS) is easier, not harder, to learn than its true competitors. (2) On the other hand, one can build quite nice graphical interfaces to more limited packages. A couple of examples that I particularly like are SAS JMP and Cook's and Weisberg's Arc (built on Lisp-Stat). (3) Similarly, my Rcmdr package was meant to be a limited-purpose GUI, useful for basic-statistics classes. Its range has grown somewhat to cover linear and generalized-linear models, and I plan a few more modest extensions (including the ability to incorporate other classes of statistical models more easily). As a technical matter, I don't think that it would be hard (although it would be time-consuming) to produce a much broader extension, but the result (in my opinion) would be as dubiously useful as the GUIs for SAS or S-PLUS. By the way, if there were something I could wish for here it would be a slightly broader set of Tk widgets to be included with the Tcl/Tk that installs with R for Windows, since using widgets outside of this set creates installation obstacles for lower-level users. (4) Several people have pointed once more to the difficulty that novice users experience in locating functions to perform particular tasks or in figuring out how to use them once found. I suspect that even people who have been using R for a while occasionally have a brain-cramp that leads to a search through documentation. I know that I do. In my experience, the various facilities for searching documentation in R work pretty well. (5) I think that examples in help files and vignettes can be useful, but are not substitutes for text-books, manuals, and journal articles. It certainly should not be the job of statistical software to teach the statistics, although of course it can be used to help do that. I doubt that many list members would look favourably on the statistical-methods decision tree in MicrOsiris, for example. One solution is to include PDF manuals with packages. I've done this, for example, with my effects and Rcmdr packages. The introductory manual supplied with Thomas Lumley's survey package is another, similar example. Maybe there's a better way of integrating such non-vignette manuals with the help system -- something like help(manual=package). (6) As has been pointed out, e.g., by Duncan Murdoch, solving the function-locating problem is best done by a method or methods that automatically accommodate the growing and changing set of contributed packages on CRAN. Why not, as previously has been proposed, replace the current static (and, in my view, not very useful) set of keywords in R documentation with the requirement that package authors supply their own keywords for each documented object? I believe that this is the intent of the concept entries in Rd files, but their use certainly is not required or even actively encouraged. (They're just mentioned in passing in the Writing R Extensions manual.) John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to get to interesting part of pattern match
Vadim Ogranovich vograno at evafunds.com writes: : I am looking for a way to extract an interesting part of the match to : a regular expression. For example the pattern [./](*.) matches a : substring that begins with either . or / followed by anything. I am : interested in this anything w/o the . or / prefix. If say I match : the pattern against abc/foo I want to get foo, not /foo. In Perl : one can simply wrap the interesting part in () and get it out of the : match. Is it possible to do a similar thing in R? : : There seems to be a way to refer to the match, see below, but I couldn't : figure out how to make gsub return it. : gsub([./](*.), \\1, abc/foo) : [1] abcfoo Assuming what was meant is the following (dot and star are transposed and gsub is sub): sub([./](.*), \\1, abc/foo) then the regular expression matches /foo and the backreference contains foo so it replaces /foo with foo which is why it returns abcfoo . To get just foo ensure that your regular expression matches the entire string so that the entire string is replaced with the backreference: sub([^./]*[./](.*), \\1, abc/foo) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Date time Differences
Mark R Laflamme, MD mlaflamme at regenstrief.org writes: : : Greetings from an R newbie : : Table imported with 4 columns containing Dates and Times, I desire to : determine the differences between said columns : Have loaded the base and chron packages for R commander. Have tried to : use format but without success. Have tried the Postix commands but : error states unused argument (s) (...), even though some of the : examples do not use (...) at the end of the command : : Example: : Table is named GvY1 : Operation.Time.End Operation.Time.Dictated : Operation.Time.Verfiy :7/10/2004 10:10:12 7/12/2004 9:18:03 : 7/28/2004 05:00:02 : : Information is mm/dd/year hh:mm:ss (time of day, e.g. the first column : is July 10th 2004 10:10 AM at 12 seconds) : What is the best way to get the difference between any of the 2 columns? : And eventually test statistics on the columns (eg. P values, if needed, : but not a priority at this time) : Thanks in advance : : Platform WinXP : IBM T40p : R v 1.8.1 : R commander : Often problems with data frames are due to storing the data as factors rather than in a datetime class but without a reproduceable example its impossible to know for sure. You might be able to solve this yourself by reading the article on dates and times in R News 4/1. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
