Re: [R] R CMD SHLIB gives error: bad value (generic) for -mtune= switch
This is clearly a compiler configuration error, not an R error. I note
that you have c:\Rtools\MinGW\libexec\gcc\mingw32\3.4.5 in your path,
which is *not* part of the instructions for R 2.6.0. Please try again
without it.
On Sat, 3 Nov 2007, McKay Curtis wrote:
Hello,
I am trying to compile C code using the R CMD SHLIB command. I get this
error:
R CMD SHLIB gibbs.c
making gibbs.d from gibbs.c
gibbs.c:0: error: bad value (generic) for -mtune= switch
make: [gibbs.d] Error 1 (ignored)
cat: gibbs.d: No such file or directory
make: [makeMakedeps] Error 1 (ignored)
gcc-sjlj -std=gnu99 -IC:/PROGRA~1/R/R-26~1.0/include-Wall -O3
-c gibbs.c -o gibbs.o
gibbs.c:1: error: bad value (generic) for -mtune= switch
make: *** [gibbs.o] Error 1
where gibbs.c contains
#include R.h
#include Rmath.h
#include gibbsiso.h
void gibbsiso(int *nmc){
Rprintf(Hello!);
}
and gibbsiso.h contains
void gibbsiso(int *);
I have installed or am using the following
* Rtools.exe 2.6.0
* R version 2.6.0 (2007-10-03)
* Windows Vista
* Toshiba Laptop, Intel Centrino Duo, T2250 @1.73 GHz w/ 1GB of RAM
My path variable is
c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;c:\Rtools\MinGW\libexec\gcc\mingw32\3.4.5;C:\Program
Files\MiKTeX
2.5\miktex\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program
Files\Common Files\Ulead Systems\MPEG;C:\Program
Files\R\R-26~1.0;C:\Program Files\R\R-26~1.0\bin;C:\Program
Files\gs\gs8.54\bin;
I would appreciate any insight into this error.
Thanks for your time!
McKay Curtis
(Stats grad student at NCSU)
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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
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Re: [R] mantel tests
Hi Simon, This is a general statistics question so I'm sorry if its outside the field of r help. Could anyone please provide a starting point? This doesn't directly answer your question, but one thing I would do is get ade4 and look at Chessel's co-inertia analysis method. It's a very general, and robust, method. It would involve treating your male and female trait tables separately, and then matching then (usually after a PCA). The method is based on (or uses) Robert Escoufier's RV-coefficient, and looks at the covariance between the two matrices. See: Dray, S., Chessel, D. and J. Thioulouse (2003) Co-inertia analysis and the linking of the ecological data tables. Ecology, 84, 11, 3078–3089 http://biomserv.univ-lyon1.fr/~dray/files/articles/SD162.pdf There is an excellent plot method, which should give you good insight, and there is a method for doing Monte-Carlo permutation tests of the match. I hope this is useful. Regards, Mark Difford. Simon Pickett wrote: This is a general statistics question so I'm sorry if its outside the field of r help. Anyway, I have a suite of female and male traits and I have made a matrix of correlation coefficients using rcorr(). This results in a 6 by 6 matrix like this.. [1] 0.11287990 0.20441361 0.23837442 0.04713234 0.04331637 0.01461611 [7] 0.22627981 0.11720108 0.14252307 0.19531625 0.29989953 0.09989502 [13] 0.03888750 0.11157971 0.02693303 0.01373447 0.08913154 0.06770636 [19] 0.01984838 0.10047978 0.05200218 0.16317234 0.2663 0.10412373 [25] 0.06269722 0.14366454 0.13123054 0.27550149 0.43863848 0.28909831 [31] 0.01454485 0.02551081 0.05645427 0.15819397 0.16508231 0.12399349 I want to test 2 hypotheses 1) is there a pattern to the matrix, does it differ from random? 2) do the top left and bottom right quadrants differ from the other 2 quadrants and if so, which one has the highest values of r2. I have read alot about permutation tests, bootstrapping and mantel tests but cant decide which is best in this situation? Could anyone please provide a starting point? Thankyou in advance, Simon [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/mantel-tests-tf4743237.html#a13571385 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help in error of mixed models
Hi R-masters I read the article: Bivariate analysis of sensitivity and specificity produces informative summary measures in diagnostic reviews. In this paper i proposed a bivariate mixed model and use SAS proc mixed to adjust the estimates. I thinks use R to make the same and try with this code: base-read.csv(base.csv) adj-.5 attach(base) sens-(VP+adj)/(VP+FN+2*adj) log.S-log(sens/(1-sens)) var.log.S-1/(sens*(1-sens)*(VP+FN)) dis-rep(1,length(log.S)) non.dis-rep(0,length(log.S)) data.S-data.frame(id,Modality,log.S,var.log.S,dis,non.dis) names(data.S)-c(id,Modality,logit,var.logit,dis,non.dis) esp-(VN+adj)/(VN+FP+2*adj) log.E-log((1-esp)/esp) var.log.E-1/(esp*(1-esp)*(VN+FP)) dis-rep(0,length(log.E)) non.dis-rep(1,length(log.E)) data.E-data.frame(id,Modality,log.E,var.log.E,dis,non.dis) names(data.E)-c(id,Modality,logit,var.logit,dis,non.dis) data.bi-rbind(data.S,data.E) require(nlme) lme(logit~dis*Modality+non.dis*Modality, random=~dis|id+non.dis| id,data=data.bi) but i recive a erro msg : Error in MEEM(object, conLin, control$niterEM) : Singularity in backsolve at level 0, block 1 How in solve this problem? Whats is wrong? Thanks in advance -- Bernardo Rangel Tura, M.D,Ph.D National Institute of Cardiology Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Where to ask general stats questions?
I see that some people ask general statistics questions here sometimes. As I understand this list is only for technical help with R-related issues. But does anyone know of a list/forum where we can ask help/questions regarding general statistics problems (and where solutions are offered possibly in the R language) . I know that usenet has some forums/groups but though those groups offer good solutions they are not necessarily in the context of the R/S langauge, in fact they are mostly either general hints without computer solution or if so then they mostly offer non-R codes. Thanks. -- View this message in context: http://www.nabble.com/Where-to-ask-general-stats-questions--tf4746189.html#a13571915 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] structure vs. matrix
Hi Edna, When creating a matrix, is it better to use the structure function or the matrix function...? I hope you have a huge (empty) jar in the kitchen, and that your pantry is empty. R isn't too difficult, except if you're trying to do stats (and don't know what you are doing --- though I am not suggesting that you don't know how to do stats;). ## see ?structure ?matrix A structure is not a matrix. So, if you want to make a matrix, use matrix(). Easy. HTH, Mark. Edna Bell wrote: Hi R Gurus! When creating a matrix, is it better to use the structure function or the matrix function, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/structure-vs.-matrix-tf4745521.html#a13572508 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problems with garch() function tseries package R 2.6.0
Hi all, I recently updated my to R 2.6.0 and tseries package tseries version: 0.10-11. When i was using R Version 2.3.1 (2006-06-01) with tseries 'tseries' version: 0.10-7, the code garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * Call: garch(x = dflnRCLC1) Coefficient(s): a0 a1 b1 4.985e+00 1.880e-01 6.210e-14 worked very quick and well. Now, with the newer version of R and tseries, this code hangs and doesnt give any result garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * its hangs forever... What happens? Regards, José Augusto Jr. University of São Paulo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Where to ask general stats questions?
francogrex [EMAIL PROTECTED] writes: But does anyone know of a list/forum where we can ask help/questions regarding general statistics problems (and where solutions are offered possibly in the R language) . You could try the newsgroup sci.stat.math or sci.stat.consult. HTH Patrick -- We are sorry, but the number you have dialed is imaginary. Please rotate your phone 90 degrees and try again. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help on error message!!!
Could anyone please help me with this one!!! I am looping some simple stuff but when I enter an if - function I get this error message: Error in if (y (2/(1 * pi) * sqrt(1 - ((x - 2)/1)^2))) c[i] = x else c[i] = 0 : missing value where TRUE/FALSE needed WHAT does it mean, what should I do [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] structure vs. matrix
On 04/11/2007 1:28 AM, Edna Bell wrote: Hi R Gurus! When creating a matrix, is it better to use the structure function or the matrix function, please? I'd use the matrix() function. You can do it with structure(), and your code might be a little faster, but it will be harder to read, will break if someone ever changes the low-level implementation of matrices, e.g. by replacing it with the Matrix class. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] structure vs. matrix
On 04/11/2007 7:43 AM, Mark Difford wrote: Hi Edna, When creating a matrix, is it better to use the structure function or the matrix function...? I hope you have a huge (empty) jar in the kitchen, and that your pantry is empty. R isn't too difficult, except if you're trying to do stats (and don't know what you are doing --- though I am not suggesting that you don't know how to do stats;). ## see ?structure ?matrix A structure is not a matrix. So, if you want to make a matrix, use matrix(). Easy. But a matrix is a structure, so you could use structure() to create one. I wouldn't normally do that, but there might be circumstances where it was appropriate. Duncan Murdoch HTH, Mark. Edna Bell wrote: Hi R Gurus! When creating a matrix, is it better to use the structure function or the matrix function, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help on error message!!!
On Sun, 2007-11-04 at 15:06 +0100, david csongor wrote: Could anyone please help me with this one!!! I am looping some simple stuff but when I enter an if - function I get this error message: Error in if (y (2/(1 * pi) * sqrt(1 - ((x - 2)/1)^2))) c[i] = x else c[i] = 0 : missing value where TRUE/FALSE needed WHAT does it mean, what should I do Try ifelse: c-ifelse(y (2/(1 * pi)*sqrt(1 -(x - 2)^2)),x,c[i]) -- Bernardo Rangel Tura, M.D,Ph.D National Institute of Cardiology Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with garch() function tseries package R 2.6.0
Hmm, did you forget to tell us the minimal information required by the posting guide? And what did the package maintainer say? A guess: you are using Windows and doing this in Rgui. I believe 'tseries' does Fortran I/O, and this is a symptom we have seen before. The workaround is to use Rterm, not Rgui. Some (maybe all) packages that attempt to do Fortran output in Rgui 2.6.0 will loop indefinitely waiting for stdout which does not exist on a console. On Sun, 4 Nov 2007, José Augusto Morais de Andrade Júnior - JAMAJ wrote: Hi all, I recently updated my to R 2.6.0 and tseries package tseries version: 0.10-11. When i was using R Version 2.3.1 (2006-06-01) with tseries 'tseries' version: 0.10-7, the code garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * Call: garch(x = dflnRCLC1) Coefficient(s): a0 a1 b1 4.985e+00 1.880e-01 6.210e-14 worked very quick and well. Now, with the newer version of R and tseries, this code hangs and doesnt give any result garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * its hangs forever... What happens? Regards, José Augusto Jr. University of São Paulo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] structure vs. matrix
On Sun, 4 Nov 2007, Duncan Murdoch wrote: On 04/11/2007 1:28 AM, Edna Bell wrote: Hi R Gurus! When creating a matrix, is it better to use the structure function or the matrix function, please? I'd use the matrix() function. You can do it with structure(), and your code might be a little faster, but it will be harder to read, will break if someone ever changes the low-level implementation of matrices, e.g. by replacing it with the Matrix class. For the record A - some data dim(A) - c(nr, rc) is faster than either matrix() or structure(), and seems at least as easy to read. matrix() has the advantage that it will replicate the data to the necessary length, but both will make copies that my version does not if you have the right length of data. But this is only worth worrying about if you have large matrices. -- 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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Why can repeated measures anova with within between subjects design not be done if group sizes are unbalanced?
Dear R people: I wish to switch from SPSS to R, but there is one particular type of ANOVA design that cannot be done in R. Or more likely, it can be done, but it is nowhere documented. The problem is typical for psychologists: You have a repeated measures design with different groups of subjects. Now, this can be done with the aov command, but the number of subjects in both groups must be equal (i.e., balanced design). SPSS allows for unbalanced designs as well. If you are still with me, let me just give you an example of what R can and cannot do so far. Imagine I have a 2x2 within subjects design and I have 2 groups (e.g., group healthy and patients, which is stored in MyGroup). And imagine I measure reaction time RT in four conditions, say, in a color condition (red vs green) and in a shape condition (square vs circle). Now, in R you would have something like, as anybody who does balanced repeated measures anova's might know: aov( RT ~ color * shape * MyGroup + Error( Subjects/( color*shape) ) In spss you would have something like this (of course with the data organized slightly differently : GLM x1 x2 x3 x4 BY MyGroup /WSFACTOR = color 2 Polynomial shape 2 Polynomial /METHOD = SSTYPE(3) /CRITERIA = ALPHA(.05) /WSDESIGN = color shape color*shape /DESIGN = VAR1 . Ok, the question is. If the group sizes are different (say 10 people in one group and 12 people in the other group) R is going to give the wrong answer. Of course that is not R's fault. BUT MY QUESTION IS: HOW TO GET THE UNBALANCED REPEATED MEASURES ANOVA RIGHT? Thanks for the answer! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why can repeated measures anova with within between subjects design not be done if group sizes are unbalanced?
'nowhere documented' ?? As the posting guide suggests, you could perform a search using RSiteSearch(repeated measures, restric=functions) say. That generates an inventory of functions that pertain to repeated measures designs. And once you have browsed through that you might focus on library(nlme) # load a library with nifty mixed model stuff ?lme # find out how to fit linear mixed models example(lme) # run some examples If that is not enough to get you started, the book J. C. Pinheiro and D. M. Bates (2000), Mixed-Effects Models in S and S-Plus., Springer, ISBN 0-387-98957-0 documents all the stops and whistles of the nlme library. Chuck On Sun, 4 Nov 2007, Gilbert G wrote: Dear R people: I wish to switch from SPSS to R, but there is one particular type of ANOVA design that cannot be done in R. Or more likely, it can be done, but it is nowhere documented. The problem is typical for psychologists: You have a repeated measures design with different groups of subjects. Now, this can be done with the aov command, but the number of subjects in both groups must be equal (i.e., balanced design). SPSS allows for unbalanced designs as well. If you are still with me, let me just give you an example of what R can and cannot do so far. Imagine I have a 2x2 within subjects design and I have 2 groups (e.g., group healthy and patients, which is stored in MyGroup). And imagine I measure reaction time RT in four conditions, say, in a color condition (red vs green) and in a shape condition (square vs circle). Now, in R you would have something like, as anybody who does balanced repeated measures anova's might know: aov( RT ~ color * shape * MyGroup + Error( Subjects/( color*shape) ) In spss you would have something like this (of course with the data organized slightly differently : GLM x1 x2 x3 x4 BY MyGroup /WSFACTOR = color 2 Polynomial shape 2 Polynomial /METHOD = SSTYPE(3) /CRITERIA = ALPHA(.05) /WSDESIGN = color shape color*shape /DESIGN = VAR1 . Ok, the question is. If the group sizes are different (say 10 people in one group and 12 people in the other group) R is going to give the wrong answer. Of course that is not R's fault. BUT MY QUESTION IS: HOW TO GET THE UNBALANCED REPEATED MEASURES ANOVA RIGHT? Thanks for the answer! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem implementing adapt()
Hello, I am trying to compute rectangle probability of bivariate
normal distribution with the following function:
bvnrectangle - function(mu, Sig, xmin, xmax, ymin, ymax){
library(adapt)
Siginv - solve(Sig)
detSig - det(Sig)
areal - adapt(ndim=2, lower=c(xmin,ymin), upper=c(xmax,ymax),
minpts=100, maxpts=1000, functn=bvnpdf, mu, Siginv, detSig)$value
areal
}
bvnpdf - function(xy, mu, Siginv, detSig){
f-numeric()
for(xloop in 1:length(xy[1])){
x - xy[[1]][xloop]
if(xy[[1]]xy[[2]] (1==2)) {
f[xloop] - 0} else {
v - rbind(xy[1], xy[2])
e - t(v-mu) %*% Siginv %*% (v-mu)
f[xloop] - exp(-e/2)/(2*pi)/sqrt(detSig)
}
}
f
}
bvnpdf works correctly (tested),
ex.: bvnpdf(c(0,0), c(0,0), solve( matrix(c(1, 0.5, 0.5, 1), nrow=2,
byrow=FALSE)), det( matrix(c(1, 0.5, 0.5, 1), nrow=2, byrow=FALSE)))
but when I run bvnrectangle, ex.: bvnrectangle(c(0,0), matrix(c(1,
0.5, 0.5, 1), nrow=2, byrow=FALSE), 0, 8, 0, 8)
I get the following error message:
Error in v - mu : non-conformable arrays
Why do I get this error message. I just can't understand what I am
doing wrong... Please, help.
Thanks in advance,
Regards,
Sergey
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[R] Problem implementing adapt()
that's the bvnpdf() code:
bvnpdf - function(xy, mu, Siginv, detSig){
f-numeric()
x - xy[[1]]
if(xy[[1]]xy[[2]] (1==2)) {
f - 0} else {
v - rbind(xy[1], xy[2])
e - t(v-mu) %*% Siginv %*% (v-mu)
f - as.numeric(exp(-e/2)/(2*pi)/sqrt(detSig))
}
f
}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] [Spam] Re: Problems with garch() function tseries package R 2.6.0
Hi, What other information should i post? I now have the two versions on the same machine. With R 2.3.1 and tseries 0.10-7 it works fine. With R 2.6.0 and tseries 0.10-11 the function garch doesnt work. The test was made with the same data, in the same machine. The maintainer did not say anything yet. Regards, José Augusto Jr. -- Cabeçalho original --- De: Prof Brian Ripley [EMAIL PROTECTED] Para: José Augusto Morais de Andrade J únior - JAMAJ [EMAIL PROTECTED] Cópia: Kurt Hornik [EMAIL PROTECTED], r-help@R-project.org Data: Sun, 4 Nov 2007 15:07:50 + (GMT) Assunto: [Spam] Re: [R] Problems with garch() function tseries package R 2.6.0 Hmm, did you forget to tell us the minimal information required by the posting guide? And what did the package maintainer say? A guess: you are using Windows and doing this in Rgui. I believe 'tseries' does Fortran I/O, and this is a symptom we have seen before. The workaround is to use Rterm, not Rgui. Some (maybe all) packages that attempt to do Fortran output in Rgui 2.6.0 will loop indefinitely waiting for stdout which does not exist on a console. On Sun, 4 Nov 2007, José Augusto Morais de Andrade Júnior - JAMAJ wrote: Hi all, I recently updated my to R 2.6.0 and tseries package tseries version: 0.10-11. When i was using R Version 2.3.1 (2006-06-01) with tseries 'tseries' version: 0.10-7, the code garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * Call: garch(x = dflnRCLC1) Coefficient(s): a0 a1 b1 4.985e+00 1.880e-01 6.210e-14 worked very quick and well. Now, with the newer version of R and tseries, this code hangs and doesnt give any result garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * its hangs forever... What happens? Regards, José Augusto Jr. University of São Paulo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 E-mail classificado pelo Identificador de Spam Inteligente Terra. Para alterar a categoria classificada, visite http://mail.terra.com.br/cgi-bin/imail.cgi?+_u=jamaj_l=1,1194188875.463773.24782.capalaba.hst.terra.com.br,3611,20031127114101,20031127114101 Esta mensagem foi verificada pelo E-mail Protegido Terra. Scan engine: McAfee VirusScan / Atualizado em 02/11/2007 / Versão: 5.1.00/5155 Proteja o seu e-mail Terra: http://mail.terra.com.br/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with garch() function tseries package R 2.6.0
Hi, I have just downloaded R 2.6.0 in other machine. The problem is the same. So, does anyone know how to make this function work again? For now, i will use my old version of R. Thanks in advance. José Augusto Jr. -- Cabeçalho original --- De: Prof Brian Ripley [EMAIL PROTECTED] Para: José Augusto Morais de Andrade J únior - JAMAJ [EMAIL PROTECTED] Cópia: Kurt Hornik [EMAIL PROTECTED], r-help@R-project.org Data: Sun, 4 Nov 2007 15:07:50 + (GMT) Assunto: [Spam] Re: [R] Problems with garch() function tseries package R 2.6.0 Hmm, did you forget to tell us the minimal information required by the posting guide? And what did the package maintainer say? A guess: you are using Windows and doing this in Rgui. I believe 'tseries' does Fortran I/O, and this is a symptom we have seen before. The workaround is to use Rterm, not Rgui. Some (maybe all) packages that attempt to do Fortran output in Rgui 2.6.0 will loop indefinitely waiting for stdout which does not exist on a console. On Sun, 4 Nov 2007, José Augusto Morais de Andrade Júnior - JAMAJ wrote: Hi all, I recently updated my to R 2.6.0 and tseries package tseries version: 0.10-11. When i was using R Version 2.3.1 (2006-06-01) with tseries 'tseries' version: 0.10-7, the code garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * Call: garch(x = dflnRCLC1) Coefficient(s): a0 a1 b1 4.985e+00 1.880e-01 6.210e-14 worked very quick and well. Now, with the newer version of R and tseries, this code hangs and doesnt give any result garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * its hangs forever... What happens? Regards, José Augusto Jr. University of São Paulo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 E-mail classificado pelo Identificador de Spam Inteligente Terra. Para alterar a categoria classificada, visite http://mail.terra.com.br/cgi-bin/imail.cgi?+_u=jamaj_l=1,1194188875.463773.24782.capalaba.hst.terra.com.br,3611,20031127114101,20031127114101 Esta mensagem foi verificada pelo E-mail Protegido Terra. Scan engine: McAfee VirusScan / Atualizado em 02/11/2007 / Versão: 5.1.00/5155 Proteja o seu e-mail Terra: http://mail.terra.com.br/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] install problem 2.6 mac os x 10.5
I am having the very SAME problem. I removed Version 2.5.1 before trying to install 2.6.0. Please help. TIA, Oscar __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD SHLIB gives error: bad value (generic) for -mtune= switch
Thanks Prof. Ripley.
I removed that snippet from my path, and R CMD SHLIB works like a dream...
Thanks again,
McKay
On Nov 4, 2007 2:32 AM, Prof Brian Ripley [EMAIL PROTECTED] wrote:
This is clearly a compiler configuration error, not an R error. I note
that you have c:\Rtools\MinGW\libexec\gcc\mingw32\3.4.5 in your path,
which is *not* part of the instructions for R 2.6.0. Please try again
without it.
On Sat, 3 Nov 2007, McKay Curtis wrote:
Hello,
I am trying to compile C code using the R CMD SHLIB command. I get this
error:
R CMD SHLIB gibbs.c
making gibbs.d from gibbs.c
gibbs.c:0: error: bad value (generic) for -mtune= switch
make: [gibbs.d] Error 1 (ignored)
cat: gibbs.d: No such file or directory
make: [makeMakedeps] Error 1 (ignored)
gcc-sjlj -std=gnu99 -IC:/PROGRA~1/R/R-26~1.0/include-Wall -O3
-c gibbs.c -o gibbs.o
gibbs.c:1: error: bad value (generic) for -mtune= switch
make: *** [gibbs.o] Error 1
where gibbs.c contains
#include R.h
#include Rmath.h
#include gibbsiso.h
void gibbsiso(int *nmc){
Rprintf(Hello!);
}
and gibbsiso.h contains
void gibbsiso(int *);
I have installed or am using the following
* Rtools.exe 2.6.0
* R version 2.6.0 (2007-10-03)
* Windows Vista
* Toshiba Laptop, Intel Centrino Duo, T2250 @1.73 GHz w/ 1GB of RAM
My path variable is
c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;c:\Rtools\MinGW\libexec\gcc\mingw32\3.4.5;C:\Program
Files\MiKTeX
2.5\miktex\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program
Files\Common Files\Ulead Systems\MPEG;C:\Program
Files\R\R-26~1.0;C:\Program Files\R\R-26~1.0\bin;C:\Program
Files\gs\gs8.54\bin;
I would appreciate any insight into this error.
Thanks for your time!
McKay Curtis
(Stats grad student at NCSU)
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] hierarchical mixed model
I would like to fit a 2-level mixed model: yit=a+a[i]+a[it] +(b+b[i]+b[it])*xit+eps[it] However, the variance of the second level components should depend on the group, i.e. sigma for a[it] and b[it] should be [i] specific. I do not know whether this is conceptually right in the mixed model context... In case it stands, how should the formula look like? Also, the data are unbalanced with different number of observations t nested in each i group and I get the warning when trying to fit the model in the traditional way. How much should I worry about this? Thank you! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with garch() function tseries package R 2.6.0
This is the sessionInfo() output immediatly before the hanging command garch(): sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=Portuguese_Brazil.1252;LC_CTYPE=Portuguese_Brazil.1252;LC_MONETARY=Portuguese_Brazil.1252;LC_NUMERIC=C;LC_TIME=Portuguese_Brazil.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] tseries_0.10-11 zoo_1.4-0 quadprog_1.4-11 loaded via a namespace (and not attached): [1] grid_2.6.0 lattice_0.17-2 -- Cabeçalho original --- De: Benilton Carvalho [EMAIL PROTECTED] Para: José Augusto Morais de Andrade Júnior - JAMAJ [EMAIL PROTECTED] Cópia: Data: Sun, 4 Nov 2007 16:26:29 -0500 Assunto: Re: [R] Problems with garch() function tseries package R 2.6.0 Augusto, a maior questao e' conseguirmos reproduzir o problema que vc esta' reportando. Como o Ripley comentou, ha' informacoes minimas para podermos dar uma melhor ajuda (sessionInfo() e' uma delas: http://www.R-project.org/posting-guide.html De qualquer forma, assumindo que vc esta' no Windows, basta apenas usar o Rterm, ao inves da interface grafica Mas sem estas informacoes extras, nao ha' como progredir em uma solucao. b On Nov 4, 2007, at 4:20 PM, José Augusto Morais de Andrade Júnior - JAMAJ wrote: Hi, I have just downloaded R 2.6.0 in other machine. The problem is the same. So, does anyone know how to make this function work again? For now, i will use my old version of R. Thanks in advance. José Augusto Jr. -- Cabeçalho original --- De: Prof Brian Ripley [EMAIL PROTECTED] Para: José Augusto Morais de Andrade J únior - JAMAJ [EMAIL PROTECTED] Cópia: Kurt Hornik [EMAIL PROTECTED], r-help@R-project.org Data: Sun, 4 Nov 2007 15:07:50 + (GMT) Assunto: [Spam] Re: [R] Problems with garch() function tseries package R 2.6.0 Hmm, did you forget to tell us the minimal information required by the posting guide? And what did the package maintainer say? A guess: you are using Windows and doing this in Rgui. I believe 'tseries' does Fortran I/O, and this is a symptom we have seen before. The workaround is to use Rterm, not Rgui. Some (maybe all) packages that attempt to do Fortran output in Rgui 2.6.0 will loop indefinitely waiting for stdout which does not exist on a console. On Sun, 4 Nov 2007, José Augusto Morais de Andrade Júnior - JAMAJ wrote: Hi all, I recently updated my to R 2.6.0 and tseries package `tseries´ version: 0.10-11. When i was using R Version 2.3.1 (2006-06-01) with tseries 'tseries' version: 0.10-7, the code garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * Call: garch(x = dflnRCLC1) Coefficient(s): a0 a1 b1 4.985e+00 1.880e-01 6.210e-14 worked very quick and well. Now, with the newer version of R and tseries, this code hangs and doesnt give any result garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * its hangs forever... What happens? Regards, José Augusto Jr. University of São Paulo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 E-mail classificado pelo Identificador de Spam Inteligente Terra. Para alterar a categoria classificada, visite http://mail.terra.com.br/cgi-bin/imail.cgi?+_u=jamaj_l=1,1194188875.463773.24782.capalaba.hst.terra.com.br,3611,20031127114101,20031127114101 Esta mensagem foi verificada pelo E-mail Protegido Terra. Scan engine: McAfee VirusScan / Atualizado em 02/11/2007 / Versão: 5.1.00/5155 Proteja o seu e-mail Terra: http://mail.terra.com.br/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. E-mail classificado pelo Identificador de Spam Inteligente Terra. Para alterar a categoria classificada, visite http://mail.terra.com.br/cgi-bin/imail.cgi?+_u=jamaj_l=1,1194211594.853911.31486.buruma.hst.terra.com.br,16362,Des15,Des15 Esta mensagem foi verificada pelo E-mail Protegido Terra. Scan engine: McAfee VirusScan / Atualizado em 02/11/2007 / Versão: 5.1.00/5155 Proteja o seu e-mail
Re: [R] Problems with garch() function tseries package R 2.6.0
Hi, Yes, you are right. With Rterm it does work. With RGui, the newer version of R and tseries package, the function Garch() does not work anymore. Thanks. -- Cabeçalho original --- De: Prof Brian Ripley [EMAIL PROTECTED] Para: José Augusto Morais de Andrade J únior - JAMAJ [EMAIL PROTECTED] Cópia: Kurt Hornik [EMAIL PROTECTED], r-help@R-project.org Data: Sun, 4 Nov 2007 15:07:50 + (GMT) Assunto: [Spam] Re: [R] Problems with garch() function tseries package R 2.6.0 Hmm, did you forget to tell us the minimal information required by the posting guide? And what did the package maintainer say? A guess: you are using Windows and doing this in Rgui. I believe 'tseries' does Fortran I/O, and this is a symptom we have seen before. The workaround is to use Rterm, not Rgui. Some (maybe all) packages that attempt to do Fortran output in Rgui 2.6.0 will loop indefinitely waiting for stdout which does not exist on a console. On Sun, 4 Nov 2007, José Augusto Morais de Andrade Júnior - JAMAJ wrote: Hi all, I recently updated my to R 2.6.0 and tseries package tseries version: 0.10-11. When i was using R Version 2.3.1 (2006-06-01) with tseries 'tseries' version: 0.10-7, the code garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * Call: garch(x = dflnRCLC1) Coefficient(s): a0 a1 b1 4.985e+00 1.880e-01 6.210e-14 worked very quick and well. Now, with the newer version of R and tseries, this code hangs and doesnt give any result garch(dflnRCLC1) * ESTIMATION WITH ANALYTICAL GRADIENT * its hangs forever... What happens? Regards, José Augusto Jr. University of São Paulo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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 E-mail classificado pelo Identificador de Spam Inteligente Terra. Para alterar a categoria classificada, visite http://mail.terra.com.br/cgi-bin/imail.cgi?+_u=jamaj_l=1,1194188875.463773.24782.capalaba.hst.terra.com.br,3611,20031127114101,20031127114101 Esta mensagem foi verificada pelo E-mail Protegido Terra. Scan engine: McAfee VirusScan / Atualizado em 02/11/2007 / Versão: 5.1.00/5155 Proteja o seu e-mail Terra: http://mail.terra.com.br/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] unable to install package ff
Hi Adrian et al, Thanks for the advice. I haven't yet tried R.huge but will do so soon. I have used filehash and it is working well now. A note: for some reason, R objects were not being 'flushed' from memory on R 2.5.1 - even when removed and after an explicit call to gc(). Originally I thought this was a problem with the filehash library but since found other instances when it occured and when not using filehash. After updating to R 2.6.0, this behavior resolved itself. So a note to others: if you're having problems with memory, you might make certain your version of R is up-to-date! Was this a documented issue with R 2.5.1? Best, Matt On 11/3/07, Adrian Dragulescu [EMAIL PROTECTED] wrote: Matthew, Did you take a look at the R.huge package? It works well with numerical data. If you describe the problem you're trying to solve in more detail, it may help us give you a better solution. Btw, we use the filehash package with great success in accessing very large amounts of data. Best, Adrian Dragulescu On 11/1/07, Matthew Keller [EMAIL PROTECTED] wrote: Hi all, I've had one of my most miserable R weeks in memory. I'm trying to deal with huge datasets (1GB each) but am running up against those pesky memory limits. The libraries filehash and g.data are not very suitable for what I need. I haven't gotten into the sql thing yet. Most recently I've been trying to install the new package ff (not yet on the CRAN repository). I can't find emails of the folks developing ff, so I was hoping someone here might have an idea how to deal with this. From http://wsopuppenkiste.wiso.uni-goettingen.de/ff/ I've downloaded the ff_1.0.tar.gz. install.packages(pkgs=ff_1.0.tar.gz,repos=NULL,destdir=/temp,type=source) much output omitted g++-4.0: installation problem, cannot exec 'i686-apple-darwin8-g++-4.0.0': No such file or directory make: *** [Error.o] Error 255 chmod: /Library/Frameworks/R.framework/Versions/2.5/Resources/library/ff/libs/i386/*: No such file or directory ERROR: compilation failed for package 'ff' So it cannot find i686-apple-darwin8-g++-4.0.0. What the hell is that? A compiler I suppose. I HAVE installed the Mac OS developer tools. I have an MacBook Pro with 4GB RAM and am using the 32bit R: sessionInfo() R version 2.5.1 (2007-06-27) i386-apple-darwin8.9.1 locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base Any ideas how to get ff to install properly on my system? Most appreciative of any advice! Matt -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] install problem 2.6 mac os x 10.5
Hi Oscara and Emelio, You guys might want to do a search on the R mailing list - this issue has been discussed and I think there's a pretty simple work-around. Best, Matt On 11/4/07, Oscar Moreno [EMAIL PROTECTED] wrote: I am having the very SAME problem. I removed Version 2.5.1 before trying to install 2.6.0. Please help. TIA, Oscar __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help in error of mixed models
Hi Bernardo, it may sound simple-minded, but it looks to me as though you have a problem with the model. Unfortunately it's difficult for us to diagnose the problem because you didn't send an example that we can reproduce. We don't have the base data. Based on my understanding of your code, you might try lme(logit ~ dis*Modality + non.dis*Modality, random = ~ dis+non.dis | id, data = data.bi) If this doesn't work, try fitting a simpler model, eg lme(logit ~ dis*Modality + non.dis*Modality, random = ~ | id, data = data.bi) and then using update() to increment towards the full model of interest. You can also change the model-fitting engine, I have sometimes had success using Nelder-Mead where nlminb failed. For more information about this see ?lmeControl Can I also recommend that you use more spaces in your code? Good luck Andrew On Sun, Nov 04, 2007 at 09:18:09AM -0200, Bernardo Rangel Tura wrote: Hi R-masters I read the article: Bivariate analysis of sensitivity and specificity produces informative summary measures in diagnostic reviews. In this paper i proposed a bivariate mixed model and use SAS proc mixed to adjust the estimates. I thinks use R to make the same and try with this code: base-read.csv(base.csv) adj-.5 attach(base) sens-(VP+adj)/(VP+FN+2*adj) log.S-log(sens/(1-sens)) var.log.S-1/(sens*(1-sens)*(VP+FN)) dis-rep(1,length(log.S)) non.dis-rep(0,length(log.S)) data.S-data.frame(id,Modality,log.S,var.log.S,dis,non.dis) names(data.S)-c(id,Modality,logit,var.logit,dis,non.dis) esp-(VN+adj)/(VN+FP+2*adj) log.E-log((1-esp)/esp) var.log.E-1/(esp*(1-esp)*(VN+FP)) dis-rep(0,length(log.E)) non.dis-rep(1,length(log.E)) data.E-data.frame(id,Modality,log.E,var.log.E,dis,non.dis) names(data.E)-c(id,Modality,logit,var.logit,dis,non.dis) data.bi-rbind(data.S,data.E) require(nlme) lme(logit~dis*Modality+non.dis*Modality, random=~dis|id+non.dis| id,data=data.bi) but i recive a erro msg : Error in MEEM(object, conLin, control$niterEM) : Singularity in backsolve at level 0, block 1 How in solve this problem? Whats is wrong? Thanks in advance -- Bernardo Rangel Tura, M.D,Ph.D National Institute of Cardiology Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] install problem 2.6 mac os x 10.5
Refer to R Mac SIG list, the mpkg installer in 2.6 binary is broken in Leopard. Until an updated version is release, you can install R by install each package in Packages folder one by one. Hope it helps. Regards, CH On 11/4/07, Emilio Gagliardi [EMAIL PROTECTED] wrote: Hi everyone, I am trying to install R-2.6 over my 2.5.1 installation on Mac OS X 10.5. R version 2.5.1 (2007-06-27) I double-click the installer package, 1) Click Continue 2) Click Continue 3) Click Continue + Click Agree On the Installation Type dialog screen, all four options are grayed out, with skip beside them. The Install button is also grayed out. If I click the Standard Install button, it allows me to change the directory to install onto, but then brings me back to the same screen. So I can't install. If I click any one the four options [R Framework, R GUI, etc] the message says There is a more recent version of this software installed on your system. There is no need to install this older version. What am I missing here? Thanks for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- CH Chan Research Assistant - KWH http://www.macgrass.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R package segmented
Has anyone successfully used R package segmented ? I tried on my data and could not get the syntax right. In addition, I wonder whether it only operates with continuous variables as I deal with discrete variables. I was contacted by its author and, upon his request, I forwarded one of my files where the plot of amplitude versus time change slopes 4-5 times. Finding the breakpoints by visual inspection is a tedious error-prone task. So far I've been unable (and had no time to seriously think of) some sort of semi-automatic way of doing that. I was hoping that someone else has already addressed and solved this problem ... Regards, -- Maura E.M [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sending E-Mail from R
Hi, Has anyone used R to send out an email via an SMTP server? I run R from a script and would like to be able to send out an email from there also. I could shell out to an email program, but was hoping maybe someone had a package for R or a smooth way to do it. Thanks, Josh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] structure vs. matrix
In general, you want to use as high level a construct as possible since then the details implementing the construct can be modified and improved without your code changing. This is really just an aspect of modularity. Thus matrix would be preferred. Actually since R allows access to the lower level details this type of benefit is not really guaranteed but as a matter of principle I would use other constructs than structure whenever possible. On Nov 4, 2007 8:32 PM, Edna Bell [EMAIL PROTECTED] wrote: I was reading S Programming and a set of the code used structure to set up a matrix. I just wondered which was better and why. On 11/4/07, Mark Difford [EMAIL PROTECTED] wrote: Hi Edna, When creating a matrix, is it better to use the structure function or the matrix function...? I hope you have a huge (empty) jar in the kitchen, and that your pantry is empty. R isn't too difficult, except if you're trying to do stats (and don't know what you are doing --- though I am not suggesting that you don't know how to do stats;). ## see ?structure ?matrix A structure is not a matrix. So, if you want to make a matrix, use matrix(). Easy. HTH, Mark. Edna Bell wrote: Hi R Gurus! When creating a matrix, is it better to use the structure function or the matrix function, please? Thanks, Edna Bell __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/structure-vs.-matrix-tf4745521.html#a13572508 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sending E-Mail from R
Try SiteSearch(blat) from within R for examples using blat. Please read the posting guide and, in particular, give your platform next time. On Nov 4, 2007 8:45 PM, Josh Kalish [EMAIL PROTECTED] wrote: Hi, Has anyone used R to send out an email via an SMTP server? I run R from a script and would like to be able to send out an email from there also. I could shell out to an email program, but was hoping maybe someone had a package for R or a smooth way to do it. Thanks, Josh [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sending E-Mail from R
On 05-Nov-07 01:45:50, Josh Kalish wrote: Hi, Has anyone used R to send out an email via an SMTP server? I run R from a script and would like to be able to send out an email from there also. I could shell out to an email program, but was hoping maybe someone had a package for R or a smooth way to do it. Thanks, Josh There is a thread in R-help starting on 10 May 1965 at https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071200.html [R] Does R have a command for sending emails? (Fernando Saldanha) Specific suggestions for specially-written R functions which can do this are at https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071212.html https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071233.html https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071235.html See also: https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071245.html https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071287.html https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071297.html Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 05-Nov-07 Time: 02:24:05 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] perl module for R
On 04/11/2007, Andrew Perrin [EMAIL PROTECTED] wrote: http://www.omegahat.org/RSPerl/ -- Andrew J Perrin - andrew_perrin (at) unc.edu - http://perrin.socsci.unc.edu Associate Professor of Sociology; Book Review Editor, _Social Forces_ University of North Carolina - CB#3210, Chapel Hill, NC 27599-3210 USA hi, can some one convert this R command into perl for me? layout(matrix(1,2,3,4,5,6), 2,3, byrow=TRUE) On Sun, 4 Nov 2007, [EMAIL PROTECTED] wrote: Hi can anyone recommend a perl module that I can use to run R? Stephen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sending E-Mail from R
On Nov 4, 2007, at 9:24 PM, (Ted Harding) wrote: On 05-Nov-07 01:45:50, Josh Kalish wrote: Hi, Has anyone used R to send out an email via an SMTP server? I run R from a script and would like to be able to send out an email from there also. I could shell out to an email program, but was hoping maybe someone had a package for R or a smooth way to do it. Thanks, Josh There is a thread in R-help starting on 10 May 1965 at I usually say that R is one step ahead... it looks like the scale has just changed to 30 years or so... :-) b https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071200.html [R] Does R have a command for sending emails? (Fernando Saldanha) Specific suggestions for specially-written R functions which can do this are at https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071212.html https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071233.html https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071235.html See also: https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071245.html https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071287.html https://www.stat.math.ethz.ch/pipermail/r-help/2005-May/071297.html Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 05-Nov-07 Time: 02:24:05 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multidensional integration with adapt
Hello,
I am trying to integrate a 2-dimensional function that already calls the
function adapt. More precisely, I am calling
adapt(2,lower=c(-100,-100),upper=c(100,100),functn=function(s){1-exp(-50*Unc
enteredGauss(c(-10,10,-10,10),60,s)})
where UncenteredGauss is given by the following code in R:
UncenteredGauss=function(limsamp,sigma2,s)
{
int=adapt(2,lower=c(limsamp[1],limsamp[3]),upper=c(limsamp[2],limsamp[4]),fu
nctn=function(u){h(sigma2,s,u)})
value=int$value
return(value)
}
h=function(sigma2,s,u){1/(2*pi*sigma2)*exp(-((u[1]-s[1])^2+(u[2]-s[2])^2)/(2
*sigma2))}
This does not return an error message but a value that is not the good one.
UncenteredGauss gives the good result, but I believe the problem comes from
calling in adapt a function that already calls adapt
Any idea on how to integrate a function that already contains an integral???
Thank you very much
Helene Morlon
Green Lab
Center for Ecology and Evolutionary Biology
University of Oregon, Eugene
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] multidimensional integration with adapt
Hello,
I apologize for eventual double-posting.
I am trying to integrate a 2-dimensional function that already calls the
function adapt. More precisely, I am calling
adapt(2,lower=c(-100,-100),upper=c(100,100),functn=function(s){1-exp(-50*Unc
enteredGauss(c(-10,10,-10,10),60,s)})
where UncenteredGauss is given by the following code in R:
UncenteredGauss=function(limsamp,sigma2,s)
{
int=adapt(2,lower=c(limsamp[1],limsamp[3]),upper=c(limsamp[2],limsamp[4]),fu
nctn=function(u){h(sigma2,s,u)})
value=int$value
return(value)
}
h=function(sigma2,s,u){1/(2*pi*sigma2)*exp(-((u[1]-s[1])^2+(u[2]-s[2])^2)/(2
*sigma2))}
This does not return an error message but a value that is not the good one.
UncenteredGauss gives the good result, but I believe the problem comes from
calling in adapt a function that already calls adapt
Any idea on how to integrate a function that already contains an integral???
Thanks!
Helene Morlon
Green Lab
Center for Ecology and Evolutionary Biology
University of Oregon, Eugene
[EMAIL PROTECTED]
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
