[R] nlm behaviour and error
Hi R-Gurus,
I've been cutting along quite nicely with nlm, until
I threw in the following condition in the function that nlm is
minimising:
if (((term*bexp) 0.0001)) {
#warning(term*bexp, =term*bexp,psi,=psi)
theta-2000
}
Now when I run this function anywhere else, there is no problem, whether
or the if's condition is met.
When I use this in nlm:
nlm(f=ssewrap.dist, p=c(292397.7,-.14053,0.03,.0005), .5, 1,
295.15,C,theta)
Error in if (((term * bexp) 1e-04)) { :
missing value where TRUE/FALSE needed
Now I know that the condition in the if should only be one logical
value, but is not the condition above evaluated to a single value, and
why does the error only occur when the function is used by nlm?
Any suggestions?
Kind regards,
Matt Redding
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Re: [R] 'asymmetric span' for 2D loess?
On Mon, 2 Jun 2008, Tokuyasu, Taku wrote: Hello, I am interested in performing a 2D loess smooth on microarray data, i.e. log2 ratios on a 2D grid, using different spans in the horizontal and vertical directions (the immediate reason being that replicate spots are laid out in the horizontal direction). Is it possible to do this in R? Functions like loess(stats) seem to apply the same span for all predictors, which carries over to functions like ma2D(marray). See the next comment. 'span' applies to 2D distances, and I think you need to rescale your inputs so Euclidean distance is appropriate. As an elementary second question, are there circumstances where one expects to see a substantial difference in the fits between say loess(y ~ x1 + x2) and loess(y ~ x1 * x2) with an interaction term (and if so, what are they)? From the help page: formula: a formula specifying the numeric response and one to four numeric predictors (best specified via an interaction, but can also be specified additively). Will be coerced to a formula if necessary. So the two versions both specify smoothing in 2D. You can use things like lo(x1) + lo(x2) in some gam fits. It often helps to read the primary sources, in this case chapters in the White Book (Chambers Hastie, nominally 1992, actually published in 1991). Many thanks, _Taku Taku A. Tokuyasu, PhD UCSF Helen Diller Family Comprehensive Cancer Center San Francisco, CA 94143-0808 -- 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] Error/Crash on start up of R (Ubuntu and Wine within Ubuntu)
Either you have a corrupt .RData file in the directory you are starting R in or the file is being read incorrectly (e.g. because of a corrupted file system or hardware issues). Reinstalling etc will not remove the .RData file, and you need to do so yourself. Starting R with --vanilla is always a good check for local configuration issues. On Mon, 2 Jun 2008, Patrick M. Joyce wrote: Hello, I'm having issues operating R under Ubuntu (Hardy 8.04) though I suspect this is not necessarily the malady. I have attempted to run R in ubuntu as is which worked for awhile and then stopped (using RKWard as the windowing environment). I tried removing then re-installing the software and the same issue (which i'll detail soon) persisted. I then tried using WINE to run R using the Windows version of R. The same error was presented. The Ubuntu and WINE errors are slightly different but are more or less the same... COMMON ASPECT--I get the following: Error in load(name, envir = .GlobalEnv): value of 'SET_ATTRIB' must be a pairlist or NULL, not a 'double' WINE Variant--I get a windowed box with the title Information noting that Fatal error: unable to restore saved data in .RData. UBUNTU Variant--I get a segmentation fault statement and abort options. I'm going to guess that this is the same issue. I would presume at this point that either there is some mistaken setting within the operating system OR something wrong with the hardware. I appreciate any help on the matter. --Patrick __ 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] nlm behaviour and error
It says the value is *missing* (NA), not that the length is wrong.
My quess is that term*bexp is NaN, but you have given us no context to go
on.
On Tue, 3 Jun 2008, Redding, Matthew wrote:
Hi R-Gurus,
I've been cutting along quite nicely with nlm, until
I threw in the following condition in the function that nlm is
minimising:
if (((term*bexp) 0.0001)) {
#warning(term*bexp, =term*bexp,psi,=psi)
theta-2000
}
Now when I run this function anywhere else, there is no problem, whether
or the if's condition is met.
When I use this in nlm:
nlm(f=ssewrap.dist, p=c(292397.7,-.14053,0.03,.0005), .5, 1,
295.15,C,theta)
Error in if (((term * bexp) 1e-04)) { :
missing value where TRUE/FALSE needed
Now I know that the condition in the if should only be one logical
value, but is not the condition above evaluated to a single value, and
why does the error only occur when the function is used by nlm?
Any suggestions?
Kind regards,
Matt Redding
DISCLAIMER**...{{dropped:15}}
__
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
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] probleme with R CMD check
c == cgenolin [EMAIL PROTECTED] on Tue, 03 Jun 2008 00:32:13 +0200 writes: c Hi the list. c I got a probleme with R CMD check. I run a package.skeleton on a very c simple code (four toy function, no probleme with the R CMD build). But c on the R CMD check packClassique, I get : c * checking for unstated dependencies in R code ... WARNING c Erreur dans .find.package(package, lib.loc) : aucun package nommé c 'packClassique' n'est trouvé c Calls: Anonymous - .find.package c Excecution hated [French=Exécution arrêtée] c See the information on DESCRIPTION files in the chapter 'Creating R c packages' of the 'Writing R Extensions' manual. c * checking S3 generic/method consistency ... WARNING c Erreur dans .find.package(package, lib.loc) : aucun package nommé c 'packClassique' n'est trouvé c Calls: Anonymous - .find.package c Exécution arrêtée c And so on. c Any idea on what is wrong ? No. c Christophe c __ c R-help@r-project.org mailing list c https://stat.ethz.ch/mailman/listinfo/r-help c PLEASE do read the posting guide http://www.R-project.org/posting-guide.html c and provide commented, minimal, self-contained, reproducible code. Please do -- both -- Martin __ 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] probleme with R CMD check
provide commented, minimal, self-contained, reproducible code. Please do -- both -- Sorry... Usualy, I do... --- 8 userA - function(x)x+1 privateA - function(x)x+2 .userB - function(x)x+10 .privateB - function(x)x+20 userC- function(x)userA(privateA(x)) privateC - function(x).userB(.privateB(x)) userD- function(x)userA(.userB(x)) privateD - function(x)privateA(.privateB(x)) --- 8 c == cgenolin [EMAIL PROTECTED] on Tue, 03 Jun 2008 00:32:13 +0200 writes: c Hi the list. c I got a probleme with R CMD check. I run a package.skeleton on a very c simple code (four toy function, no probleme with the R CMD build). But c on the R CMD check packClassique, I get : c * checking for unstated dependencies in R code ... WARNING c Erreur dans .find.package(package, lib.loc) : aucun package nommé c 'packClassique' n'est trouvé c Calls: Anonymous - .find.package c Excecution hated [French=Exécution arrêtée] c See the information on DESCRIPTION files in the chapter 'Creating R c packages' of the 'Writing R Extensions' manual. c * checking S3 generic/method consistency ... WARNING c Erreur dans .find.package(package, lib.loc) : aucun package nommé c 'packClassique' n'est trouvé c Calls: Anonymous - .find.package c Exécution arrêtée c And so on. c Any idea on what is wrong ? No. c Christophe c __ c R-help@r-project.org mailing list c https://stat.ethz.ch/mailman/listinfo/r-help c PLEASE do read the posting guide http://www.R-project.org/posting-guide.html c and provide commented, minimal, self-contained, reproducible code. Please do -- both -- Martin __ 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] regsubsets - package(leaps)
Please, can someone suggest me where to find a description for the attributes of the summary of regsubsets, that is: which rsqrssadjr2 cp bicoutmat obj ?? Thank you so much. -- 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] discrete parameter
hello dear sir, Inbsp;wonder whether ifnbsp;anybody try to constructnbsp;acontinous parameternbsp;AR(P) from the discrete parameter AR(P) execuse me for my bad english lang. and thank you for your helpful. nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; [[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] Need advise in grab the line number of sorted list in R
On Tue, Jun 03, 2008 at 10:37:33AM +1000, Jason Lee wrote: Hi, If there are more than one item having the same value, how can i use R to take the average of the position. E.g:- X Y Z 131 22.2 3.4 4.4 132 20.0 3.4 4.4==Position 2 if queried 150 20.0 12.2 4.5 =Position 3 if queried 134 20.0 3.4 4.4 == Position4 if queried 159 20.0 12.2 4.5==Position 5 if queried 160 22.0 12.2 4.5 When I query 150 using which, it gives 3 but since in other position the value are same which is 20.0, how can i get the average of the position which is (2+3+4+5)/3 aggregate() will do what you want. A little warning: of course aggregate will group by elements which are EXACTLY the same so make sure the floats in columns X really behave the way you want. Otherwise you may want to have a look at cut(). cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany and Institut für Bioinformatik und Systembiologie / MIPS Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt Ingolstädter Landstrasse 1 85764 Neuherberg, Germany http://mips.gsf.de/staff/pagel __ 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] exit function in R?
Thank everybody for the answers! The stop and quit functions are what I
need (it is a script, not a function what needs to be terminated. I was
talking about an exit function, what can be confusing).
Best,
Federico
Gregory. R. Warnes wrote:
Since Frederico indeicated he was running a script, rather than a
function, I suspect that he would be better served by the
quit(no)
function.
Jun 2, 2008, at 5:15PM , Rolf Turner wrote:
On 3/06/2008, at 1:18 AM, Federico Abascal wrote:
Hi,
This is likely an stupid question, but I cannot find the solution.
I am searching for an exit function, to end the execution of an R
script if some condition is not filled.
Any clue?
Others have suggested using stop(). It might be the case that the
condition not being fulfilled is not actually a sign of an error,
but simply of a different, perhaps ``marginal'' situation in which
a different sort of action or calculation is required. In which
case what you want is return().
Trivial e.g.:
foo - function(x) {
if(any(x=0)) return(42)
y - sum(log(x))
y
}
cheers,
Rolf Turner
##
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Gregory R. Warnes, Ph.D.
Associate Professor
Center for Biodefence Immune Modeling
and
Department of Biostatistics and Computational Biology
University of Rochester
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Re: [R] Odp: Aggregation and the meaning of class
Hi Chip Maybe some more experienced users can direct you to proper source of information but in case of programming there are several books which can be of some use (I do not have any of them so its only my guess from their names). See items 1, 3 and 5 from CRAN Books page. Regards Petr [EMAIL PROTECTED] 724008364, 581252140, 581252257 [EMAIL PROTECTED] napsal dne 02.06.2008 16:14:32: Hi Petr, Thanks for your reply. See below. At 05:58 AM 6/2/2008, Petr PIKAL wrote: Hi I did not see any response yet so I try a kick. Each object in R has some attributes which can be revealed by attributes(object) Some of them are useful for methods and tell R how to handle particular object with a method. There are other options how to evaluate your object e.g. str, typeof, mode. If you went through intro manual you could find that there are different types of objects like vectors, matrices, data.frames, arrays, and lists. And probably some others. Output from by is list or array and you can handle such objects in many ways. I understand all this in general. I am a C++ programmer with decades of experience, so I fully understand object-oriented concepts. My question is: How does one learn the specifics? For the case at hand, what are the specialized methods associated with class by? Are there clever things I can do with it? Is there documentation for class by? What are the browsing/exploring approaches one might use to learn about that class? So far, the main approach I have is interactive experimentation, yielding slow knowledge accretion. Is there anything more efficient? I have a moderate pile of R books, they are helpful, but obviously don't cover every detail of every situation. BTW it is hard to tell what is desired result is as we do not have D60. Agreed and I could supply some example data if you want. I speculated that experienced users could answer my question on formal grounds, but perhaps this speaks to my general issue: questions like this aren't easily answered without running experiments. At the moment, my code seems to be working. I don't find that very reassuring. I may have to get used to an R culture that is different from my prior world. Eg. when I do WM = by( D60, D60[ KeyProfA], FUN=function(x) weighted.mean( x$IAC, x$Wt)) Error in by(D60, D60[KeyProfA], FUN = function(x) weighted.mean(x$IAC, : object D60 not found I get an error. Better then using by is maybe to use ave which retains number of rows, but I am not sure if it can be adopted to weighted mean. Regards Petr [EMAIL PROTECTED] 724008364, 581252140, 581252257 [EMAIL PROTECTED] napsal dne 30.05.2008 16:00:50: Dear R-ers, My aggregation saga continues. Using the following sequence, I can calculate any statistic for row groups and merge the result back to all associated rows ... WM = by( D60, D60[ KeyProfA], FUN=function(x) weighted.mean( x$IAC, x$Wt)) D60$IAC.WM = as.numeric( WM[ D60$KeyProfA]) class( WM) [1] by Questions ... 1) Is this a reasonable way to obtain the desired result? 2) What can one glean by knowing the class of WM (by)? It appears to me that class is a pretty shallow attribute in R ... just an associated string that selects among methods in some contexts. Is that really all there is to it? Is there a way to discover what generic methods are aware of a given class? In other words, who cares if WM is a by ... what does that do for me? In my traditional universe (C++) I can grep and discover what methods are virtual, who inherits from whom, etc. In R, the documentation appears silent on what is a by (correct me if I'm wrong). In addition, I have found no way to broadly search code to learn things. (Displaying single functions is useful but hardly broad.) How does one learn R more efficiently than randomly discovering how to avoid error messages? (For example, I now know that a by cannot be coerced into a data.frame (although it seems to me that such a conversion could be usefully defined), so now I don't hit myself on the head with that particular hammer.) Chip Barnaby - Chip Barnaby [EMAIL PROTECTED] Vice President of Research Wrightsoft Corp. 781-862-8719 x118 voice 131 Hartwell Ave 781-861-2058 fax Lexington, MA 02421 www.wrightsoft.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. - Chip Barnaby [EMAIL
Re: [R] probleme with R CMD check
c == cgenolin [EMAIL PROTECTED] on Tue, 03 Jun 2008 09:55:15 +0200 writes: provide commented, minimal, self-contained, reproducible code. Please do -- both -- c Sorry... Usualy, I do... c --- 8 c userA - function(x)x+1 c privateA - function(x)x+2 c .userB - function(x)x+10 c .privateB - function(x)x+20 c userC- function(x)userA(privateA(x)) c privateC - function(x).userB(.privateB(x)) c userD- function(x)userA(.userB(x)) c privateD - function(x)privateA(.privateB(x)) c --- 8 If I execute these in an empty R session, and do package.skeleton(EXpkg) system(R CMD check EXpkg) I can NOT see the problem you describe below. Probably you'd rather should upload the pkg.tar.gz to a public place, to make your problem reproducible. Martin c == cgenolin [EMAIL PROTECTED] on Tue, 03 Jun 2008 00:32:13 +0200 writes: c Hi the list. c I got a probleme with R CMD check. I run a package.skeleton on a very c simple code (four toy function, no probleme with the R CMD build). But c on the R CMD check packClassique, I get : c * checking for unstated dependencies in R code ... WARNING c Erreur dans .find.package(package, lib.loc) : aucun package nommé c 'packClassique' n'est trouvé c Calls: Anonymous - .find.package c Excecution hated [French=Exécution arrêtée] c See the information on DESCRIPTION files in the chapter 'Creating R c packages' of the 'Writing R Extensions' manual. c * checking S3 generic/method consistency ... WARNING c Erreur dans .find.package(package, lib.loc) : aucun package nommé c 'packClassique' n'est trouvé c Calls: Anonymous - .find.package c Exécution arrêtée c And so on. c Any idea on what is wrong ? No. c Christophe c __ c R-help@r-project.org mailing list c https://stat.ethz.ch/mailman/listinfo/r-help c PLEASE do read the posting guide http://www.R-project.org/posting-guide.html c and provide commented, minimal, self-contained, reproducible code. Please do -- both -- Martin c c Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre __ 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] Rpart and case weights: working with functions
I can't get rpart accept case weights defined inside a function.
It keeps using the copy defined in the global environment (if they
exists) instead of the function-defined ones.
Here is what I do:
test.function - function (formula, data) {
weights - rep(.1, 100)
rpart(formula, data, weights)
}
test.function(x~y, data)
And I get an error:
Error in model.frame(formula, rownames, variables, varnames, extras, extranames, :
invalid type (closure) for variable '(weights)'
If I define weights in the global environment, it uses this instead of
the function-defined one (which can be verified by
.Last.value$frame$wt[1]: it should equal sum(weights) and actually
equals the sum of global weights, not the function one).
I tried to pass a named argument (weights=weights), using other names
(w, foo, ...), or both, but still it doesn't work. I found nothing in
rpart doc about that behaviour...
It was tested on R 2.7.0 (Windows XP) and R 2.5.1 (Linux kernel 2.6.9).
For the moment, the only workaround I found is to use/modify the global
weights using - (not very satisfying).
What did I wrong? And what should I do to get it work (i.e. using the
copy of weights defined inside the function)?
Thanks in advance for your help.
Xavier Robin
--
Xavier Robin
Biomedical Proteomics Research Group (BPRG)
Department of Structural Biology and Bioinformatics (DBSB)
Geneva University Medical Center (CMU)
1, rue Michel Servet - CH-1211 Genève 4 - Switzerland
Tel: (+41 22) 379 53 21
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] mtable and plm
Dear all, I'm trying to generate latex-formatted tables for panel data regressions using the mtable function of the memisc package, which is quite good. I use the plm package for panel data regression. Unfortunately, it seems that mtable works very well when using either lm or glm, but it encounters some problems when using plm. In particular, the error message I get is: (mtable.my.example-mtable(My_example=zzwith)) Error in FUN(X[[1]], ...) : no applicable method for getSummary I guess I'm missing something (I'm not an expert neither in R nor in generating latex-formatted tables) and perhaps by specifying some options my problems would be fixed. Kind regards, Emili __ 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] matlab eigs function in R
Hello Does anybody know how one can compute d largest eigenvalues/eigenvectors in R, like in MATLAB eigs function ? eigen function computes all eigenvectors/eigenvalues, and they are slightly different than those generated by matlab eigs. Thanks in advance -- View this message in context: http://www.nabble.com/matlab-eigs-function-in-R-tp17619641p17619641.html 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 using jri0.4-1 y R 2.7.0
Hello, this is the first time I send a mail to r-help mailing list. I'm developing a program in java with calls in R and I can`t use jri 0.4-1 with R 2.7 or 2.6 .but it runs with 2.4. The problem that I get when using the latest version of R is as follows: Cannot find JRI native library! Please make sure that the JRI native library is in a directory listed in java.library.path. java.lang.UnsatisfiedLinkError: C:\JRI_0.4-1\JRI\jri.dll: No se encontró el proceso especificado at java.lang.ClassLoader$NativeLibrary.load(Native Method) at java.lang.ClassLoader.loadLibrary0(Unknown Source) at java.lang.ClassLoader.loadLibrary(Unknown Source) at java.lang.Runtime.loadLibrary0(Unknown Source) at java.lang.System.loadLibrary(Unknown Source) at org.rosuda.JRI.Rengine.clinit(Rengine.java:9) at vista.main.Main.main(Main.java:12) C:\JRI_0.4-1\JRI\j is included in the system path (in fact, the program runs fine with R 2.4.0). I wonder if someone also has this problem and how it can solve. Any suggestions are highly appreciated, Thanks, Borja [[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] Rpart and case weights: working with functions
'weights' should be a column in your 'data': that is the standard way to
specify weights to a model-fitting function.
On Tue, 3 Jun 2008, Xavier Robin wrote:
I can't get rpart accept case weights defined inside a function.
It keeps using the copy defined in the global environment (if they exists)
instead of the function-defined ones.
Here is what I do:
test.function - function (formula, data) {
weights - rep(.1, 100)
rpart(formula, data, weights)
}
test.function(x~y, data)
And I get an error:
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames, : invalid type (closure) for variable '(weights)'
If I define weights in the global environment, it uses this instead of the
function-defined one (which can be verified by .Last.value$frame$wt[1]: it
should equal sum(weights) and actually equals the sum of global weights, not
the function one).
I tried to pass a named argument (weights=weights), using other names (w,
foo, ...), or both, but still it doesn't work. I found nothing in rpart doc
about that behaviour...
It was tested on R 2.7.0 (Windows XP) and R 2.5.1 (Linux kernel 2.6.9).
For the moment, the only workaround I found is to use/modify the global
weights using - (not very satisfying).
What did I wrong? And what should I do to get it work (i.e. using the copy of
weights defined inside the function)?
Thanks in advance for your help.
Xavier Robin
--
Xavier Robin
Biomedical Proteomics Research Group (BPRG)
Department of Structural Biology and Bioinformatics (DBSB)
Geneva University Medical Center (CMU)
1, rue Michel Servet - CH-1211 Genève 4 - Switzerland
Tel: (+41 22) 379 53 21
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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] wildcard symbol or character
At 03:07 03/06/2008, john.polo wrote: hello all, i want to split a list into smaller lists. the list looks like this: CW-W730 CW-W720 CW-W710 CW-W700 CW-W690 CW-W680 CW-W670 CW-W660 CE-W997 CE-W987 CE-W977 CE-W967 CE-W956 CE-W944 CE-W934 CE-W924 7W-W760 7W-W750 7W-967W-941 7W-932 7W-923 7W-914 7W-905 7E-W565 7E-W555 7E-W545 7E-W535 7E-W525 7E-906 7E-850 7E-840 ... i want the smaller lists to be based on the first two characters, like CW or 7E. i tried split() where the f variable = c(1E-*,1W-*,2E-*,2W-*,5E-*,5W-*,7E-*,7W-*,CE-*,CW-*), but * doesn't work as a wildcard as i had hoped. can someone tell me the appropriate wildcard character/symbol to use, please? Did you really use split()? I suspect that ?strsplit might help you and you can follow the link to regular expressions or do ?regexp for enlightenment on the wonders of regular expressions. As another poster has mentioned you can of course use substr() in this case but regular expressions enable you to do far more. john Michael Dewey http://www.aghmed.fsnet.co.uk __ 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] Rpart and case weights: working with functions
A bit of fiddling suggests that the problem is less to do with rpart
(which will quite happily acept weights defined inside a function) and
more to do with the formula argument to the test function.
This is probably because defining the formula in the global environment
(as you implicitly do by placing it in the function call) drags the
original formula environment along with it; try
f-function(form) str(form)
f(y~x)
to see what I mean.
As a work-round, try something lik
test.function - function (formula.str, data) {
weights - rep(.1, 8)
rpart(as.formula(formula.str), data, weights)
}
which works if formula.str is a string instead of a formula object.
Alternatively,
test.function - function (form, data) {
weights - rep(.1, 8)
environment(form)-environment() #re-sets the formula environment
rpart(form, data, weights)
}
test.function(y~x,df)
### SEEMED to work - though it looks like the sort of kludge an expert
would quail at; there's
### bound to be a right way to get the formula evaluated in the current
environment.
Xavier Robin [EMAIL PROTECTED] 03/06/2008 10:33:06
I can't get rpart accept case weights defined inside a function.
It keeps using the copy defined in the global environment (if they
exists) instead of the function-defined ones.
***
This email and any attachments are confidential. Any use...{{dropped:8}}
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[R] predict arfima
I noticed that both in the fArma and fracdiff packages it is not possible to predict an object fitted with an ARFIMA model. Moreover, the ox link is no more available. However, is it possible to find the coefficient d of differentiation of a time series, and then predict the time series by apply an arma model to the filtered time series ?? Are there better or other methods to predict ARFIMA models ? -- View this message in context: http://www.nabble.com/predict-arfima-tp17621431p17621431.html 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] Cluster analysis with numeric and categorical variables
Dear all, I would like to perform a clustering analysis on a data frame with two coordinate variables (X and Y) and a categorical variable where only a != b can be established. As far as I understood classification analyses, they are not an option as they partition the training set only in k classes of the test set. By searching through the book Modern Applied Statistics with S I did not find a satisfactory solution. I will be grateful for any suggestions. Best regards Miha __ can.html __ 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] Swap variables in data.frame
Birgit Lemcke wrote: I have a dataframe and two of my variables are in the wrong position and I would like to swap those variables. In addition to the other solutions posted, if you prefer to reference the columns by name rather than by index, you could use subset() dat - data.frame(a = letters[1:3], b = LETTERS[1:3], c = 1:3, d = 3:1) subset(dat, select = c(b, a, c, d)) ## or equivalently, something like: subset(dat, select = c(b:a, c:d)) --Jim James A. Rogers, Ph.D. Associate Director, Neuroscience Statistics Pfizer Global RD New London 50 Pequot Avenue (MS 6025-B2131) New London, CT 06320 office: (860) 732-0783 cell: (860) 501-7228 fax: (860) 686-7866 __ 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] regsubsets - package(leaps)
Maura E Monville maura.monville at gmail.com writes: Please, can someone suggest me where to find a description for the attributes of the summary of regsubsets, that is: which rsqrssadjr2 cp bicoutmat obj ?? The docs say: An object of class regsubsets containing no user-serviceable parts. It is designed to be processed by summary.regsubsets. So if you don't want to dissect the code that generates it, it is probably best to look what summary.regsubsets does the non-serviceable parts, and copy/modify the code to adapt to your needs. Dieter __ 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] matlab eigs function in R
Dear kayteck, Function eigen (see ?eigen) will do what you want. HTH, Jorge On Tue, Jun 3, 2008 at 5:42 AM, kayteck_master [EMAIL PROTECTED] wrote: Hello Does anybody know how one can compute d largest eigenvalues/eigenvectors in R, like in MATLAB eigs function ? eigen function computes all eigenvectors/eigenvalues, and they are slightly different than those generated by matlab eigs. Thanks in advance -- View this message in context: http://www.nabble.com/matlab-eigs-function-in-R-tp17619641p17619641.html 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. [[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] transforming output of grid.locator() to coordinates of a leaf viewport
Paul,
Thanks very much! Your example code below shows exactly how to do what I wanted.
-Ben
p.s., For the record,
transRight - current.transform()
after the second call to pushViewport() seems to have gotten deleted from you
example code below, but that was obvious.
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Paul Murrell
Sent: Monday, June 02, 2008 10:05 PM
To: Wittner, Ben, Ph.D.
Cc: [EMAIL PROTECTED]
Subject: Re: [R] transforming output of grid.locator() to coordinates of a
leaf viewport
Hi
Wittner, Ben, Ph.D. wrote:
Hadley, In my application the leaf viewports will not overlap, but I
guess that
would not necessarily be the case for all applications. In any event, do
you
happen to know how to transform coordinates in the top-level viewport to
coordinates in another viewport in the tree? Thanks. -Ben
current.transform() transforms from *inches* within the current viewport
to *inches* on the overall device. Sounds like you need the inverse
transform.
If you are in a position to be able to enumerate all of your leaf
viewports, then this may be a possible approach:
- for each leaf viewport, visit the viewport and record the
current.transform() for each leaf viewport. Also record the size of the
current viewport (in inches).
- capture a click on the device (current viewport should be ROOT) in
*inches*, then iterate through the leaf viewports to determine which one
was clicked in.
- to determine whether the click was within the viewport, use something
like the following function (and check whether both new locations are
positive and smaller than the size of the viewport (in inches)):
newloc - function(loc, trans) {
temploc - c(loc, 1) %*% trans
(temploc/temploc[3])[-3]
}
Here's a simple example:
# two leaf viewports
# (one on the left half of the device, one on the right)
grid.newpage()
pushViewport(viewport(x=0, width=.5, just=left, name=left))
transLeft - current.transform()
sizeLeft - c(convertWidth(unit(1, npc), inches, valueOnly=TRUE),
convertHeight(unit(1, npc), inches, valueOnly=TRUE))
# Draw a rect for visual reference
grid.rect(gp=gpar(fill=hcl(240, 60, 80)))
upViewport()
pushViewport(viewport(x=.5, width=.5, just=left, name=right))
sizeRight - c(convertWidth(unit(1, npc), inches, valueOnly=TRUE),
convertHeight(unit(1, npc), inches, valueOnly=TRUE))
heightRight - convertHeight(unit(1, npc), inches, valueOnly=TRUE)
grid.rect(gp=gpar(fill=hcl(120, 60, 80)))
upViewport()
# Get a click
# (current viewport is the ROOT viewport)
click - grid.locator(unit=inches)
# For each leaf viewport, calculate where the click was
leftClick - newloc(unlist(click), solve(transLeft))
rightClick - newloc(unlist(click), solve(transRight))
# Which one was it in ?
all(leftClick 0 leftClick sizeLeft)
all(rightClick 0 rightClick sizeRight)
Does that help ?
Paul
From: hadley wickham [mailto:[EMAIL PROTECTED]
Sent: Sun 6/1/2008 3:24 PM
To: Wittner, Ben, Ph.D.
Cc: [EMAIL PROTECTED]
Subject: Re: [R] transforming output of grid.locator() to coordinates of
a leaf
viewport
Ben,
What if the click occurs over multiple viewports?
Hadley
On Mon, Jun 2, 2008 at 6:50 AM, Wittner, Ben, Ph.D.
[EMAIL PROTECTED] wrote:
Short form:
How do I transform the output of grid.locator() (or
grid.locator(unit='npc')) to the native (or npc) coordinates of a
viewport
other
than the top-level viewport?
Thanks in advance. -Ben
Long form:
I would like the user to be able to click anywhere on
the R
graphics window. I would then like to figure out which leaf viewport
the user
clicked in and compute the native coordinates in that leaf viewport of
the
user's click.
I saw a 2005 response by Paul Murrell to a post by Gabor
Grothendieck roughly on this topic in which Paul suggested looking at
trellis.focus(). I've looked at trellis.focus() and
trellis.clickFocus(), but
they don't appear to do what I want in that a) it would appear that my
user
would have to click twice, once to specify which leaf viewport and then
again
to
specify which point in that viewport and b) trellis.clickFocus()
appears to
use
lots of information from the trellis package, which I'm not using.
So I decided to try to figure out the native coordinates
of the
click in each leaf viewport, to a) see whether the click is within the
plotting
region for that viewport and b) use those coordinates to take the
appropriate
action if it is. But I don't seem to be able to figure out how to
translate
from
the top-level viewport coordinates to those of a leaf viewport. I tried
interpreting the 3X3 matrix returned by current.transform() as an
affine
transformation in the x,y plane in
Re: [R] Cluster analysis with numeric and categorical variables
Dear Miha, a general way to do this is as follows: Define a distance measure by aggregating the Euclidean distance on the (X,Y)-space and the trivial 0-1 distance (0 if category is the same) on the categorial variable. Perform cluster analysis (whichever you want) on the resulting distance matrix. Note that there is more than one way to do this. The 0-1-distance could be incorporated in the definition of the Euclidean distance (instead of (x_i-y_i)^2), or a weighted average of the distances in X-, Y- and categorial space could be computed. Weights of variables (including possibly rescaling) have to be decided. How to do this precisely should depend on the subject matter and prior information about variable importance etc. In absence of such information, you may standardise the variablewise sums of squared pairwise distances to be equal. Hope this helps (and you can figure out the relevant R code yourself). Christian On Tue, 3 Jun 2008, Miha Staut wrote: Dear all, I would like to perform a clustering analysis on a data frame with two coordinate variables (X and Y) and a categorical variable where only a != b can be established. As far as I understood classification analyses, they are not an option as they partition the training set only in k classes of the test set. By searching through the book Modern Applied Statistics with S I did not find a satisfactory solution. I will be grateful for any suggestions. Best regards Miha __ can.html __ 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. *** --- *** Christian Hennig University College London, Department of Statistical Science Gower St., London WC1E 6BT, phone +44 207 679 1698 [EMAIL PROTECTED], www.homepages.ucl.ac.uk/~ucakche __ 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] JGR / linux
Hi all,
i'm trying to install JGR on linux (see bottom), but it runs into errors.
The bottom of the sequence below shows JavaJD could not be found
Any suggestion, please?
$ sudo apt-get install sun-java6-jdk
$ sudo update-alternatives --config java
There are 5 alternatives which provide `java'.
Selection Alternative
---
1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
2 /usr/bin/gij-4.1
3 /usr/bin/gij-4.2
4 /usr/lib/jvm/java-gcj/jre/bin/java
+ 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
$sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_03
Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64
-L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib
-L/usr/lib -ljvm
JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
Updating Java configuration in /etc/R
Done.
$ sudo R
R version 2.5.1 (2007-06-27)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
install.packages('JGR', dep=TRUE)
Warning in install.packages(JGR, dep = TRUE) :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ‘JavaGD’
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
Content type 'application/x-gzip' length 86505 bytes
opened URL
==
downloaded 84Kb
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
Content type 'application/x-gzip' length 426244 bytes
opened URL
==
downloaded 416Kb
* Installing *source* package 'JavaGD' ...
checking for gcc... gcc-4.2 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags : '-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux -Iinclude -fpic -g
-O2 -c
Re: [R] matlab eigs function in R
Jorge Ivan Velez [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Dear kayteck, Function eigen (see ?eigen) will do what you want. HTH, He had looked, but since eigen returns both eigenvalues and eigenvectors, and does so in a list, perhaps he needs advice about how to extract his values from the list structure. x - matrix(c(1:5, (1:5)^2, (1:5)^(1/2), 0,0,0,1,0, 0,0,0,0,1),5, 5) str(eigen(x)) #List of 2 # $ values : cplx [1:5] 7.43+0i 1.00+0i 1.00+0i ... # $ vectors: cplx [1:5, 1:5] 0.0699+0i 0.1600+0i 0.2894+0i ... d - 3 eigen(x)$values[1:d] [1] 7.431675+0i 1.00+0i 1.00+0i #no need to sort since eigen does that by default. Not sure we can help him out regarding the slight difference btwn Matlab values and R values due to the unnecessary vagueness of his concern. -- David Winsemius Jorge On Tue, Jun 3, 2008 at 5:42 AM, kayteck_master [EMAIL PROTECTED] wrote: Hello Does anybody know how one can compute d largest eigenvalues/eigenvectors in R, like in MATLAB eigs function ? eigen function computes all eigenvectors/eigenvalues, and they are slightly different than those generated by matlab eigs. Thanks in advance -- __ 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] Rpart and case weights: working with functions
S Ellison a écrit :
As a work-round, try something lik
test.function - function (formula.str, data) {
weights - rep(.1, 8)
rpart(as.formula(formula.str), data, weights)
}
which works if formula.str is a string instead of a formula object.
Ok, I think I got the point. The only problem with transforming the
string to a formula is that rpart raises another error:
Error in t.default(x) : argument is not a matrix
test.function - function (form, data) {
weights - rep(.1, 8)
environment(form)-environment() #re-sets the formula environment
rpart(form, data, weights)
}
This works perfectly well. It will be good enough for what I need.
Thanks a lot ;-)
Xavier
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Re: [R] Swap variables in data.frame
Thanks might be easier in my case because I have so many variables. Could have found this solution on my own. Birgit Rogers, James A [PGRD Groton] wrote: Birgit Lemcke wrote: I have a dataframe and two of my variables are in the wrong position and I would like to swap those variables. In addition to the other solutions posted, if you prefer to reference the columns by name rather than by index, you could use subset() dat - data.frame(a = letters[1:3], b = LETTERS[1:3], c = 1:3, d = 3:1) subset(dat, select = c(b, a, c, d)) ## or equivalently, something like: subset(dat, select = c(b:a, c:d)) --Jim James A. Rogers, Ph.D. Associate Director, Neuroscience Statistics Pfizer Global RD New London 50 Pequot Avenue (MS 6025-B2131) New London, CT 06320 office: (860) 732-0783 cell: (860) 501-7228 fax: (860) 686-7866 __ 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. - The art of living is more like wrestling than dancing. (Marcus Aurelius) -- View this message in context: http://www.nabble.com/Swap-variables-in-data.frame-tp17597476p17626237.html 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] JGR / linux
Your R is way too old: please follow the advice in the posting guide.
I suspect the current JavaJD requires R = 2.7.0 from the errors you are
getting below.
On Tue, 3 Jun 2008, g-h-d wrote:
Hi all,
i'm trying to install JGR on linux (see bottom), but it runs into errors.
The bottom of the sequence below shows JavaJD could not be found
Any suggestion, please?
$ sudo apt-get install sun-java6-jdk
$ sudo update-alternatives --config java
There are 5 alternatives which provide `java'.
Selection Alternative
---
1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
2 /usr/bin/gij-4.1
3 /usr/bin/gij-4.2
4 /usr/lib/jvm/java-gcj/jre/bin/java
+ 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
$sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_03
Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64
-L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib
-L/usr/lib -ljvm
JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
Updating Java configuration in /etc/R
Done.
$ sudo R
R version 2.5.1 (2007-06-27)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
install.packages('JGR', dep=TRUE)
Warning in install.packages(JGR, dep = TRUE) :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ‘JavaGD’
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
Content type 'application/x-gzip' length 86505 bytes
opened URL
==
downloaded 84Kb
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
Content type 'application/x-gzip' length 426244 bytes
opened URL
==
downloaded 416Kb
* Installing *source* package 'JavaGD' ...
checking for gcc... gcc-4.2 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags : '-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
[R] surprising predicting capabilities
Hi,
I noticed the following fortune in R 2.7 and 2.6.2:
fortune('Spreads')
If anything, there should be a Law: Thou Shalt Not Even Think Of Producing A
Graph That Looks Like Anything From A Spreadsheet.
-- Ted Harding (in a discussion about producing graphics)
R-help (August 2008)
Just wondering, what function and library gave this detailed prediction?
Cheers
__
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] JGR / linux
Thanks.
I basically followed the steps in http://lib.stat.cmu.edu/R/CRAN/, and those
below for JGR and it worked.
...but there are problems with help files e.g. ?matrix generates the
following message:
/tmp/RtmpvxsnQa/.R/doc/html/packages.html (No such file or directory)
g-h-d wrote:
Hi all,
i'm trying to install JGR on linux (see bottom), but it runs into errors.
The bottom of the sequence below shows JavaJD could not be found
Any suggestion, please?
$ sudo apt-get install sun-java6-jdk
$ sudo update-alternatives --config java
There are 5 alternatives which provide `java'.
Selection Alternative
---
1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
2 /usr/bin/gij-4.1
3 /usr/bin/gij-4.2
4 /usr/lib/jvm/java-gcj/jre/bin/java
+ 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
$sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_03
Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Java library path:
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm
JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
Updating Java configuration in /etc/R
Done.
$ sudo R
R version 2.5.1 (2007-06-27)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
install.packages('JGR', dep=TRUE)
Warning in install.packages(JGR, dep = TRUE) :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ‘JavaGD’
trying URL
'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
Content type 'application/x-gzip' length 86505 bytes
opened URL
==
downloaded 84Kb
trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
Content type 'application/x-gzip' length 426244 bytes
opened URL
==
downloaded 416Kb
* Installing *source* package 'JavaGD' ...
checking for gcc... gcc-4.2 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags : '-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib
Re: [R] 'asymmetric span' for 2D loess?
Dear Prof Ripley, Hello, I am interested in performing a 2D loess smooth on microarray data, i.e. log2 ratios on a 2D grid, using different spans in the horizontal and vertical directions (the immediate reason being that replicate spots are laid out in the horizontal direction). Is it possible to do this in R? Functions like loess(stats) seem to apply the same span for all predictors, which carries over to functions like ma2D(marray). See the next comment. 'span' applies to 2D distances, and I think you need to rescale your inputs so Euclidean distance is appropriate. That's a great idea. As an elementary second question, are there circumstances where one expects to see a substantial difference in the fits between say loess(y ~ x1 + x2) and loess(y ~ x1 * x2) with an interaction term (and if so, what are they)? From the help page: formula: a formula specifying the numeric response and one to four numeric predictors (best specified via an interaction, but can also be specified additively). Will be coerced to a formula if necessary. So the two versions both specify smoothing in 2D. You can use things like lo(x1) + lo(x2) in some gam fits. Hadn't thought of that, I will explore this. It often helps to read the primary sources, in this case chapters in the White Book (Chambers Hastie, nominally 1992, actually published in 1991). -- 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 Thanks very much for the help. Nice photos on the Web, by the way. Regards, _Taku Taku A. Tokuyasu, PhD UCSF Helen Diller Family Comprehensive Cancer Center San Francisco, CA 94143-0808 __ 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] surprising predicting capabilities
That is actually from August 2007 (typo in the fortunes package).
If you do
RSiteSearch('Thou Shalt Not Even Think Graph Spreadsheet')
Then it will bring up the actual post and you can read it in context (along
with the posts that lead to it and those that followed).
Basically, Ted was trying to shorten my soapbox without knocking me off of it
after I replied to someone who wanted to add the values to a barchart like a
particular spreadsheet.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of chaogai
Sent: Tuesday, June 03, 2008 10:16 AM
To: r-help@r-project.org
Subject: [R] surprising predicting capabilities
Hi,
I noticed the following fortune in R 2.7 and 2.6.2:
fortune('Spreads')
If anything, there should be a Law: Thou Shalt Not Even Think
Of Producing A Graph That Looks Like Anything From A Spreadsheet.
-- Ted Harding (in a discussion about producing graphics)
R-help (August 2008)
Just wondering, what function and library gave this detailed
prediction?
Cheers
__
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] gam and prior
Hi. I am running a gam for covariate forward inclusions/ backward exclusions, using the weight options as follow. library(gam) gam.object1-gam(ET~1, data=nonp.dat, weights=PROBA) summary(gam.object1) step.object1-step.gam(gam.object1, direction=both , trace=T, scope=list(CRCL=~1+CRCL+ns(CRCL,2), HT=~1+HT+ns(HT,2), WT=~1+WT+ns(WT,2), SER=~1+SER+ns(SER,2), ALAT=~1+ALAT+ns(ALAT,2), AGE=~1+AGE+ns(AGE,2), UNI1=~1+UNI1+ns(UNI1,2), as.factor(SEX)=~1+as.factor(SEX), as.factor(COME)=~1+as.factor(COME), as.factor(SMOK)=~1+as.factor(SMOK))) summary(step.object1) The problem is that I am not sure how to use this weight since my AIKAIKE criteria goes really high as soon as I include the weights (that is, by the way, a probability (very small number then)) and then, it includes all the covariates in the scope while it should include only the one created in a previous step. I heard about a prior.weights() option as well but using it does not affect the results at all. Some suggestions or help on how to use prior.weights or weights in gam or even in glm will be very welcome as it is not really well documented. __ 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] request: An array declarion problem
Dear R users
I tried a lot to solve the following problem but could not. I have two arrays
having same order i.e 1 by 150.
j=10; ss=150; r=array(0 , c( j , ss )); rr=array(0 , c( j , ss )); r1=array(0 ,
c( j-1 , ss )); r2=array(0 , c( j-1 , ss ));
r3=array(0 , c( 2 , ss ))
for(i in 1:j-1){
r1[ i , ] - r[ j+1, ]-r[ j, ]; r2[ i , ] - rr[ j+1,
]-rr[ j, ]
}
Now i want to rbind the results of r1 and r2 for each time. Now the order of
r3[ j, ] will become 2 by 150. I used the following form in the loop
r3[ i,]=rbind(r1[ i, ], r2[ i, ])
But there is an error message
Error in r3[i, ] = rbind(r1[i, ], r2[i, ]) : number of items to replace is not
a multiple of replacement length
I am looking for some suggestion to solve the problem. Thanks and
best regards
Muhammad Azam
Ph.D. Student
Department of Medical Statistics,
Informatics and Health Economics
University of Innsbruck, Austria
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] wildcard symbol or character
Michael Dewey wrote: split() where the f variable = c(1E-*,1W-*,2E-*,2W-*,5E-*,5W-*,7E-*,7W-*,CE-*,CW-*), but * doesn't work as a wildcard as i had hoped. can someone tell me the appropriate wildcard character/symbol to use, please Did you really use split()? yes, i did. the output looked like this: split(rtt,RTT) $`1E-.` [1] CW-W739 CW-W729 CW-W719 CW-W709 CW-W699 CW-W689B CW-W679 CW-W669 ... $`1W-.` [1] CW-W738 CW-W728 CW-W718 CW-W708 CW-W698 CW-W688 CW-W678 CW-W668 ... I suspect that ?strsplit might help you and you can follow the link to regular expressions or do ?regexp for enlightenment on the wonders of regular expressions. As another poster has mentioned you can of course use substr() in this case but regular expressions enable you to do far more. i haven't tried any of other solution suggested in other posts yet. thanks for your reply. john __ 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] matlab eigs function in R
Presumably the original poster was looking for a function that would compute just the largest five eigenvalues and associated vectors, because that is enormously more efficient for a large matrix than computing all of them. eigen() computes all of them. One way to compute just a few is to use svd(), where you can specify the number of left and right singular vectors to compute. -thomas On Tue, 3 Jun 2008, David Winsemius wrote: Jorge Ivan Velez [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Dear kayteck, Function eigen (see ?eigen) will do what you want. HTH, He had looked, but since eigen returns both eigenvalues and eigenvectors, and does so in a list, perhaps he needs advice about how to extract his values from the list structure. x - matrix(c(1:5, (1:5)^2, (1:5)^(1/2), 0,0,0,1,0, 0,0,0,0,1),5, 5) str(eigen(x)) #List of 2 # $ values : cplx [1:5] 7.43+0i 1.00+0i 1.00+0i ... # $ vectors: cplx [1:5, 1:5] 0.0699+0i 0.1600+0i 0.2894+0i ... d - 3 eigen(x)$values[1:d] [1] 7.431675+0i 1.00+0i 1.00+0i #no need to sort since eigen does that by default. Not sure we can help him out regarding the slight difference btwn Matlab values and R values due to the unnecessary vagueness of his concern. -- David Winsemius Jorge On Tue, Jun 3, 2008 at 5:42 AM, kayteck_master [EMAIL PROTECTED] wrote: Hello Does anybody know how one can compute d largest eigenvalues/eigenvectors in R, like in MATLAB eigs function ? eigen function computes all eigenvectors/eigenvalues, and they are slightly different than those generated by matlab eigs. Thanks in advance -- __ 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. Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ 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] wildcard symbol or character
Jorge Ivan Velez wrote: Dear John, Assuming that your information is in the list x, does substr(x,1,2) work for you? HTH, Jorge thanks for your reply Jorge. i will try substr(). john __ 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-2.7.0 rJava installation failure on x86_64
attempting to install rJava on R-2.7.0, x86_64 platform, config.log shows the following error: configure:3880: checking whether JNI programs can be compiled configure:3898: gcc -m64 -std=gnu99 -o conftest -g -O2 -I/path/to/x86-64-linux/jdk-1.6.0_06/jre/../include conftest.c -L/path/to/x86-64-linux/jdk-1.6.0_06/jre/lib/amd64/server -L/path/to/x86-64-linux/jdk-1.6.0_06/jre/lib/amd64 -L/path/to/x86-64-linux/jdk-1.6.0_06/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm 5 /path/to/x86-64-linux/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib/libc.a: could not read symbols: File format is ambiguous collect2: ld returned 1 exit status It looks like the command above could use /lib64/libc.so.6, but running R CMD javareconf shows that JNI linker flags don't contain any entry similar to '-L/lib64': -bash-3.00$ /path/to/noarch/bin/statcomp R-2.7.0 CMD javareconf Java interpreter : /path/to/x86-64-linux/bin/java Java version : 1.6.0_06 Java home path : /path/to/x86-64-linux/jdk-1.6.0_06/jre Java compiler : /path/to/x86-64-linux/bin/javac Java headers gen.: /path/to/x86-64-linux/bin/javah Java archive tool: /path/to/x86-64-linux/bin/jar Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm JNI cpp flags: -I$(JAVA_HOME)/../include Suggests on the root of the problem or best workarounds? -- Nathan __ 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 on plotting adjacent bars with barplot. Help request, please
hi ladyes and gentlemans of the R comunity.
i have the following graphical issue:
# say y is a matrix or a dataframe with
dim(51,nrow=17),hence 3 columns;
l-51
# now the 3 colums represents 3 different aspects of
my continuous variable (3 factors),plotted against a
categorical one;
n-levels(factor(x))
# i want to plot those 3 factors adjacently using the
barplot(), and possibly show error bars as well;
err-rep(1.2,17)
this is the function that i unsuccesfully wrote to do
this:
adj.bars-function(y,e,n,l){
both-numeric(l)
both[1:l%%2==1]-y[,1]
both[1:l%%2!=c(0,1)]-y[,2]
both[1:l%%2==0]-y[,3]
labels-character(l)
labels[1:l%%2==1]-n
xv-barplot(both,col=rep(c(1,2,3),17),
ylim=c(0,max(y)+e[1]),names=labels)
up-x[,1]+e
down-x[,1]-e
arrows(xv,up,xv,down,code=3,angle=90,length=0.025)
up2-x[,2]+e
down2-x[,2]-e
arrows(xv,up,xv,down,code=3,angle=90,length=0.025)
up3-x[,3]+e
down3-x[,3]-e
arrows(xv,up,xv,down,code=3,angle=90,length=0.025)
}
i guess the both instruction is fake 'cause the plot
looks really wrong.
i have also tried this other one.
rm(l)
l-17
adj.bars-function(y,e,n,l){
both-rep(c(1,1.5,2),l)
both[1:l%%2==1]-y[,1]
both[1:l%%2==1.5]-y[,2]
both[1:l%%2==0]-y[,3]
...
i thank you all for the attention, and i'll be
grateful if someone had simple tip to all this.
FEDERICO, undergraduate student in Insubria University
Varese, Italy.
___
http://www.ymailblogit.com/blog/
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] splitting data frame based on a criteria
Hi, I have a data frame that I want to split into two based on the values of a variable in it. The variable Y has numeric values ranging between 0 through 70. I want to plot the frequencies of another variable X in two different cases: - When Y = 0 and - When Y 0 How does one go about doing this? In general, I want to do several analyses with this data frame that are a variation of the above situation, i.e. they require splitting the data into different age, gender etc. and then calculating separate means, correlations and so on for the different groups into which the data frame would split. I am struggling with the correct syntax for achieving this. Reading through the documentation suggests that tapply and split may be the functions to use for my purposes but the examples in the documentations didn't help me understand how I could achieve this. I would appreciate any suggestions and help. Thanks, Marvin [[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] JGR / linux
On 3 June 2008 at 08:42, g-h-d wrote:
| I basically followed the steps in http://lib.stat.cmu.edu/R/CRAN/, and those
| below for JGR and it worked.
|
| ...but there are problems with help files e.g. ?matrix generates the
| following message:
|
| /tmp/RtmpvxsnQa/.R/doc/html/packages.html (No such file or directory)
I think you can ignore that. It's just a warning. The rest of your steps
were very sound.
In particular ...
| g-h-d wrote:
|
| Hi all,
|
| i'm trying to install JGR on linux (see bottom), but it runs into errors.
| The bottom of the sequence below shows JavaJD could not be found
|
| Any suggestion, please?
|
|
| $ sudo apt-get install sun-java6-jdk
|
| $ sudo update-alternatives --config java
|
| There are 5 alternatives which provide `java'.
|
| Selection Alternative
| ---
| 1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
| 2 /usr/bin/gij-4.1
| 3 /usr/bin/gij-4.2
| 4 /usr/lib/jvm/java-gcj/jre/bin/java
| + 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
... a very good idea to realign what command will default to being 'java' ...
| $sudo R CMD javareconf
| Java interpreter : /usr/bin/java
| Java version : 1.6.0_03
| Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/jre
| Java compiler : /usr/bin/javac
| Java headers gen.: /usr/bin/javah
| Java archive tool: /usr/bin/jar
... but given that javareconf also looks after javac and javah, I recommend
doing the same update-alternatives call for 'javah' and 'javac'.
I just re-did that on a Ubuntu 8.04, 32bit, machine and it re-built rJava,
JGR, JavaGD, ... without a hitch.
Dirk
| Java library path:
|
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
| JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
| -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
| -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm
| JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
| -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
|
| Updating Java configuration in /etc/R
| Done.
|
| $ sudo R
|
| R version 2.5.1 (2007-06-27)
| Copyright (C) 2007 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
|
| R is free software and comes with ABSOLUTELY NO WARRANTY.
| You are welcome to redistribute it under certain conditions.
| Type 'license()' or 'licence()' for distribution details.
|
| Natural language support but running in an English locale
|
| R is a collaborative project with many contributors.
| Type 'contributors()' for more information and
| 'citation()' on how to cite R or R packages in publications.
|
| Type 'demo()' for some demos, 'help()' for on-line help, or
| 'help.start()' for an HTML browser interface to help.
| Type 'q()' to quit R.
|
| install.packages('JGR', dep=TRUE)
| Warning in install.packages(JGR, dep = TRUE) :
| argument 'lib' is missing: using '/usr/local/lib/R/site-library'
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| also installing the dependency JavaGD
|
| trying URL
| 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
| Content type 'application/x-gzip' length 86505 bytes
| opened URL
| ==
| downloaded 84Kb
|
| trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
| Content type 'application/x-gzip' length 426244 bytes
| opened URL
| ==
| downloaded 416Kb
|
| * Installing *source* package 'JavaGD' ...
| checking for gcc... gcc-4.2 -std=gnu99
| checking for C compiler default output file name... a.out
| checking whether the C compiler works... yes
| checking whether we are cross compiling... no
| checking for suffix of executables...
| checking for suffix of object files... o
| checking whether we are using the GNU C compiler... yes
| checking whether gcc-4.2 -std=gnu99 accepts -g... yes
| checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
| checking how to run the C preprocessor... gcc-4.2 -std=gnu99 -E
| checking for grep that handles long lines and -e... /bin/grep
| checking for egrep... /bin/grep -E
| checking for ANSI C header files... yes
| checking for sys/wait.h that is POSIX.1 compatible... yes
| checking for sys/types.h... yes
| checking for sys/stat.h... yes
| checking for stdlib.h... yes
| checking for string.h... yes
| checking for memory.h... yes
| checking for strings.h... yes
| checking for inttypes.h... yes
| checking for stdint.h... yes
| checking for unistd.h... yes
| checking for string.h... (cached) yes
| checking sys/time.h usability... yes
| checking sys/time.h presence... yes
| checking for sys/time.h... yes
| checking for unistd.h... (cached) yes
| checking for an ANSI C-conforming const... yes
| checking whether time.h and
[R] adding column and pulling data from table
Hello to everyone, I have a general question about how to add a column to a table.I have a table that has 62 columns and 2000 rows.I am wanting to add a column on the left most row.I am wanting to label the rows g1 to g2000 I have the code of (g,c(1:nrow(dat)),sep=) for the right side of the assignment but do not know what function to use for the left side of the equation.I also have a similiar question as to how to select a particular portion of the table and to plot this. For example to select column 1 and 3 and to take the data from the first twenty rows from those columns and put this data onto a plot which I have allready coded.Lastly I would like to take all the points in a column (2000) and put them into a scatter plot.What is the command or function I would use to do this? Thank You Paul [[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] splitting data frame based on a criteria
?by may be helpful here eg if dat is your data.frame and yf is a factor (created using ifelse) use by(dat,yf,mean) to compute the means for each level of yf hth, Ingmar On Jun 3, 2008, at 8:37 PM, Marvin Lists wrote: Hi, I have a data frame that I want to split into two based on the values of a variable in it. The variable Y has numeric values ranging between 0 through 70. I want to plot the frequencies of another variable X in two different cases: - When Y = 0 and - When Y 0 How does one go about doing this? In general, I want to do several analyses with this data frame that are a variation of the above situation, i.e. they require splitting the data into different age, gender etc. and then calculating separate means, correlations and so on for the different groups into which the data frame would split. I am struggling with the correct syntax for achieving this. Reading through the documentation suggests that tapply and split may be the functions to use for my purposes but the examples in the documentations didn't help me understand how I could achieve this. I would appreciate any suggestions and help. Thanks, Marvin [[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] robust mlm in R?
Dear Michael,
I don't think that anyone else has suggested a fix, so here's one:
snip ---
# Mahalanobis Dsq for a matrix of variables
dsq - function(x, Sigma) {
if (missing(Sigma)) Sigma - cov(x, use=complete.obs)
dev - scale(x, scale=FALSE)
# DSQ - dev %*% solve(Sigma) %*% t(dev )
DSQ - apply(dev * (dev %*% solve(Sigma)), 1, sum)
return(DSQ)
}
# robust mlm via multivariate trimming a la Gnanadesikan, Kettering Wilks
rmlm.GKW - function(formula, weights, data, iter=3, pvalue=.01, ...) {
if (missing(data)) data - model.frame(formula)
if (missing(weights)) weights - rep(1, nrow(data))
last.weights - weights
for (i in 1:iter) {
data$weights - weights
mod - lm(formula=formula, data=data, weights=weights, ...)
res - residuals(mod)
coef - mod$coefficients
print (coef)
p - ncol(res)
DSQ - dsq(res)
prob - pchisq(DSQ, p, lower.tail=FALSE)
weights - ifelse( probpvalue, 0, weights)
nzero - which(weights==0)
print (nzero)
if (isTRUE(all.equal(weights, last.weights))) { break }
}
mod
}
snip ---
There were a scoping problem in the call to lm() and some other errors as
well.
I think that this revised function does what you want, but I'd also probably
program it differently, handling the standard model arguments in the
function and calling lm.wfit() for the computations.
I hope this helps,
John
--
John Fox, Professor
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
web: socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On
Behalf Of Michael Friendly
Sent: June-02-08 9:51 AM
To: [EMAIL PROTECTED]
Subject: Re: [R] robust mlm in R?
I had no on-list replies, so I cobbled up a function for the simplest
method I could think of -- iterative multivariate trimming, following
Gnanadesikan, Kettering Wilks, assigning 0 weights to observations
based on the Mahalanobis D^2 of residuals.
But I'm getting an error I don't understand, and neither traceback()
nor browser() gives me any insight. Can anyone tell me what is wrong
with the lm() call in rmlm.GKW below?
iris.rmod - rmlm.GKW(cbind(Sepal.Length, Sepal.Width, Petal.Length,
Petal.Width)~Species, data=iris)
Error in model.frame.default(formula = formula, data = data, subset =
subset, :
invalid type (closure) for variable '(weights)'
Here are the functions:
# Mahalanobis Dsq for a matrix of variables
dsq - function(x, Sigma) {
if (missing(Sigma)) Sigma - cov(x, use=complete.obs)
dev - scale(x, scale=FALSE)
# DSQ - dev %*% solve(Sigma) %*% t(dev )
DSQ - apply(dev * (dev %*% solve(Sigma)), 1, sum)
return(DSQ)
}
# robust mlm via multivariate trimming a la Gnanadesikan, Kettering
Wilks
rmlm.GKW - function(formula, data, subset, weights=NULL, iter=3,
pvalue=.01) {
if (missing(weights) | is.null(weights)) { weights - rep(1,
nrow(data)) }
last.weights - weights
for (i in 1:iter) {
mod - lm(formula=formula, data=data, subset=subset, weights=weights)
res - residuals(mod)
coef - mod$coefficients
print (coef)
p - ncol(res)
DSQ - dsq(res)
prob - pchisq(DSQ, p, lower.tail=FALSE)
weights - ifelse( probpvalue, 0, weights)
nzero - which(weights=0)
print (nzero)
if (all.equal(weights, last.weights)) { break }
}
}
Michael Friendly wrote:
I'm looking for something in R to fit a multivariate linear model
robustly, using
an M-estimator or any of the myriad of other robust methods for linear
models
implemented in robustbase or methods based on MCD or MVE covariance
estimation (package rrcov).
E.g., one can fit an mlm for the iris data as:
iris.mod - lm(cbind(Sepal.Length, Sepal.Width, Petal.Length,
Petal.Width) ~ Species, data=iris)
What I'd like is something like rlm() in MASS, but handling an mlm,
e.g.,
iris.mod - rmlm(cbind(Sepal.Length, Sepal.Width, Petal.Length,
Petal.Width) ~ Species, data=iris)
and returning a vector of observation weights in its result.
There's a burgeoning literature on this topic, but I haven't yet found
computational methods.
Any pointers or suggestions would be appreciated.
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
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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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the
Re: [R] matlab eigs function in R
Dear Thomas Yes, you're right. But I'm looking for this not only for computational cost reasons. eigen function from R has identical behavior to matlab function eig, but not to eigs. Even in matlab you can check that those function are not giving identical results. Here you have a short example : Suppose we have given a matrix M M = 1.2607 -3.55752.2968 0 0 0 -3.5575 10.1429 -6.5855 0 0 0 2.2968 -6.58554.2887 0 0 0 0 0 02.6359 -4.84892.2130 0 0 0 -4.84898.9217 -4.0728 0 0 02.2130 -4.07281.8598 For eig (R's eigen)we have: [V,eiggg]=eig(M); V = 0.5774 0 0 -0.7663 00.2820 0.5774 0 00.1389 0 -0.8046 0.5774 0 00.6273 00.5226 00.5774 -0.6857 00.4432 0 00.5774 -0.0410 0 -0.8155 0 00.57740.7267 00.3723 0 eiggg = -0. 0 0 0 0 0 0 -0. 0 0 0 0 0 00.0011 0 0 0 0 0 00.0252 0 0 0 0 0 0 13.4163 0 0 0 0 0 0 15.6671 And for matlab's eigs we have: [Y,eigenvals] = eigs(M,4,0,options) ; Y = -0.8147 -0.0106 -0. -0.5774 0.3802 -0.0143 -0. -0.5774 0.43440.02490. -0.5774 -0.03320.6871 -0.57740. 0.04300.0379 -0.57740. -0.0098 -0.7250 -0.57740. eigenvals = 0.0331 0 0 0 00.0011 0 0 0 00. 0 0 0 0 -0. As you can see, columns of chosen eigenvectors are different. I'm looking for function similar to eigs in R. I'll try with svd, which you have mentioned. Thank you for that idea, maybe it will be what i'm looking for. Kayteck -- View this message in context: http://www.nabble.com/matlab-eigs-function-in-R-tp17619641p17629655.html 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] adding column and pulling data from table
Paul
It is not entirely clear to me what you want to do. However, if you are
wanting to add row names then try
row.names(dat) - paste('g', 1:nrow(dat), sep='')
First twenty rows of columns 1:3 are obtained by
dat[1:20,1:3]
Regarding putting all the points in a column onto a scatterplot. One
usually has two variates for a scatterplot. Thus to make a scatter plot
of column 2 against column 1
plot(dat[,1], dat[,2])
Incidentally, subsetting is covered in the introductory manual and some
online texts.
HTH ..
Peter Alspach
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Paul Adams
Sent: Wednesday, 4 June 2008 7:08 a.m.
To: r-help@r-project.org
Subject: [R] adding column and pulling data from table
Hello to everyone,
I have a general question about how to add a column to a
table.I have a table that has 62 columns and 2000 rows.I am
wanting to add a column on the left most row.I am wanting to
label the rows g1 to g2000 I have the code of
(g,c(1:nrow(dat)),sep=) for the right side of the
assignment but do not know what function to use for the left
side of the equation.I also have a similiar question as to
how to select a particular portion of the table and to plot
this. For example to select column 1 and 3 and to take the
data from the first twenty rows from those columns and put
this data onto a plot which I have allready coded.Lastly I
would like to take all the points in a column (2000) and put
them into a scatter plot.What is the command or function I
would use to do this?
Thank You
Paul
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
The contents of this e-mail are privileged and/or confidential to the named
recipient and are not to be used by any other person and/or organisation.
If you have received this e-mail in error, please notify the sender and delete
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and provide commented, minimal, self-contained, reproducible code.
[R] How to solve a non-linear system of equations using R
Dear R-list members,
I've had a hard time trying to solve a non-linear system (nls) of equations
which structure for the equation i, i=1,...,4, is as follows:
f_i(d_1,d_2,d_3,d_4)-k_i(l,m,s) = 0(1)
In the expression above, both f_i and k_i are known functions and l, m and s
are known constants. I would like to estimate the vector d=(d_1,d_2,d_3,d_4)
which is solution of (1). Functions in R to estimate f_i-k_i are at the end
of this message.
Any help/suggestions/comments would be greatly appreciated.
Thanks in advance,
Jorge
# --
# Constants
# --
l=1
m=0.4795
s=0.4795
# --
# Functions to estimate f_i-k_i
# --
f1=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=2*d1+2*sqrt(2)*d1*d2+2*sqrt(3)*d2*d3+4*d3*d4-l*m*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f2=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=2*sqrt(2)*d2+2*d1^2+2*sqrt(6)*d1*d3+4*d2^2+4*sqrt(3)*d2*d4+6*d3^2+8*d4^2-l*(m^2+m^3*s^(-1))*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f3=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=6*d1+12*sqrt(2)*d1*d2+18*sqrt(3)*d2*d3+48*d3*d4+2*sqrt(6)*d3+4*sqrt(6)*d1*d4-l*(m^3+3*m^4*s^(-1)+3*m^6*s^(-2))*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f4=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=12*sqrt(2)*d2+12*d1^2+36*d2^2+72*d3^2+120*d4^2+20*sqrt(6)*d1*d3+56*sqrt(3)*d2*d4+4*sqrt(6)*d4-l*((m^4+6*m^6*s^(-1)+15*m^6*s^(-2)+15*m^7*s^(-3))-3*l^(2)*(m^2+m^3*s^(-1))^2)*(1+d1^2+d2^2+d3^2+d4^2)
res
}
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to solve a non-linear system of equations using R
Hi Jorge,
Have you tried to use systemfit package. In this package, this is a
function call nlsystemfit . This might help.
Chunhao
Quoting Jorge Ivan Velez [EMAIL PROTECTED]:
Dear R-list members,
I've had a hard time trying to solve a non-linear system (nls) of equations
which structure for the equation i, i=1,...,4, is as follows:
f_i(d_1,d_2,d_3,d_4)-k_i(l,m,s) = 0(1)
In the expression above, both f_i and k_i are known functions and l, m and s
are known constants. I would like to estimate the vector d=(d_1,d_2,d_3,d_4)
which is solution of (1). Functions in R to estimate f_i-k_i are at the end
of this message.
Any help/suggestions/comments would be greatly appreciated.
Thanks in advance,
Jorge
# --
# Constants
# --
l=1
m=0.4795
s=0.4795
# --
# Functions to estimate f_i-k_i
# --
f1=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=2*d1+2*sqrt(2)*d1*d2+2*sqrt(3)*d2*d3+4*d3*d4-l*m*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f2=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=2*sqrt(2)*d2+2*d1^2+2*sqrt(6)*d1*d3+4*d2^2+4*sqrt(3)*d2*d4+6*d3^2+8*d4^2-l*(m^2+m^3*s^(-1))*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f3=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=6*d1+12*sqrt(2)*d1*d2+18*sqrt(3)*d2*d3+48*d3*d4+2*sqrt(6)*d3+4*sqrt(6)*d1*d4-l*(m^3+3*m^4*s^(-1)+3*m^6*s^(-2))*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f4=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=12*sqrt(2)*d2+12*d1^2+36*d2^2+72*d3^2+120*d4^2+20*sqrt(6)*d1*d3+56*sqrt(3)*d2*d4+4*sqrt(6)*d4-l*((m^4+6*m^6*s^(-1)+15*m^6*s^(-2)+15*m^7*s^(-3))-3*l^(2)*(m^2+m^3*s^(-1))^2)*(1+d1^2+d2^2+d3^2+d4^2)
res
}
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] A question about environments
I have been using separate environments to partition my data and functions
into logical groups but I have been having an odd (to me) problem.
To load and manipulate the data environments, I wrote a couple of small
functions (see below). The problem seems to be that when I initially try to
load the environment, often no data can be found but if I repeat the
function call, it then works.
It appears that the CreateEnv function sometimes returns a different
environment value than as.environment does. Not always, this is puzzling. I
discovered this by saving the returned value. That environment contains the
data.
Can someone tell me where I am going wrong?
Thanks,
DAV
---
# return a named environment or, if needed, create and attach it
CreateEnv -
function(name, clear=FALSE) {
if (name %in% search()) {
env - as.environment(name)
if (clear)
rm(list=ls(name),envir=env)
return(env)
}
env - new.env()
attach(env, name=name)
env
}
LoadEnv -
function (envname, fname=NULL, ret=FALSE) {
if (is.null(fname)) fname - paste(envname,'Rdata',sep='.')
env - CreateEnv(envname)
load(file=fname, envir=env)
if (ret)
return(env)
}
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and provide commented, minimal, self-contained, reproducible code.
[R] using function from specific packages
hello, useRs- i have a function that i wrote myself, for example, lag(x). however, when i load 'zoo' packages and try to lag 'zoo' object, it gave me error. (R try to pass 'zoo' object into my function.) i typed 'lag.zoo' in R, but it can't find it. how can i access 'lag.zoo' function? and in general, how can i deal with such problem as to access functions from specific packages -- View this message in context: http://www.nabble.com/using-function-from-specific-packages-tp17632885p17632885.html 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] R-2.7.0 make check failure
Hello,
I am fairly new to using R and am trying to install it on my Linux
machine, running Scientific Linux. I get through running 'configure'
and 'make' OK, but when I run 'make check', I get the following error:
make check
make[1]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests'
make[2]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests'
make[3]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests/
Examples'
make[4]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests/
Examples'
make[4]: `Makedeps' is up to date.
make[4]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests/
Examples'
make[4]: Entering directory `/home/gruchti/Programs/R-2.7.0/tests/
Examples'
running code in 'base-Ex.R' .../bin/sh: line 1: 4233 Segmentation
fault ../../bin/R --vanilla base-Ex.R base-Ex.Rout 21
make[4]: *** [base-Ex.Rout] Error 1
make[4]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests/
Examples'
make[3]: *** [test-Examples-Base] Error 2
make[3]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests/
Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/home/gruchti/Programs/R-2.7.0/tests'
make: *** [check] Error 2
I took a look at the 'base-Ex.Rout.fail' file to see where the problem
occured and get the following at the end of the file:
## R code version of choose() [simplistic; warning for k 0]:
mychoose - function(r,k)
+ ifelse(k = 0, (k==0),
+sapply(k, function(k) prod(r:(r-k+1))) / factorial(k))
k - -1:6
cbind(k=k, choose(1/2, k), mychoose(1/2, k))
*** caught segfault ***
address 0x200, cause 'memory not mapped'
Traceback:
1: doWithOneRestart(return(expr), restart)
2: withOneRestart(expr, restarts[[1]])
3: withRestarts({.Internal(.signalCondition(simpleWarning(msg,
call), msg, call)).Internal(.dfltWarn(msg, call))},
muffleWarning = function() NULL)
4: .signalSimpleWarning(NaNs produced, quote(gamma(x + 1)))
5: factorial(k)
6: ifelse(k = 0, (k == 0), sapply(k, function(k) prod(r:(r - k
+ 1)))/factorial(k))
7: mychoose(1/2, k)
8: cbind(k = k, choose(1/2, k), mychoose(1/2, k))
aborting ...
I really am not sure how to interpret this, or how to fix it. Any
help would be greatly appreciated!
Regards,
Greg
--
Gregory Ruchti
Bloomberg Center for Physics and Astronomy
Johns Hopkins University
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Re: [R] JGR / linux
Dirk Eddelbuettel wrote:
On 3 June 2008 at 08:42, g-h-d wrote:
| I basically followed the steps in http://lib.stat.cmu.edu/R/CRAN/, and
those
| below for JGR and it worked.
|
| ...but there are problems with help files e.g. ?matrix generates the
| following message:
|
| /tmp/RtmpvxsnQa/.R/doc/html/packages.html (No such file or directory)
I think you can ignore that. It's just a warning. The rest of your steps
were very sound.
In particular ...
| g-h-d wrote:
|
| Hi all,
|
| i'm trying to install JGR on linux (see bottom), but it runs into
errors.
| The bottom of the sequence below shows JavaJD could not be found
|
| Any suggestion, please?
|
|
| $ sudo apt-get install sun-java6-jdk
|
| $ sudo update-alternatives --config java
|
| There are 5 alternatives which provide `java'.
|
| Selection Alternative
| ---
| 1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
| 2 /usr/bin/gij-4.1
| 3 /usr/bin/gij-4.2
| 4 /usr/lib/jvm/java-gcj/jre/bin/java
| + 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java
... a very good idea to realign what command will default to being 'java'
...
| $sudo R CMD javareconf
| Java interpreter : /usr/bin/java
| Java version : 1.6.0_03
| Java home path : /usr/lib/jvm/java-6-sun-1.6.0.03/jre
| Java compiler : /usr/bin/javac
| Java headers gen.: /usr/bin/javah
| Java archive tool: /usr/bin/jar
... but given that javareconf also looks after javac and javah, I
recommend
doing the same update-alternatives call for 'javah' and 'javac'.
I just re-did that on a Ubuntu 8.04, 32bit, machine and it re-built rJava,
JGR, JavaGD, ... without a hitch.
Dirk
| Java library path:
|
$(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
| JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server
| -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
| -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm
| JNI cpp flags : -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
| -I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux
|
| Updating Java configuration in /etc/R
| Done.
|
| $ sudo R
|
| R version 2.5.1 (2007-06-27)
| Copyright (C) 2007 The R Foundation for Statistical Computing
| ISBN 3-900051-07-0
|
| R is free software and comes with ABSOLUTELY NO WARRANTY.
| You are welcome to redistribute it under certain conditions.
| Type 'license()' or 'licence()' for distribution details.
|
| Natural language support but running in an English locale
|
| R is a collaborative project with many contributors.
| Type 'contributors()' for more information and
| 'citation()' on how to cite R or R packages in publications.
|
| Type 'demo()' for some demos, 'help()' for on-line help, or
| 'help.start()' for an HTML browser interface to help.
| Type 'q()' to quit R.
|
| install.packages('JGR', dep=TRUE)
| Warning in install.packages(JGR, dep = TRUE) :
| argument 'lib' is missing: using '/usr/local/lib/R/site-library'
| --- Please select a CRAN mirror for use in this session ---
| Loading Tcl/Tk interface ... done
| also installing the dependency JavaGD
|
| trying URL
| 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz'
| Content type 'application/x-gzip' length 86505 bytes
| opened URL
| ==
| downloaded 84Kb
|
| trying URL
'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz'
| Content type 'application/x-gzip' length 426244 bytes
| opened URL
| ==
| downloaded 416Kb
|
| * Installing *source* package 'JavaGD' ...
| checking for gcc... gcc-4.2 -std=gnu99
| checking for C compiler default output file name... a.out
| checking whether the C compiler works... yes
| checking whether we are cross compiling... no
| checking for suffix of executables...
| checking for suffix of object files... o
| checking whether we are using the GNU C compiler... yes
| checking whether gcc-4.2 -std=gnu99 accepts -g... yes
| checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none
needed
| checking how to run the C preprocessor... gcc-4.2 -std=gnu99 -E
| checking for grep that handles long lines and -e... /bin/grep
| checking for egrep... /bin/grep -E
| checking for ANSI C header files... yes
| checking for sys/wait.h that is POSIX.1 compatible... yes
| checking for sys/types.h... yes
| checking for sys/stat.h... yes
| checking for stdlib.h... yes
| checking for string.h... yes
| checking for memory.h... yes
| checking for strings.h... yes
| checking for inttypes.h... yes
| checking for stdint.h... yes
| checking for unistd.h... yes
| checking for string.h... (cached) yes
| checking sys/time.h usability... yes
| checking sys/time.h
[R] Summarizing dummy coefficients in sem package
Greetings,
I am working in the sem package on a model with 3 exogenous variables (2
are nominal-categorical), and 4 endogenous, continuous variables. To
use sem with the nominal variables, I created dummy variables. Now, in
my sem output I have estimates for path coefficients for the
relationship between each level of the nominal variables and the
endogenous variables they are associated with. However, what I am
interested are the overall path coefficients from each nominal variable
to the various endogenous variables, not the relationship between each
level of this and the endogenous variables. How might I go about
achieving this?
Here is my model ('sex' and 'trt' are the nominal variables with 2 and 4
levels, respectively) followed by the relevant output:
Path Parameter
1 sexMale-nect sexnect
2 sexMale-cono sexcono
3 sexMale-herb sexherb
4 sexMale-para sexpara
5 trtControl-nect trtContnect
6 trtControl-cono trtContcono
7 trtControl-herb trtContherb
8 trtControl-para trtContpara
9 trtNoFemale-nect trtNoFemnect
10 trtNoFemale-cono trtNoFemcono
11 trtNoFemale-herb trtNoFemherb
12 trtNoFemale-para trtNoFempara
13 trtNoMale-nect trtNoMalenect
14 trtNoMale-cono trtNoMalecono
15 trtNoMale-herb trtNoMaleherb
16 trtNoMale-para trtNoMalepara
17 area-nectareanect
18 area-conoareacono
19 area-herbareaherb
20 area-paraareapara
21 nect-para nect-para
22 nect-herb nectherb
23 nect-cono nectcono
24 cono-herb conoherb
25 cono-para conopara
26 area-area errorarea
27 nect-nect errornect
28 cono-cono errorcono
29 herb-herb errorherb
30 para-para errorpara
31 trtControl-trtControl errortrtControl
32 trtNoFemale-trtNoFemale errorNoFemale
33 trtNoMale-trtNoMale errortrtNoMale
34 sexMale-sexMale errorsexMale
Parameter Estimates
EstimateStd Error z valuePr(|z|)
sexnect -0.01929179 0.06376330 -0.3025532 7.6223e-01
sexcono -2.66789515 0.36084653 -7.3934344 1.4300e-13
sexherb -0.00743378 0.00566452 -1.3123412 1.8941e-01
sexpara 0.01097552 0.00980425 1.1194652 2.6294e-01
trtContnect 0.21164052 0.08736725 2.4224240 1.5417e-02
trtContcono -0.44791548 0.54528423 -0.8214349 4.1140e-01
trtContherb -0.00038585 0.00756348 -0.0510144 9.5931e-01
trtContpara -0.00015034 0.06098602 -0.0024651 9.9803e-01
trtNoFemnect 0.11658323 0.08786423 1.3268566 1.8456e-01
trtNoFemcono-0.10709039 0.55754523 -0.1920748 8.4768e-01
trtNoFemherb-0.00412156 0.00777418 -0.5301598 5.9600e-01
trtNoFempara 0.00420467 0.03406450 0.1234325 9.0176e-01
trtNoMalenect0.23656338 0.08897775 2.6586801 7.8447e-03
trtNoMalecono0.07633944 0.60103928 0.1270124 8.9893e-01
trtNoMaleherb -0.00156381 0.00788036 -0.1984436 8.4270e-01
trtNoMalepara0.00910566 0.03304680 0.2755383 7.8290e-01
areanect 0.01097847 0.02250164 0.4878965 6.2562e-01
areacono 0.37431397 0.12725982 2.9413367 3.2680e-03
areaherb-0.00169721 0.00200841 -0.8450508 3.9808e-01
areapara 0.00044190 0.00365491 0.1209054 9.0377e-01
nect-para 0.00399596 0.00425721 0.9386334 3.4792e-01
nectherb-0.00028131 0.00245373 -0.1146438 9.0873e-01
nectcono 0.52509632 0.15739193 3.3362340 8.4922e-04
conoherb 0.01380912 0.01401081 0.9856041 3.2433e-01
conopara 0.01752004 0.02413323 0.7259716 4.6786e-01
errorarea1.90255983 0.08980542 21.1853566 0.e+00
errornect0.82560204 0.03897074 21.1851759 0.e+00
errorcono 26.60775814 1.25597309 21.1849746 0.e+00
errorherb0.00661525 0.00031226 21.1851940 0.e+00
errorpara0.01967170 0.00092856 21.1852827 0.e+00
errortrtControl 0.19005279 0.00897095 21.1853556 0.e+00
errorNoFemale0.18331925 0.00865314 21.1852797 0.e+00
errortrtNoMale 0.19059782 0.00899668 21.1853547 0.e+00
errorsexMale 0.24736468 0.01167625 21.1852846 0.e+00
Thanks,
Gus
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Re: [R] using function from specific packages
zoo has a namespace and lag.zoo is not exported so zoo:::lag.zoo is how to access it directly. See help(:::) On Tue, Jun 3, 2008 at 4:31 PM, jiho.han [EMAIL PROTECTED] wrote: hello, useRs- i have a function that i wrote myself, for example, lag(x). however, when i load 'zoo' packages and try to lag 'zoo' object, it gave me error. (R try to pass 'zoo' object into my function.) i typed 'lag.zoo' in R, but it can't find it. how can i access 'lag.zoo' function? and in general, how can i deal with such problem as to access functions from specific packages -- View this message in context: http://www.nabble.com/using-function-from-specific-packages-tp17632885p17632885.html 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.
Re: [R] probleme with R CMD check
I find the problem: the name of my base directory (the one that contain R, man and test) was not the same than the name of the package... I thaught this was allowed, I guess I was wrong. Christophe c == cgenolin [EMAIL PROTECTED] on Tue, 03 Jun 2008 09:55:15 +0200 writes: provide commented, minimal, self-contained, reproducible code. Please do -- both -- c Sorry... Usualy, I do... c --- 8 c userA - function(x)x+1 c privateA - function(x)x+2 c .userB - function(x)x+10 c .privateB - function(x)x+20 c userC- function(x)userA(privateA(x)) c privateC - function(x).userB(.privateB(x)) c userD- function(x)userA(.userB(x)) c privateD - function(x)privateA(.privateB(x)) c --- 8 If I execute these in an empty R session, and do package.skeleton(EXpkg) system(R CMD check EXpkg) I can NOT see the problem you describe below. Probably you'd rather should upload the pkg.tar.gz to a public place, to make your problem reproducible. Martin c == cgenolin [EMAIL PROTECTED] on Tue, 03 Jun 2008 00:32:13 +0200 writes: c Hi the list. c I got a probleme with R CMD check. I run a package.skeleton on a very c simple code (four toy function, no probleme with the R CMD build). But c on the R CMD check packClassique, I get : c * checking for unstated dependencies in R code ... WARNING c Erreur dans .find.package(package, lib.loc) : aucun package nommé c 'packClassique' n'est trouvé c Calls: Anonymous - .find.package c Excecution hated [French=Exécution arrêtée] c See the information on DESCRIPTION files in the chapter 'Creating R c packages' of the 'Writing R Extensions' manual. c * checking S3 generic/method consistency ... WARNING c Erreur dans .find.package(package, lib.loc) : aucun package nommé c 'packClassique' n'est trouvé c Calls: Anonymous - .find.package c Exécution arrêtée c And so on. c Any idea on what is wrong ? No. c Christophe c __ c R-help@r-project.org mailing list c https://stat.ethz.ch/mailman/listinfo/r-help c PLEASE do read the posting guide http://www.R-project.org/posting-guide.html c and provide commented, minimal, self-contained, reproducible code. Please do -- both -- Martin c c Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre __ 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-2.7.0 rJava installation failure on x86_64
From: Nathan Coulter It looks like the command above could use /lib64/libc.so.6, but running R CMD javareconf shows that JNI linker flags don't contain any entry similar to '-L/lib64': It turns out that /usr/lib64/libc.so is what is needed. I was able to install rJava after adding /usr/lib64 to the JAVA_LIBS and JAVA_LD_LIBRARY_PATH env JAVA_LIBS='-L/path/to/x86-64/jdk-1.6.0_06/jre/lib/amd64/server -L/path/to/x86-64/jdk-1.6.0_06/jre/lib/amd64 -L/path/to/x86-64/jdk-1.6.0_06/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib -L/usr/lib -ljvm' JAVA_LD_LIBRARY_PATH='/path/to/x86-64/jdk-1.6.0_06/jre/lib/amd64/server:/path/to/x86-64/jdk-1.6.0_06/jre/lib/amd64:/path/to/x86-64/jdk-1.6.0_06/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib:/usr/lib' R-2.7.0 CMD javareconf -- Nathan __ 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] probleme with R CMD check
c == cgenolin [EMAIL PROTECTED] on Wed, 04 Jun 2008 00:30:08 +0200 writes: c I find the problem: the name of my base directory (the c one that contain R, man and test) was not the same than c the name of the package... Aha! c I thaught this was allowed, I guess I was wrong. It has been documented to be allowed; and it has been, but in some circumstances, R CMD check gave wrong warnings, as you found. I had found and fixed this buglet on May 22, both for R-devel and R-patched (which will become R 2.7.1 ...) Could you try 'R-patched' and confirm that the problem is solved? Regards, Martin c Christophe c == cgenolin [EMAIL PROTECTED] on Tue, 03 Jun 2008 09:55:15 +0200 writes: provide commented, minimal, self-contained, reproducible code. Please do -- both -- c Sorry... Usualy, I do... c --- 8 userA - function(x)x+1 privateA - c function(x)x+2 .userB - function(x)x+10 .privateB - c function(x)x+20 userC - function(x)userA(privateA(x)) c privateC - function(x).userB(.privateB(x)) userD - c function(x)userA(.userB(x)) privateD - c function(x)privateA(.privateB(x)) --- 8 If I execute these in an empty R session, and do package.skeleton(EXpkg) system(R CMD check EXpkg) I can NOT see the problem you describe below. Probably you'd rather should upload the pkg.tar.gz to a public place, to make your problem reproducible. Martin c == cgenolin [EMAIL PROTECTED] on Tue, 03 Jun 2008 00:32:13 +0200 writes: c Hi the list. I got a probleme with R CMD check. I run a c package.skeleton on a very simple code (four toy c function, no probleme with the R CMD build). But on the R c CMD check packClassique, I get : c * checking for unstated dependencies in R code c ... WARNING Erreur dans .find.package(package, lib.loc) : c aucun package nommé 'packClassique' n'est trouvé Calls: c Anonymous - .find.package Excecution hated c [French=Exécution arrêtée] c See the information on DESCRIPTION files in the chapter c 'Creating R packages' of the 'Writing R Extensions' c manual. * checking S3 generic/method consistency c ... WARNING Erreur dans .find.package(package, lib.loc) : c aucun package nommé 'packClassique' n'est trouvé Calls: c Anonymous - .find.package Exécution arrêtée c And so on. c Any idea on what is wrong ? No. c Christophe c __ c R-help@r-project.org mailing list c https://stat.ethz.ch/mailman/listinfo/r-help c PLEASE do read the posting guide http://www.R-project.org/posting-guide.html c and provide commented, minimal, self-contained, c reproducible code. Please do -- both -- Martin c c Ce message a ete envoye par IMP, grace a l'Universite c Paris 10 Nanterre __ c R-help@r-project.org mailing list c https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do c read the posting guide c http://www.R-project.org/posting-guide.html and provide c 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] merging two data sets with no column header
Thanks for your reply. In your last step If I create a duplicate ( two similar records ) # create a duplicate vv[8,1] - 7 vv[8,2]-'g' and then I merge vv with vv2 ,both duplicates are merged. Is there a way to tell R to merge only the unique records. Thanks and appreciate your help. -- View this message in context: http://www.nabble.com/merging-two-data-sets-with-no-column-header-tp17613296p17634368.html 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] IBM-AIX 5.2 (GCC 4.2.4 installed) - Error while executing 'make'
Hi, The following error occurs while executing 'make' after the successful configuration (./configure) on IBM-AIX 5.2 (GCC 4.2.4 installed): gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O2 -c vfonts.c -o vfonts.o gfortran -g -O2 -c xxxpr.f -o xxxpr.o gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O2 -c mkdtemp.c -o mkdtemp.o ar cr libR.a CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o apse.o arithmetic.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o inlined.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o mkdtemp.o libs/*o ranlib libR.a gcc -std=gnu99 -Wl,-brtl -Wl,-bexpall -lc -Wl,-bE:../../etc/R.exp -L/usr/local/lib -o R.bin Rmain.o libR.a -lgfortran -lm /opt/pware/lib/gcc/powerpc-ibm-aix5.2.0.0/4.2.4/libgcc.a -lg -lintl -ldl -lm ld: 0711-317 ERROR: Undefined symbol: .dcopy ld: 0711-317 ERROR: Undefined symbol: .dtrsm ld: 0711-317 ERROR: Undefined symbol: .ddot ld: 0711-317 ERROR: Undefined symbol: .dnrm2 ld: 0711-317 ERROR: Undefined symbol: .dtrsl ld: 0711-317 ERROR: Undefined symbol: .dscal ld: 0711-317 ERROR: Undefined symbol: .dpofa ld: 0711-317 ERROR: Undefined symbol: .daxpy ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information. collect2: ld returned 8 exit status make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. Can anyone help to resolve this issue? Or at least help me to define the linker options '-bloadmap' or '-bnoquiet' while executing 'make'? Thanks, Senthil 414-931-2436. -- View this message in context: http://www.nabble.com/IBM-AIX-5.2-%28GCC-4.2.4-installed%29---Error-while-executing-%27make%27-tp17634911p17634911.html 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] JGR / linux
Dirk Eddelbuettel wrote: On 3 June 2008 at 13:44, g-h-d wrote: | | $ sudo apt-get install sun-java6-jdk | | | | $ sudo update-alternatives --config java | | | | There are 5 alternatives which provide `java'. | | | | Selection Alternative | | --- | | 1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java | | 2 /usr/bin/gij-4.1 | | 3 /usr/bin/gij-4.2 | | 4 /usr/lib/jvm/java-gcj/jre/bin/java | | + 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java | | About the message resulting from calling say ?matrix: the message may be a | warning, but ?matrix just doesnt work, I can't use it (or any other help | command). I see. That appears to be the same at my end. You may want to bring that to the attention of the rosuda.org folks. | About doing the same update-alternatives call for 'javah' and 'javac'. I | actually don't know what you mean exactly. Could you please clarify? Thanks. See what I left from your initial post -- besides running $ sudo update-alternatives --config java it may be prudent to also redirect via $ sudo update-alternatives --config javac $ sudo update-alternatives --config javah as 'R CMD javareconf' checkes for all three. But as you got JGR built, this may not matter. I always found that other java compilers from gij, gcj, ecj, ... would get in the way. Hope this helps, Dirk -- Three out of two people have difficulties with fractions. __ 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. Thanks for clarifying. -- View this message in context: http://www.nabble.com/JGR---linux-tp17622071p17635209.html 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] splitting data frame based on a criteria
Also check ?aggregate --- On Wed, 4/6/08, Ingmar Visser [EMAIL PROTECTED] wrote: From: Ingmar Visser [EMAIL PROTECTED] Subject: Re: [R] splitting data frame based on a criteria To: Marvin Lists [EMAIL PROTECTED] Cc: r-help@r-project.org Received: Wednesday, 4 June, 2008, 5:11 AM ?by may be helpful here eg if dat is your data.frame and yf is a factor (created using ifelse) use by(dat,yf,mean) to compute the means for each level of yf hth, Ingmar On Jun 3, 2008, at 8:37 PM, Marvin Lists wrote: Hi, I have a data frame that I want to split into two based on the values of a variable in it. The variable Y has numeric values ranging between 0 through 70. I want to plot the frequencies of another variable X in two different cases: - When Y = 0 and - When Y 0 How does one go about doing this? In general, I want to do several analyses with this data frame that are a variation of the above situation, i.e. they require splitting the data into different age, gender etc. and then calculating separate means, correlations and so on for the different groups into which the data frame would split. I am struggling with the correct syntax for achieving this. Reading through the documentation suggests that tapply and split may be the functions to use for my purposes but the examples in the documentations didn't help me understand how I could achieve this. I would appreciate any suggestions and help. Thanks, Marvin [[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. __ 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] Stacked barplot of timeseries data
Hi, I'm trying to plot time-series data where each sample breaks down the percentage of CPU time spent in each of four states (usr, nice, sys, idle) 19:08:15 %usr %nice %sys %idle 19:08:165 0 10 86 19:08:17 17 0 14 69 19:08:185 0 8 87 19:08:19 10 0 10 81 19:08:203 0 7 90 19:08:214 0 8 88 [on and on for many samples] The plot I'm aiming for would stack the first three states in a colored barplot, so you get a visual sense of how busy the system is over the course of the day, and which state the CPU is spending its time in. (I've done this as area charts as well). barplot() looked promising, but it wants to stack the columns instead of the rows. Anybody have a good solution for this? Thanks! ...Demetri __ 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] Stacked barplot of timeseries data
On Tue, 3 Jun 2008, Demetri S. Mouratis wrote: Hi, I'm trying to plot time-series data where each sample breaks down the percentage of CPU time spent in each of four states (usr, nice, sys, idle) 19:08:15 %usr %nice %sys %idle 19:08:165 0 10 86 19:08:17 17 0 14 69 19:08:185 0 8 87 19:08:19 10 0 10 81 19:08:203 0 7 90 19:08:214 0 8 88 [on and on for many samples] The plot I'm aiming for would stack the first three states in a colored barplot, so you get a visual sense of how busy the system is over the course of the day, and which state the CPU is spending its time in. (I've done this as area charts as well). barplot() looked promising, but it wants to stack the columns instead of the rows. Anybody have a good solution for this? The zoo package provides a barplot() method for zoo series. Example with some artificial data: library(zoo) x - matrix(runif(44), ncol = 4) colnames(x) - c(%usr, %nice, %sys, %idle) z - zoo(x, Sys.time() - c(10:0)) barplot(z, legend = TRUE) hth, Z Thanks! ...Demetri __ 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] How to solve a non-linear system of equations using R
Since k_i(l,m,s) are known constants, you actually have a system of four
non-linear equations with 4 unknowns.
One possibility is to use optim (check ?optim).
Another one is to use the very recently released package - look at
https://stat.ethz.ch/pipermail/r-help/attachments/20080423/da0b7f6c/attachment.pl
--- On Wed, 4/6/08, Jorge Ivan Velez [EMAIL PROTECTED] wrote:
From: Jorge Ivan Velez [EMAIL PROTECTED]
Subject: [R] How to solve a non-linear system of equations using R
To: R mailing list r-help@r-project.org
Received: Wednesday, 4 June, 2008, 7:09 AM
Dear R-list members,
I've had a hard time trying to solve a non-linear
system (nls) of equations
which structure for the equation i, i=1,...,4, is as
follows:
f_i(d_1,d_2,d_3,d_4)-k_i(l,m,s) = 0(1)
In the expression above, both f_i and k_i are known
functions and l, m and s
are known constants. I would like to estimate the vector
d=(d_1,d_2,d_3,d_4)
which is solution of (1). Functions in R to estimate
f_i-k_i are at the end
of this message.
Any help/suggestions/comments would be greatly appreciated.
Thanks in advance,
Jorge
# --
# Constants
# --
l=1
m=0.4795
s=0.4795
# --
# Functions to estimate f_i-k_i
# --
f1=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=2*d1+2*sqrt(2)*d1*d2+2*sqrt(3)*d2*d3+4*d3*d4-l*m*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f2=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=2*sqrt(2)*d2+2*d1^2+2*sqrt(6)*d1*d3+4*d2^2+4*sqrt(3)*d2*d4+6*d3^2+8*d4^2-l*(m^2+m^3*s^(-1))*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f3=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=6*d1+12*sqrt(2)*d1*d2+18*sqrt(3)*d2*d3+48*d3*d4+2*sqrt(6)*d3+4*sqrt(6)*d1*d4-l*(m^3+3*m^4*s^(-1)+3*m^6*s^(-2))*(1+d1^2+d2^2+d3^2+d4^2)
res
}
f4=function(d){
d1=d[1]
d2=d[2]
d3=d[3]
d4=d[4]
res=12*sqrt(2)*d2+12*d1^2+36*d2^2+72*d3^2+120*d4^2+20*sqrt(6)*d1*d3+56*sqrt(3)*d2*d4+4*sqrt(6)*d4-l*((m^4+6*m^6*s^(-1)+15*m^6*s^(-2)+15*m^7*s^(-3))-3*l^(2)*(m^2+m^3*s^(-1))^2)*(1+d1^2+d2^2+d3^2+d4^2)
res
}
[[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] 1501-511 Compilation failed for file ch2inv.f - R on AIX 5.2.
Hi, Installed GCC 4.2.4 on IBM-AIX 5.2 and configured 'R' successfully. Although the below error was resolved after installing GCC 4.2.4, the 'make' failed in another step (related msg posted on June 03). Senthilkumaran wrote: Hi, Thanks for the response. We do have a IBM XL Fortran Enterprise Edition for AIX, V11.1 coupled with IBM XL C/C++ Enterprise Edition for AIX, V9.0 specifically on our IBM-AIX 5.2 system for the 'R' software. The 'f95' represents Fortran 95 compiler and I presume the 'R' sources can be compiled with 'f95' compiler too. Any thoughts? Thanks, Senthil - Original Message From: Prof Brian Ripley [EMAIL PROTECTED] To: Senthilkumaran [EMAIL PROTECTED] Cc: r-help@r-project.org Sent: Friday, May 23, 2008 1:39:16 AM Subject: Re: [R] 1501-511 Compilation failed for file ch2inv.f - R on AIX 5.2. Look like you need to use a Fortran compiler set to accept Fortran 77 (which the R sources are). We don't know what 'f95' is, and this is not really an R issue so please ask your sysadmins for help. On Thu, 22 May 2008, Senthilkumaran wrote: Hi, While executing the make after successful configuration (./configure --with-readline=no --without-iconv), the following error occurs: mbf2n11s (Regatta) /saswork/R/R-2.7.0$ make Target R is up to date. Target R is up to date. Target R is up to date. Target R is up to date. Target Makedeps is up to date. Target libbz2.a is up to date. Target Makedeps is up to date. Target libpcre.a is up to date. Target Makedeps is up to date. Target libz.a is up to date. Target Makedeps is up to date. f95 -g -c ch2inv.f -o ch2inv.o ch2inv.f, line 1.2: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 2.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 3.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 4.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 5.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 6.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 7.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 7.39: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 8.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 9.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 9.41: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 10.8: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 11.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 12.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 13.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 13.38: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 14.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 15.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 16.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 17.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 18.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 18.32: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 19.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 20.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 21.2: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 22.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 23.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 24.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 25.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 26.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 27.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 28.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 29.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 30.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 30.30: 1515-018 (S) Incorrect character found in source at line 30 in column 30. Hexadecimal value of character is 7B. ch2inv.f, line 30.39: 1515-018 (S) Incorrect character found in source at line 30 in column 39. Hexadecimal value of character is 7D. ch2inv.f, line 31.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 32.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 33.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 34.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 35.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 36.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 37.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 38.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 39.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 40.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 41.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 42.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 43.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 44.0: 1515-010 (S) String is missing a closing delimiter. Closing delimiter assumed at end of line. ch2inv.f, line 44.4: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 45.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 46.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 47.3: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 48.1: 1515-019 (S) Syntax is incorrect. ch2inv.f, line 49.0:
[R] unable to get plot in R
Hi everyone, I use R to plot my data set (x,y) in Windows XP, but keep getting error message like follows, ... plot(x, y) Error in windows() : unable to start device devWindows How can I solve this problem? Thanks for any suggestion or help. CC _ sh_skydrive_062008 [[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] IBM-AIX 5.2 (GCC 4.2.4 installed) - Error while executing 'make'
Hi, Added -Wl,-bnoquiet in Makeconf and executed 'make'. The following error occured: gcc -std=gnu99 -I. -I../../../src/include -I../../../src/include -I/usr/local/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O2 -c Lapack.c -o Lapack.o gcc -std=gnu99 -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc -Wl,-bnoquiet -L/usr/local/lib -o lapack.so Lapack.o-lintl -Ltop_builddir/lib -lRlapack -lgfortran -lm /opt/pware/lib/gcc/powerpc-ibm-aix5.2.0.0/4.2.4/libgcc.a -lg collect2: library libRlapack not found make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. Where do we find this library libRlapack? Any thoughts? -Senthil. Senthilkumaran wrote: Hi, The following error occurs while executing 'make' after the successful configuration (./configure) on IBM-AIX 5.2 (GCC 4.2.4 installed): gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O2 -c vfonts.c -o vfonts.o gfortran -g -O2 -c xxxpr.f -o xxxpr.o gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O2 -c mkdtemp.c -o mkdtemp.o ar cr libR.a CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o apse.o arithmetic.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o inlined.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o mkdtemp.o libs/*o ranlib libR.a gcc -std=gnu99 -Wl,-brtl -Wl,-bexpall -lc -Wl,-bE:../../etc/R.exp -L/usr/local/lib -o R.bin Rmain.o libR.a -lgfortran -lm /opt/pware/lib/gcc/powerpc-ibm-aix5.2.0.0/4.2.4/libgcc.a -lg -lintl -ldl -lm ld: 0711-317 ERROR: Undefined symbol: .dcopy ld: 0711-317 ERROR: Undefined symbol: .dtrsm ld: 0711-317 ERROR: Undefined symbol: .ddot ld: 0711-317 ERROR: Undefined symbol: .dnrm2 ld: 0711-317 ERROR: Undefined symbol: .dtrsl ld: 0711-317 ERROR: Undefined symbol: .dscal ld: 0711-317 ERROR: Undefined symbol: .dpofa ld: 0711-317 ERROR: Undefined symbol: .daxpy ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information. collect2: ld returned 8 exit status make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 1. Stop. Can anyone help to resolve this issue? Or at least help me to define the linker options '-bloadmap' or '-bnoquiet' while executing 'make'? Thanks, Senthil 414-931-2436. -- View this message in context: http://www.nabble.com/IBM-AIX-5.2-%28GCC-4.2.4-installed%29---Error-while-executing-%27make%27-tp17634911p17636258.html 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] merge two data sets
I would like to merge “data1 “that contains 100 unique ID’s with another data set “data 2” with 150 ID’s and the age of those individuals ( the ID in data1 is a subset of the ID in data 2) I would like to merge these data1 with data2 and have the result of the merge to have the ID ordered as in data1. Can this be done in R? -- View this message in context: http://www.nabble.com/merge-two-data-sets-tp17636278p17636278.html 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] Model simplification using anova()
Hello all, I've become confused by the output produced by a call to anova(model1,model2). First a brief background. My model used to predict final tree height is summarised here: Df Sum Sq Mean Sq F valuePr(F) Treatment 2 748.35 374.17 21.3096 7.123e-06 *** HeightInitial1 0.31 0.31 0.01780.89519 DiameterInitial 1 0.52 0.52 0.02980.86460 Frost 1 38.2938.292.18070.15392 HeightInitial:Frost1 85.83 85.83 4.88820.03774 * DiameterInitial:Frost 1 97.9097.905.57540.02749 * Residuals22 386.30 17.56 --- Based on this, I should not remove either of the interaction terms, so I turned my attention to the main factors. Based on p-values, I removed HeightInitial and used a call to anova(model1,model2) to see if this resulted in a weaker model. Here is the output: Model 1: HeightFinal ~ Treatment + HeightInitial + DiameterInitial + Frost + HeightInitial:Frost + DiameterInitial:Frost Model 2: AbsoluteDiameterDiff ~ Treatment + DiameterInitial + Frost + HeightInitial:Frost + DiameterInitial:Frost Res.Df RSS Df Sum of Sq F Pr(F) 1 22 386.3 2 22 386.3 0 -1.08e-12 This is not the output that I'm used to seeing. Typically, a pvalue would be provided to suggest if the models differ significantly from one another. Can anyone explain why there's no pvalue in this situation and whether or not removing HeightInitial was justified. Thanks, Jacob Freel -- View this message in context: http://www.nabble.com/Model-simplification-using-anova%28%29-tp17636012p17636012.html 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] Stacked barplot of timeseries data
Here is a variation of the example below which uses your data. Paste this into an R session: Lines - 19:08:15 %usr %nice %sys %idle 19:08:165 0 10 86 19:08:17 17 0 14 69 19:08:185 0 8 87 19:08:19 10 0 10 81 19:08:203 0 7 90 19:08:214 0 8 88 library(zoo) library(chron) # in reality the commented line next replaces the one after it # z - read.csv(myfile.dat, header = TRUE, FUN = times) z - read.zoo(textConnection(Lines), header = TRUE, FUN = times) colnames(z) - sub(X., % , colnames(z)) barplot(z[, 1:3], legend = TRUE, col = 1:3) On Tue, Jun 3, 2008 at 7:47 PM, Achim Zeileis [EMAIL PROTECTED] wrote: On Tue, 3 Jun 2008, Demetri S. Mouratis wrote: Hi, I'm trying to plot time-series data where each sample breaks down the percentage of CPU time spent in each of four states (usr, nice, sys, idle) 19:08:15 %usr %nice %sys %idle 19:08:165 0 10 86 19:08:17 17 0 14 69 19:08:185 0 8 87 19:08:19 10 0 10 81 19:08:203 0 7 90 19:08:214 0 8 88 [on and on for many samples] The plot I'm aiming for would stack the first three states in a colored barplot, so you get a visual sense of how busy the system is over the course of the day, and which state the CPU is spending its time in. (I've done this as area charts as well). barplot() looked promising, but it wants to stack the columns instead of the rows. Anybody have a good solution for this? The zoo package provides a barplot() method for zoo series. Example with some artificial data: library(zoo) x - matrix(runif(44), ncol = 4) colnames(x) - c(%usr, %nice, %sys, %idle) z - zoo(x, Sys.time() - c(10:0)) barplot(z, legend = TRUE) hth, Z Thanks! ...Demetri __ 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] unable to get plot in R
On 03/06/2008 6:53 PM, Chin-Cheng Su wrote: Hi everyone, I use R to plot my data set (x,y) in Windows XP, but keep getting error message like follows, ... plot(x, y) Error in windows() : unable to start device devWindows How can I solve this problem? Thanks for any suggestion or help. Somehow you appear to have set options(device) to devWindows. If you set it to windows using options(device=windows), things should be fine. 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.
[R] Question about subsetting data
I have a data set(Bill) of with 1 variable (var1), with 100 obs that are in ascending order. I want to sample every 10 observations and save them in 10 different groups such as Group1 is obs 1-10 Group 2 is obs-11-20 and so on. First step is to subset them into the 10 groups, then calculate the mean of var1 for each of the 10 groups. Any help would be appreciated. Thanks. _ sh_skydrive_062008 [[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] How to add space between main title to leave space for legend?
On Sat, May 31, 2008 at 2:45 PM, Peter Dalgaard [EMAIL PROTECTED] wrote: Paul Johnson wrote: Hell (1) par(xpd=TRUE) allows you to write outside the plotting region O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B As usual, PD right on the money. Here's a working demo program for posterity. For most random samples, this gives a good looking graph. For a the other few, well, they happen less than 0.05 of the time :) ### histogramWithDensityLinesAndLegend.R ### Paul Johnson 2008-06-02 ### Thanks to r-help members for tips. x - rnorm(100) ###Allows writing outside plotting region par(mai=c(1,1,2.5,1)) par(xpd=TRUE) myhist - hist(x, freq=F, main=Different Meanings of Normality) lines(density(x)) xseq1 - seq( min(x), max(x), length.out=100) m1 - mean(x) sd1 - sd(x) obsNormal - dnorm(xseq1, mean=m1, sd=sd1) lines( xseq1, obsNormal, lty=2, col=red) truNormal - dnorm(xseq1) lines(xseq1, truNormal, lty=3, col=green) legend(min(xseq1),1.3*max(myhist$density), legend=c(observed density, normal with observed mean sd, normal with 'true' mean and sd), lty=c(1,2,3), col=c(black, red, blue)) -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ 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] Minimizing the negative log likelihood function...
Hey,
The following is a function I wrote which generates random variables from a
Kappa (2-parameter) distribution.
rkappa - function(n,beta,alpha){
if(alpha = 0)
stop(alpha must be greater than zero!)
if(beta = 0)
stop(beta must be greater than zero!)
Vec - beta*exp((1/alpha)*(log(-(alpha/(-1 +
exp(alpha*log(runif(n,0,1))+ alpha*log(runif(n,0,1
return(Vec)
}
Now I would like to estimate the parameters of such a distribution using the
Maximum likelihood method.
I know that I have to minimize the following negative log likelihood
function:
Neg.Log.Like - function(beta,alpha,x){
-(sum( log((alpha/beta)*(alpha + (x/beta)^alpha)^( -(alpha + 1)/alpha
}
I have tried several R's functions for optimization but the results I yield
are not correct.
Is there anybody who can help me?
Thanks!
Francois Aucoin
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Re: [R] merge two data sets
Where do you want to place ID's which are in data2 but NOT in data1? --- On Wed, 4/6/08, kayj [EMAIL PROTECTED] wrote: From: kayj [EMAIL PROTECTED] Subject: [R] merge two data sets To: r-help@r-project.org Received: Wednesday, 4 June, 2008, 9:45 AM I would like to merge “data1 “that contains 100 unique ID’s with another data set “data 2” with 150 ID’s and the age of those individuals ( the ID in data1 is a subset of the ID in data 2) I would like to merge these data1 with data2 and have the result of the merge to have the ID ordered as in data1. Can this be done in R? -- View this message in context: http://www.nabble.com/merge-two-data-sets-tp17636278p17636278.html 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.
Re: [R] Question about subsetting data
One possibility is: x - ceiling((1:100)/10) aggregate(var1,by=list(x),mean) --- On Wed, 4/6/08, William Pepe [EMAIL PROTECTED] wrote: From: William Pepe [EMAIL PROTECTED] Subject: [R] Question about subsetting data To: r-help@r-project.org Received: Wednesday, 4 June, 2008, 10:35 AM I have a data set(Bill) of with 1 variable (var1), with 100 obs that are in ascending order. I want to sample every 10 observations and save them in 10 different groups such as Group1 is obs 1-10 Group 2 is obs-11-20 and so on. First step is to subset them into the 10 groups, then calculate the mean of var1 for each of the 10 groups. Any help would be appreciated. Thanks. _ sh_skydrive_062008 [[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] Question about subsetting data
Will this do it for you: Bill - 1:100 # test data # partition Bill.p - split(Bill, rep(1:10, each=10)) Bill.p $`1` [1] 1 2 3 4 5 6 7 8 9 10 $`2` [1] 11 12 13 14 15 16 17 18 19 20 $`3` [1] 21 22 23 24 25 26 27 28 29 30 $`4` [1] 31 32 33 34 35 36 37 38 39 40 $`5` [1] 41 42 43 44 45 46 47 48 49 50 $`6` [1] 51 52 53 54 55 56 57 58 59 60 $`7` [1] 61 62 63 64 65 66 67 68 69 70 $`8` [1] 71 72 73 74 75 76 77 78 79 80 $`9` [1] 81 82 83 84 85 86 87 88 89 90 $`10` [1] 91 92 93 94 95 96 97 98 99 100 sapply(Bill.p, mean) 123456789 10 5.5 15.5 25.5 35.5 45.5 55.5 65.5 75.5 85.5 95.5 On Tue, Jun 3, 2008 at 8:35 PM, William Pepe [EMAIL PROTECTED] wrote: I have a data set(Bill) of with 1 variable (var1), with 100 obs that are in ascending order. I want to sample every 10 observations and save them in 10 different groups such as Group1 is obs 1-10 Group 2 is obs-11-20 and so on. First step is to subset them into the 10 groups, then calculate the mean of var1 for each of the 10 groups. Any help would be appreciated. Thanks. _ sh_skydrive_062008 [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[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 understanding why #function(x, y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})# doesn't work like I think it should
Hello R users and developers,
I am trying to write several functions (fairly new at this) in order
to avoid using loops on large data frames (because they are slow). I
wrote the function below and it seems to get hung on the first part of
the if statement and then applies that condition to rest of the
function. So if (x-y) is greater than 0 the function uses the true
statement for the calculations. Could someone please offer some
advise on how to write these functions a little better or a type
apply that I may use with two (or more) different vectors of data
required by a single functions.
### Examples
###
## example 1 ###
x-c(5,6,4,3,5,3,1)
y-c(1,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z-folds(x,y)
check-cbind(x,y,z)
View(check)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
### why will it only use the first element and how to I get around
this
## example 2 making the fist comparison negative ###
x1-c(5,6,4,3,5,3,1)
y1-c(11,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z1-folds(x1,y1)
check2-cbind(x1,y1,z1)
View(check2)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
loop I am trying to avoid writing many many times #
folds2-NULL
xy-as.data.frame(cbind(x,y))
for (i in 1:nrow(xy)) {
diff-xy$x[i]-xy$y[i]
folds2[i]-if(diff=0) {2^diff} else{-(2^abs(diff))}
}
xyz-cbind(xy,folds2)
View(xyz)
#
Thank you,
Alan
P.S. why does ?function not work
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[R] column and row
-fit1$coefficients y.control y.lowy.high (Intercept)19.628713 21.883999 20.023814 log(1 + (age - 45)/10) -7.383725 -6.017342 -5.084431 here is my outcome,I need one vector say b1=first row without the intercept ,like:(19.628713, 21.883999, 20.023814) and another b2=second row without the log(1 + (age - 45)/10),only the data,how to do this in R? [[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] (re-titled) help with if.
This is an FAQ (although it doesn't seem to be listed in the official
FAQs.
The ``if'' command compares scalars (only, in effect).
See ?if
You need to use the ifelse() function:
folds - function(x,y) ifelse(x-y=0,2^(x-y),-2^(y-x))
This if for illustrative purposes only. The foregoing would be
better done as:
folds - function(x,y) sign(x-y)*2^abs(x-y)
cheers,
Rolf Turner
On 4/06/2008, at 1:47 PM, ALAN SMITH wrote:
Hello R users and developers,
I am trying to write several functions (fairly new at this) in order
to avoid using loops on large data frames (because they are slow). I
wrote the function below and it seems to get hung on the first part of
the if statement and then applies that condition to rest of the
function. So if (x-y) is greater than 0 the function uses the true
statement for the calculations. Could someone please offer some
advise on how to write these functions a little better or a type
apply that I may use with two (or more) different vectors of data
required by a single functions.
### Examples
###
## example 1 ###
x-c(5,6,4,3,5,3,1)
y-c(1,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z-folds(x,y)
check-cbind(x,y,z)
View(check)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
### why will it only use the first element and how to I get around
this
## example 2 making the fist comparison negative ###
x1-c(5,6,4,3,5,3,1)
y1-c(11,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z1-folds(x1,y1)
check2-cbind(x1,y1,z1)
View(check2)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
##
##
loop I am trying to avoid writing many many times #
folds2-NULL
xy-as.data.frame(cbind(x,y))
for (i in 1:nrow(xy)) {
diff-xy$x[i]-xy$y[i]
folds2[i]-if(diff=0) {2^diff} else{-(2^abs(diff))}
}
xyz-cbind(xy,folds2)
View(xyz)
#
Thank you,
Alan
P.S. why does ?function not work
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guide.html
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##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] help understanding why #function(x, y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})# doesn't work like I think it should
Use ifelse() rather than if () {} else {}. It's vectorized and very
useful for applying to elements along vectors. The latter idiom is much
better for control of flow in programs and functions.
folds - function (x, y) ifelse(x-y = 0, 2^(x-y), -(2^abs(x-y)))
z - folds(x, y)
z
[1] 16144 -44 -256
?function works for me. Here's my setup:
R version 2.7.0 (2008-04-22)
x86_64-pc-linux-gnu
Cheers,
Simon.
On Tue, 2008-06-03 at 20:47 -0500, ALAN SMITH wrote:
Hello R users and developers,
I am trying to write several functions (fairly new at this) in order
to avoid using loops on large data frames (because they are slow). I
wrote the function below and it seems to get hung on the first part of
the if statement and then applies that condition to rest of the
function. So if (x-y) is greater than 0 the function uses the true
statement for the calculations. Could someone please offer some
advise on how to write these functions a little better or a type
apply that I may use with two (or more) different vectors of data
required by a single functions.
### Examples
###
## example 1 ###
x-c(5,6,4,3,5,3,1)
y-c(1,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z-folds(x,y)
check-cbind(x,y,z)
View(check)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
### why will it only use the first element and how to I get around
this
## example 2 making the fist comparison negative ###
x1-c(5,6,4,3,5,3,1)
y1-c(11,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z1-folds(x1,y1)
check2-cbind(x1,y1,z1)
View(check2)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
loop I am trying to avoid writing many many times #
folds2-NULL
xy-as.data.frame(cbind(x,y))
for (i in 1:nrow(xy)) {
diff-xy$x[i]-xy$y[i]
folds2[i]-if(diff=0) {2^diff} else{-(2^abs(diff))}
}
xyz-cbind(xy,folds2)
View(xyz)
#
Thank you,
Alan
P.S. why does ?function not work
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--
Simon Blomberg, BSc (Hons), PhD, MAppStat.
Lecturer and Consultant Statistician
Faculty of Biological and Chemical Sciences
The University of Queensland
St. Lucia Queensland 4072
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Room 320 Goddard Building (8)
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Re: [R] help understanding why #function(x, y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})# doesn't work like I think it should
Alan -
ALAN SMITH wrote:
Hello R users and developers,
I am trying to write several functions (fairly new at this) in order
to avoid using loops on large data frames (because they are slow). I
wrote the function below and it seems to get hung on the first part of
the if statement and then applies that condition to rest of the
function. So if (x-y) is greater than 0 the function uses the true
statement for the calculations. Could someone please offer some
advise on how to write these functions a little better or a type
apply that I may use with two (or more) different vectors of data
required by a single functions.
### Examples
###
## example 1 ###
x-c(5,6,4,3,5,3,1)
y-c(1,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z-folds(x,y)
check-cbind(x,y,z)
View(check)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
### why will it only use the first element and how to I get around
this
When learning R, you have the power of the interpreter at all times.
You have defined x and y above to be numeric vectors of length 7 each.
Try typign x - y at the interpreter, and you'll see you get another
numeric vector of length 7. Now try (x - y) = 0 , and you'll get a
logical vector of length 7. However, if does not want a logical vector
of length 7, it wants a logical vector of length 1, see the 'cond'
argument of ?if. However, the ifelse function should do what you want,
see ?ifelse.
Here's an example using it
folds2 - function(x, y) {
ifelse(x - y = 0, 2^(x - y), -(2^abs(x - y)))
}
folds2(x, y) should give you your answer...
## example 2 making the fist comparison negative ###
x1-c(5,6,4,3,5,3,1)
y1-c(11,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z1-folds(x1,y1)
check2-cbind(x1,y1,z1)
View(check2)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
Same idea as above here...
loop I am trying to avoid writing many many times #
folds2-NULL
xy-as.data.frame(cbind(x,y))
for (i in 1:nrow(xy)) {
diff-xy$x[i]-xy$y[i]
folds2[i]-if(diff=0) {2^diff} else{-(2^abs(diff))}
}
xyz-cbind(xy,folds2)
View(xyz)
#
I'm not exactly sure what you'd like here, but hopefully with the above
you can figure it out. Let me know if you have any questions!
Best,
Erik Iverson
Thank you,
Alan
P.S. why does ?function not work
What do you expect it to do? It shows the help page for 'function' here.
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and provide commented, minimal, self-contained, reproducible code.
__
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Re: [R] help understanding why #function(x, y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})# doesn't work likeI think it should
Hi Alan,
-Original Message-
From: [EMAIL PROTECTED] on behalf of ALAN SMITH
Sent: Tue 6/3/2008 6:47 PM
To: r-help@r-project.org
Subject: [R] help understanding why #function(x,y) (if((x-y)=0) {2^(x-y)}
else{-(2^abs(x-y))})# doesn't work likeI think it should
Hello R users and developers,
I am trying to write several functions (fairly new at this) in order
to avoid using loops on large data frames (because they are slow). I
wrote the function below and it seems to get hung on the first part of
the if statement and then applies that condition to rest of the
function. So if (x-y) is greater than 0 the function uses the true
statement for the calculations. Could someone please offer some
advise on how to write these functions a little better or a type
apply that I may use with two (or more) different vectors of data
required by a single functions.
### Examples
###
## example 1 ###
x-c(5,6,4,3,5,3,1)
y-c(1,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z-folds(x,y)
check-cbind(x,y,z)
View(check)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
### why will it only use the first element and how to I get around
this
You probably want to use ifelse() instead of if()
folds - function(x, y) (ifelse( ((x - y) = 0), 2^(x - y), -(2^abs(x - y
x - c(5,6,4,3,5,3,1)
y - c(1,6,2,1,7,1,9)
folds - function(x, y) (ifelse( ((x - y) = 0), 2^(x - y), -(2^abs(x - y
z - folds(x, y)
check - cbind(x, y, z)
check
R x - c(5,6,4,3,5,3,1)
R y - c(1,6,2,1,7,1,9)
R folds - function(x, y) (ifelse( ((x - y) = 0), 2^(x - y), -(2^abs(x - y
R z - folds(x, y)
R check - cbind(x, y, z)
R check
x yz
[1,] 5 1 16
[2,] 6 61
[3,] 4 24
[4,] 3 14
[5,] 5 7 -4
[6,] 3 14
[7,] 1 9 -256
## example 2 making the fist comparison negative ###
x1-c(5,6,4,3,5,3,1)
y1-c(11,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z1-folds(x1,y1)
check2-cbind(x1,y1,z1)
View(check2)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be
used
x1 - c(5,6,4,3,5,3,1)
y1 - c(11,6,2,1,7,1,9)
folds - function(x, y) {ifelse( ((x - y) = 0), {2^(x - y)}, {-(2^abs(x - y))}
) }
z1-folds(x1,y1)
check2-cbind(x1,y1,z1)
check2
R x1 - c(5,6,4,3,5,3,1)
R y1 - c(11,6,2,1,7,1,9)
R folds - function(x, y) {ifelse( ((x - y) = 0), {2^(x - y)}, {-(2^abs(x -
y))} ) }
R z1-folds(x1,y1)
R check2-cbind(x1,y1,z1)
R check2
x1 y1 z1
[1,] 5 11 -64
[2,] 6 61
[3,] 4 24
[4,] 3 14
[5,] 5 7 -4
[6,] 3 14
[7,] 1 9 -256
loop I am trying to avoid writing many many times #
folds2-NULL
xy-as.data.frame(cbind(x,y))
for (i in 1:nrow(xy)) {
diff-xy$x[i]-xy$y[i]
folds2[i]-if(diff=0) {2^diff} else{-(2^abs(diff))}
}
xyz-cbind(xy,folds2)
View(xyz)
#
Thank you,
Alan
P.S. why does ?function not work
It does work in my ESS R session buffer, so
it depends on your setup.
try
R ?function
?function
might not work as the R parser doesn't think you have
finished typing in the expression (function objects
are typically terminated by the final '}' brace).
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Best
Steve McKinney
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[R] Similar question about subsetting data
This is just a slight modification of a question I asked earlier. Thanks to all the responders. I have a data set(Bill) of with 1 variable (var1), with 100 obs that are in ascending order. I want to sample every 10 observations and save them in 10 different groups such as Group1 is obs 1-10 Group 2 is obs-11-20 Subset data into the 10 groups, then calculate the mean/0.8 of var1 for each of the 10 groups. The mean/0.8 is the modification. Thanks. _ Its easy to add contacts from Facebook and other social sites through Wi https://www.invite2messenger.net/im/?source=TXT_EML_WLH_LearnHow [[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] help understanding why #function(x, y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})# doesn't work like I think it should
Try this:
data.frame(x, y, folds = (x == y) + sign(x - y) * 2 ^ abs(x - y))
or replace data.frame with cbind if you prefer a matrix result.
On Tue, Jun 3, 2008 at 9:47 PM, ALAN SMITH [EMAIL PROTECTED] wrote:
Hello R users and developers,
I am trying to write several functions (fairly new at this) in order
to avoid using loops on large data frames (because they are slow). I
wrote the function below and it seems to get hung on the first part of
the if statement and then applies that condition to rest of the
function. So if (x-y) is greater than 0 the function uses the true
statement for the calculations. Could someone please offer some
advise on how to write these functions a little better or a type
apply that I may use with two (or more) different vectors of data
required by a single functions.
### Examples
###
## example 1 ###
x-c(5,6,4,3,5,3,1)
y-c(1,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z-folds(x,y)
check-cbind(x,y,z)
View(check)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
### why will it only use the first element and how to I get around
this
## example 2 making the fist comparison negative ###
x1-c(5,6,4,3,5,3,1)
y1-c(11,6,2,1,7,1,9)
folds-function(x,y) (if((x-y)=0) {2^(x-y)} else{-(2^abs(x-y))})
z1-folds(x1,y1)
check2-cbind(x1,y1,z1)
View(check2)
Warning message:
In if ((x - y) = 0) { :
the condition has length 1 and only the first element will be used
loop I am trying to avoid writing many many times #
folds2-NULL
xy-as.data.frame(cbind(x,y))
for (i in 1:nrow(xy)) {
diff-xy$x[i]-xy$y[i]
folds2[i]-if(diff=0) {2^diff} else{-(2^abs(diff))}
}
xyz-cbind(xy,folds2)
View(xyz)
#
Thank you,
Alan
P.S. why does ?function not work
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] how to extract a specific group of data from a table?
a table with three varialbe:treatment (low,high),size(large,small),response y I want all response y with treatment=low and size=large, I try to write as : treatment-c(low,low,high,high) size-c(small,large,small,large) y-c(1,2,4,5) table1-data.frame(treatment,size,y) x=table1$y(treatment==low size==large) this does not work out~ thank you for the help~ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to extract a specific group of data from a table?
Dear Manli, Try this: table1[table1$treatment==low table1$size==large,] HTH, Jorge On Tue, Jun 3, 2008 at 11:19 PM, Manli Yan [EMAIL PROTECTED] wrote: a table with three varialbe:treatment (low,high),size(large,small),response y I want all response y with treatment=low and size=large, I try to write as : treatment-c(low,low,high,high) size-c(small,large,small,large) y-c(1,2,4,5) table1-data.frame(treatment,size,y) x=table1$y(treatment==low size==large) this does not work out~ thank you for the help~ [[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. [[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] Similar question about subsetting data
Dear William, Following Jim Holtman's solution to your previous post, you can do something similar to Bill - 1:100 # test data Bill.p - split(Bill, rep(1:10, each=10)) sapply(Bill.p, function(x) mean(x)/0.8) 1 2 3 4 5 6 7 8 9 10 6.875 19.375 31.875 44.375 56.875 69.375 81.875 94.375 106.875 119.375 HTH, Jorge On Tue, Jun 3, 2008 at 10:36 PM, William Pepe [EMAIL PROTECTED] wrote: This is just a slight modification of a question I asked earlier. Thanks to all the responders. I have a data set(Bill) of with 1 variable (var1), with 100 obs that are in ascending order. I want to sample every 10 observations and save them in 10 different groups such as Group1 is obs 1-10 Group 2 is obs-11-20 Subset data into the 10 groups, then calculate the mean/0.8 of var1 for each of the 10 groups. The mean/0.8 is the modification. Thanks. _ It's easy to add contacts from Facebook and other social sites through Wi https://www.invite2messenger.net/im/?source=TXT_EML_WLH_LearnHow [[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. [[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] code for automating the sem package
Greetings, I am wondering if anyone has written programs to automate model fitting with the sem package, where one could specify a 'saturated' model and sequentially fit models with different combinations of parameters removed, while outputting fit data/parameters involved for each model. Thanks Gus __ 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] for loop or by group in EF function
Hello, I would like to apply the EF function (a goodness of fit test between predicted (ts2) and observed (Tw) values in the qualV package) to each of the Sites in my data frame. However, when I try the following script, R gives an error message that lists unused arguments, which include the Tw and ts2 that are explicitly in the function: nsc = by(tsdem16, tsdem16['Site'], function(x) EF(Tw, ts2, data = x)) Error in EF(Tw, ts1, data = x) : unused argument(s) (data = list(ts2 = c(11.9967554700039, ... I tried a for loop, but it didn't perform the function on each Site, rather it performed one calculation for the entire data set. Are there any suggestions to improving my script? Thanks, Ingrid [[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] unable to get plot in R
Please look at what I tried, attach(my.data) options(device=windows) plot(x,y) Error in windows() : unable to start device devWindows However, as i tried something else, it went like options(device=devWindows) plot(x,y) Error in plot.new() : no active or default device Any idea? Thanks CC Date: Tue, 3 Jun 2008 20:25:51 -0400 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@r-project.org Subject: Re: [R] unable to get plot in R On 03/06/2008 6:53 PM, Chin-Cheng Su wrote: Hi everyone, I use R to plot my data set (x,y) in Windows XP, but keep getting error message like follows, ... plot(x, y) Error in windows() : unable to start device devWindows How can I solve this problem? Thanks for any suggestion or help. Somehow you appear to have set options(device) to devWindows. If you set it to windows using options(device=windows), things should be fine. Duncan Murdoch _ sh_skydrive_062008 [[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] linear model in the repeated data type~
here is the data: y-c(5,2,3,7,9,0,1,4,5) id-c(1,1,6,6,7,8,15,15,19) t-c(50,56,50,56,50,50,50,60,50) table1-data.frame(y,id,t)//longitudinal data what I want to do is to use the linear model for each id ,then get the estimate value,like: fit1-lm(y~t,data=table1,subset=(id==1)) but ,you can see the variable id is quite irregular,they are not arranaged in order and many number missing,if I write a loop by using for,it will give me a lot NA, and for sure ,I dont want to type id=## for about 500 times,any one know how to deal with it? [[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] splitting data frame based on a criteria
Or ?gsummary Quoting Moshe Olshansky [EMAIL PROTECTED]: Also check ?aggregate --- On Wed, 4/6/08, Ingmar Visser [EMAIL PROTECTED] wrote: From: Ingmar Visser [EMAIL PROTECTED] Subject: Re: [R] splitting data frame based on a criteria To: Marvin Lists [EMAIL PROTECTED] Cc: r-help@r-project.org Received: Wednesday, 4 June, 2008, 5:11 AM ?by may be helpful here eg if dat is your data.frame and yf is a factor (created using ifelse) use by(dat,yf,mean) to compute the means for each level of yf hth, Ingmar On Jun 3, 2008, at 8:37 PM, Marvin Lists wrote: Hi, I have a data frame that I want to split into two based on the values of a variable in it. The variable Y has numeric values ranging between 0 through 70. I want to plot the frequencies of another variable X in two different cases: - When Y = 0 and - When Y 0 How does one go about doing this? In general, I want to do several analyses with this data frame that are a variation of the above situation, i.e. they require splitting the data into different age, gender etc. and then calculating separate means, correlations and so on for the different groups into which the data frame would split. I am struggling with the correct syntax for achieving this. Reading through the documentation suggests that tapply and split may be the functions to use for my purposes but the examples in the documentations didn't help me understand how I could achieve this. I would appreciate any suggestions and help. Thanks, Marvin [[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. __ 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] linear model in the repeated data type~
How about library(nlme) allFits - lmList(y ~ t|id, data=table1, pool=FALSE) or allFits - by(table1, table1$id, function(x) lm(y ~ t, data=x)) Both ways store the results as a list, so you can access individual results using list extraction. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Manli Yan Sent: Tuesday, June 03, 2008 9:07 PM To: r-help@r-project.org Subject: [R] linear model in the repeated data type~ here is the data: y-c(5,2,3,7,9,0,1,4,5) id-c(1,1,6,6,7,8,15,15,19) t-c(50,56,50,56,50,50,50,60,50) table1-data.frame(y,id,t)//longitudinal data what I want to do is to use the linear model for each id ,then get the estimate value,like: fit1-lm(y~t,data=table1,subset=(id==1)) but ,you can see the variable id is quite irregular,they are not arranaged in order and many number missing,if I write a loop by using for,it will give me a lot NA, and for sure ,I dont want to type id=## for about 500 times,any one know how to deal with it? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] linear model in the repeated data type~
Try something like this:
fits - list(500)
for (i in 1:500)
{
if (sum(table1$id == i) == 0) fits[[i]] - NA
else fits[[i]] - lm(y~t,data=table1,subset=(id==i))
}
--- On Wed, 4/6/08, Manli Yan [EMAIL PROTECTED] wrote:
From: Manli Yan [EMAIL PROTECTED]
Subject: [R] linear model in the repeated data type~
To: r-help@r-project.org
Received: Wednesday, 4 June, 2008, 2:06 PM
here is the data:
y-c(5,2,3,7,9,0,1,4,5)
id-c(1,1,6,6,7,8,15,15,19)
t-c(50,56,50,56,50,50,50,60,50)
table1-data.frame(y,id,t)//longitudinal data
what I want to do is to use the linear model for each id
,then get the
estimate value,like:
fit1-lm(y~t,data=table1,subset=(id==1))
but ,you can see the variable id is quite
irregular,they are not arranaged
in order and many number missing,if I write a loop by using
for,it will
give me a lot NA,
and for sure ,I dont want to type id=## for about 500
times,any one know how
to deal with it?
[[alternative HTML version deleted]]
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http://www.R-project.org/posting-guide.html
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reproducible code.
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[R] how to automatically create objects with names from a string list?
Suppose I have a string of objects names:
name - c(foo, bar, baz)
and I would like to use a for loop to automatically create three
objects called foo, bar and baz accordingly. Then how can this
be done (so that in the workspace, foo = 1, bar = 2 and baz=3)
for (i in name) {
.
}
Thanks!
Mark
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to automatically create objects with names from a string list?
You can use either assign or eval.
Something like
name - c(foo, bar, baz)
for (i in 1:length(name)) assign(name[i],i)
--- On Wed, 4/6/08, Mark Farnell [EMAIL PROTECTED] wrote:
From: Mark Farnell [EMAIL PROTECTED]
Subject: [R] how to automatically create objects with names from a string
list?
To: R-help@r-project.org
Received: Wednesday, 4 June, 2008, 3:15 PM
Suppose I have a string of objects names:
name - c(foo, bar,
baz)
and I would like to use a for loop to automatically create
three
objects called foo, bar and
baz accordingly. Then how can this
be done (so that in the workspace, foo = 1, bar = 2
and baz=3)
for (i in name) {
.
}
Thanks!
Mark
__
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.
