Re: [R] row-wise conditional update in dataframe
On 2008-January-22 , at 03:10 , Jon Erik Ween wrote: > That got me there. I suppose R prefers absolute field references in > scripts rather than macrosubstitutions of field names like you would > do in pearl or shell scripts? no, actually, the problem is that apply works on arrays/matrices[1], not data.frames. So it converts the rows of your data.frame in an array instead of using a one row data.frame, hence you cannot refer to the elements of this array by name. This behavior has also bitten me several times and I would love to have an apply function that works on data.frames directly. Is there such a modified apply in some package? [1] ?apply says "If X is not an array but has a dimension attribute, apply attempts to coerce it to an array via as.matrix if it is two-dimensional (e.g., data frames) or via as.array." JiHO --- http://jo.irisson.free.fr/ __ 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] Reading Genepop files
Thanks, but I think this function (in the the ARES package) reads a dataset in genepop input format, not the result file from genepop.exe. hans On 1/21/08, Henrique Dallazuanna <[EMAIL PROTECTED]> wrote: > > Perhaps: > > http://finzi.psych.upenn.edu/R/library/ARES/html/read.genepop.html > > On 21/01/2008, H. Skaug <[EMAIL PROTECTED]> wrote: > > Dear list, > > > > Does there exist R routines for reading output files from Genepop? > > > > (GENEPOP is a population genetics software package by Raymond & Rousset; > > http://genepop.curtin.edu.au/ ) > > > > I find several R packages that contain function for writing Genepop > input > > files, but > > non that does the reverse. > > > > Regards, > > > > hans > > > > [[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. > > > > > -- > Henrique Dallazuanna > Curitiba-Paraná-Brasil > 25° 25' 40" S 49° 16' 22" O > [[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] geometric transformation
Hi everyone, I've got a set of thousands points (2D) located on a pixel image, and I know that four points in this pixels image correspond to four points in a real space on which I need to locate the mapping of all the thousand source points from the pixel set. For this I've got four reference points (corners.px), and the corresponding four destination points (corners.r): > corners.px [,1] [,2] [1,] 212.5 275.5 [2,] 562.5 275.5 [3,] 212.5 625.5 [4,] 562.5 625.5 > corners.r [,1] [,2] [1,] 139463 8386 [2,] 139579 -1294 [3,] 131921 8180 [4,] 132002 -1256 I think I must find a transformation matrix and apply this transformation matrix to all the set in the pixel space, but cannot find the way to contruct this transformation matrix. I guess this is not a question just pertaining to R, but perhaps you can help me with this. Thank you and best regards! Javier - __ 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 an Sweave Vignette to a package
In R, type
Sys.getenv("PATH")
and you will probably find that the PATH does not include the path of
the pdflatex executable of the mikTeX distribution.
Uwe
Doran, Harold wrote:
> Jim
>
> First thanks for your patience. I use MikTex as well. I do have both
> (texti2dvi and pdflatex) on my local machine. I copied and pasted the
> code below and stepped through it. I think this break down with the
> following error. Indeed, I think there is a path problem.
>
> However, I don't see a resolution in either Writing R Extensions or the
> Leisch paper. So, I'm not quite sure what path to modify and/or how.
>
> Error in texi2dvi("TheVignette.tex", pdf = TRUE) :
> unable to run pdflatex on 'TheVignette.tex'
> In addition: Warning message:
> In system(paste(shQuote(latex), "-interaction=nonstopmode", texfile)) :
> "pdflatex" not found
>
>> -Original Message-
>> From: James W. MacDonald [mailto:[EMAIL PROTECTED]
>> Sent: Monday, January 21, 2008 4:53 PM
>> To: Doran, Harold
>> Cc: R Help
>> Subject: Re: [R] Adding an Sweave Vignette to a package
>>
>> What TeX variant are you using? If texi2dvi() can't find
>> texi2dvi, it tries to fall back on pdflatex which has to be
>> in the path.
>>
>> I have always had good luck with MikTeX, which does have texi2dvi.
>>
>> You could always try
>>
>> library(tools)
>> Sweave("TheVignette.Rnw")
>> debug(texi2dvi)
>> texi2dvi("TheVignette.tex", pdf=TRUE)
>>
>> and step through to see where it fails, although on the
>> surface it looks like a path problem.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> Doran, Harold wrote:
>>> There is now and it looks like I got through the first
>> phase. But, now
>>> I get the error below.
>>>
>>> * DONE (MiscPsycho)
>>> * creating vignettes ... ERROR
>>> Loading required package: statmod
>>> Below is what alpha *would be* if the item were removed
>>>
>>> Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
>>> quiet)
>>> :
>>> unable to run pdflatex on 'MP.tex'
>>> Calls: buildVignettes -> texi2dvi
>>> In addition: Warning messages:
>>> 1: In readLines(f[1]) : incomplete final line found on 'MP.Rnw'
>>> 2: In system(paste(shQuote(latex), "-interaction=nonstopmode",
>>> texfile))
>>> :
>>> "pdflatex" not found
>>> Execution halted
>>>
>>> I do have pdflatex, it's what I use all of the time.
>> However, how do I
>>> point to it for this build process?
>>>
-Original Message-
From: James W. MacDonald [mailto:[EMAIL PROTECTED]
Sent: Monday, January 21, 2008 4:09 PM
To: Doran, Harold
Cc: R Help
Subject: Re: [R] Adding an Sweave Vignette to a package
Hi Harold,
Doran, Harold wrote:
> I'm finalizing development of a package that will include a
vignette.
> Without the vignette, the package builds fine with no
warnings and is
> ready for distribution. Now, I am following the directions for
> developing vignettes "Sweave, Part II: Package Vignettes"
by Friedrich
> Leisch.
>
> I am using a windows XP machine (other session info
>> below). Here is
> what I have done.
>
> 1) I add the 'inst/doc' directory to the package source tree.
> 2) I have added the following information in the preamble
of the .Rnw
> file
>
> % \VignetteIndexEntry{An \texttt{R} Package for Miscellaneous
> Psychometric Analyses} % \VignetteDepends{MiscPsycho, statmod} %
> \VignetteKeyword{misc}
>
> 3) I then copy the file "MP.Rnw" to the 'inst/doc' directory.
> 4) I then run Rcmd build g:\MiscPsycho
>
> The process begins as usual and it even tries to create the
vignette.
> However, it runs into an error at code chunk 1
>> complaining that it
> cannot find the function called simRasch(). This simRasch
function is
> one of the functions developed for this package and one that will
> exist only when the package is built. The build process is halted.
>
> I'm not sure how to handle this. Any advice is appreciated.
Is there a library(MiscPsycho) at the beginning of that code chunk?
Best,
Jim
> Harold
>
>> sessionInfo()
> R version 2.6.1 (2007-11-26)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets
>> methods base
>
> other attached packages:
> [1] statmod_1.3.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.6.1
>
> __
> 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, repr
[R] ODE's in R
Dear all, Has anybody tried numerical solving of ODE's and/or transport equations in R? (Don't ask how we ended up in using R for this job, in the first place!) More precisely, does anybody know any technical issue that could make the work insecure in the sense of propagation of errors? Is there any track of evidence that R is, in this kind of task, less reliable than e.g. MatLab? We use just a simple discretisation written in a for loop and a variable (i.e. user-fed) time step. Maybe, I'm too neurotic about this, but I guess I just want some comfort after seeing a few particularly nasty orbits. Best, Markku Karhunen National Public Health Institute, Finland __ 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] Stationarity of a Time Series
Hello Stephen,
stationarity tests as well as unit root tests have been implemented in a
couple of packages. For instance, as already mentioned: tseries, but
also uroot, fUnitRoots and urca. See the annotated task view
"Econemtrics" and "Finance" for further information.
Best,
Bernhard
>
>kpss.test in the tsereis package should do the trick
>
>On Jan 21, 2008 12:36 PM, stephen sefick <[EMAIL PROTECTED]> wrote:
>
>> Does anyone know of a test for stationarity of a time series, or like
>> all ordination techniques it is a qualitative assessment of a
>> quantitative result. Books, papers, etc. suggestions welcome.
>> thanks
>>
>> Stephen
>>
>> --
>> Let's not spend our time and resources thinking about things that are
>> so little or so large that all they really do for us is puff
>us up and
>> make us feel like gods. We are mammals, and have not exhausted the
>> annoying little problems of being mammals.
>>
>>
> -K. Mullis
>>
>> __
>> 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.
>>
>
> [[alternative HTML version deleted]]
>
>__
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>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
>
*
Confidentiality Note: The information contained in this ...{{dropped:10}}
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Re: [R] Bugs through R in Mac
Bill Northcott wrote: > On 21/01/2008, at 10:00 PM, Uwe Ligges wrote: >> Fredrik Lundgren wrote: >>> Hello, >>> >>> I recently changed from Win XP to Mac OS X (10.5.1). >>> Is there a way to run Bugs (in any version) in R (R version 2.6.0 >>> (2007-10-03)) on this platform? >>> >> >> Which way to "run Bugs in R" did you use in Windows? >> On MacOS X, a solution that should work but is completely inelegant is >> using the package R2WinBUGS, and running WinBUGS within DarWINE. There >> are some rumors that OpenBUGS development will be forced within the next >> couple of months, but I am not that confident that we will have a >> natively working BRugs version on Mac OS X or Linux this year ... > > I just posted a message about this on r-sig-mac. > > I spent a little time on this late last year. > > WinBUGS runs happily under DarWINE or the commercial package > CrossoverMac. There is nothing inelegant about it. It is inelegant in at least two points: 1. R2WinBUGS is a mess per se, we all want to use something that runs natively within R, such as BRugs or jags. 2. running the WinBUGS instance in xyz-WINE things does not make things faster and more elegant from my point of view. > > R2WinBUGS is another can of worms. The code to support running WinBUGS > in WINE on Linux or Mac is thoroughly broken. The problem is in the > need to convert Windows paths to UNIX ones. R2WinBUGS does this using > undocumented and unsupported features of some versions of WINE. As is > the way with unsupported features these have been changed on recent > versions of WINE and broken R2WinBUGS. > > The fix is not trivial, and the WINE support stuff in R2WinBUGS needs to > be completely rewritten. I can see what needs to be done, and if I find > the time, I will fix it. Contributions are welcome. I do not touch that xyz...-WINE conversion stuff at all. Best wishes, uwe > You can also use JAGS ( http://www-fis.iarc.fr/~martyn/software/jags/ ) > which has now reached version 1.0.1 and has an R support package rjags. > I hope to post a fat Mac binary for this before the end of the week. In > testing, this works on Leopard with a 32 bit R controlling a 64 bit JAGS > binary which is sort of cool. Now all we need is to be able to run > multiple chains on different CPUs but there are some issues with the > RNGs from R which are used in JAGS. > > Bill Northcott > __ 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] select repositories under linux
Hi all, I am trying to install the package "GEOquery" in unix. I have downloaded the standard version of R and this package is not contained in the default. I know that I can select repositories under windows but I don't know how to do it in unix. Does anyone have any idea on this? Thank you in advance, Eleni [[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] R: determinants and inverses
hello all sorry for the following "none" R related question. does anyone know of a reference to calculate the following identity: |I + ABC| where I is an identity matrix and A, B,C may not have to be square matrices? you help will be greatly appreciated. H. V. Henderson; S. R. Searle SIAM Review, Vol. 23, No. 1. (Jan., 1981), pp. 53-60. provides a result to calculate the inverse of I + ABC. (for those interested!!!) thanking you in advance Allan Clark Lecturer in Statistical Sciences Department University of Cape Town 7701 Rondebosch South Africa TEL (Office): +27-21-650-3228 FAX: +27-21-650-4773 http://web.uct.ac.za/depts/stats/aclark.htm [[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] Problems saving the workspace image
Thanks for your help! I change the starting directory to one I own. I start up R from the same directory. Now it`s working. Best regards, Ana -Mensagem original- De: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Enviada: segunda-feira, 21 de Janeiro de 2008 16:09 Para: Erin Hodgess Cc: Ana Azevedo; r-help@r-project.org Assunto: Re: [R] Problems saving the workspace image On Mon, 21 Jan 2008, Erin Hodgess wrote: > In Windows Vista, you have to "run as administrator". Please don't: the point of not running as administrator is to protect you and your OS from rogue processes. *If* you use a starting directory you own, there is no problem on Vista (for me, or many other Vista users). > > I ran into the same thing myself. > > Hope this helps! > Sincerely, > Erin > > > On Jan 21, 2008 5:46 AM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: >> On Mon, 21 Jan 2008, Ana Azevedo wrote: >> >>> Hi! >>> >>> I use R with Windows for a long time. In the last week I change to Windows >>> Vista. Now I can´t save the workspace image when I exit R. The system >>> presents the following message "Unable to open .Rhistory". Does anyone can >>> help me? >> >> Did you change the shortcut from which you run R to start in a user >> directory, as advised in the rw-FAQ? >> >> Start R, run 'getwd()' and check it is a directory which you own. >> If not, alter the shortcut until it is. >> >> >>> >>> I thank you in advance, >>> >>> Ana >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> >> >> -- >> 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. >> >> > > > > -- > Erin Hodgess > Associate Professor > Department of Computer and Mathematical Sciences > University of Houston - Downtown > mailto: [EMAIL PROTECTED] > -- 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] select repositories under linux
Eleni, download the package (I assume you know where it is),
on Linux you will need the source package. Then from R type
install.packages("", repos=NULL)
Gabor
On Tue, Jan 22, 2008 at 11:26:12AM +0200, Eleni Christodoulou wrote:
> Hi all,
>
> I am trying to install the package "GEOquery" in unix. I have downloaded the
> standard version of R and this package is not contained in the default. I
> know that I can select repositories under windows but I don't know how to do
> it in unix. Does anyone have any idea on this?
>
> Thank you in advance,
> Eleni
>
> [[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.
--
Csardi Gabor <[EMAIL PROTECTED]>UNIL DGM
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Re: [R] geometric transformation
Javier,
You can use two lm-models for that. One for each coordinate. Then use
predict() to calculate the coordinates of the other points. And by the
way: four points is not very much data to calculate a transformation. I
mlight work if the image is not very much distorted and you have precise
measurement of the reference points coordinates.
corners.px <- matrix(c(212.5, 275.5, 562.5, 275.5, 212.5, 625.5, 562.5,
625.5), ncol = 2, byrow = TRUE)
corners.r <- matrix(c(139463, 8386, 139579, -1294, 131921, 8180, 132002,
-1256), ncol = 2, byrow = TRUE)
dataset <- data.frame(cbind(corners.px, corners.r))
colnames(dataset) <- c("X", "Y", "U", "V")
lm(U ~ X + Y, data = dataset)
lm(V ~ X + Y, data = dataset)
HTH,
Thierry
PS R-sig-GEO would be more suitable for this kind of question.
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
[EMAIL PROTECTED]
www.inbo.be
Do not put your faith in what statistics say until you have carefully
considered what they do not say. ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney
-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
Namens [EMAIL PROTECTED]
Verzonden: dinsdag 22 januari 2008 9:56
Aan: r-help@r-project.org
Onderwerp: [R] geometric transformation
Hi everyone,
I've got a set of thousands points (2D) located on a pixel image, and I
know that four points in this pixels image correspond to four points in
a
real space on which I need to locate the mapping of all the thousand
source points from the pixel set.
For this I've got four reference points (corners.px), and the
corresponding four destination points (corners.r):
> corners.px
[,1] [,2]
[1,] 212.5 275.5
[2,] 562.5 275.5
[3,] 212.5 625.5
[4,] 562.5 625.5
> corners.r
[,1] [,2]
[1,] 139463 8386
[2,] 139579 -1294
[3,] 131921 8180
[4,] 132002 -1256
I think I must find a transformation matrix and apply this
transformation
matrix to all the set in the pixel space, but cannot find the way to
contruct this transformation matrix.
I guess this is not a question just pertaining to R, but perhaps you can
help me with this.
Thank you and best regards!
Javier
-
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Re: [R] select repositories under linux
hits=-2.6 tests=BAYES_00 X-USF-Spam-Flag: NO On Tue, 2008-01-22 at 11:26 +0200, Eleni Christodoulou wrote: > Hi all, > > I am trying to install the package "GEOquery" in unix. I have downloaded the > standard version of R and this package is not contained in the default. I > know that I can select repositories under windows but I don't know how to do > it in unix. Does anyone have any idea on this? > > Thank you in advance, > Eleni GEOquery is part of the Bioconductor project. See the web site for this project for instructions on how to install bioconductor and associated packages: http://www.bioconductor.org/ Installation instructions for GEOquery appear to be here: http://bioconductor.org/packages/2.1/bioc/html/GEOquery.html HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.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.
[R] R object as a function
I want to use a function as an argument to ingtegrate it twice.
See the following (senseless) example of a double integration:
test<-function(sf,lo,up,rest) {
innerFkn<-function(sf,lo) {
inte=integrate(f=sf,lower=lo,upper=4)
return( inte$value )
}
integral=integrate(f=innerFkn,lower=1,upper=2,sf=sf,lo=lo,up=up)
return( integral$vlaue+rest )
}
test(sf=stepfun(c(0,1),c(2,-1,3)),lo=0,up=2,rest=12)
Why isn't it possible to define the "innerFkn" inside "test"?
"sf" is a stepfun, but it should possibly be any function.
How can I define some R object like a stepfun (depending on variables)
which can be evaluated like a function at some "lo"?
Thanks for help,
Thomas
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Re: [R] ODE's in R
> "MK" == Markku Karhunen <[EMAIL PROTECTED]> > on Tue, 22 Jan 2008 10:57:25 +0200 writes: MK> Dear all, MK> Has anybody tried numerical solving of ODE's and/or transport equations MK> in R? (Don't ask how we ended up in using R for this job, in the first MK> place!) MK> More precisely, does anybody know any technical issue that could make MK> the work insecure in the sense of propagation of errors? Is there any MK> track of evidence that R is, in this kind of task, less reliable than MK> e.g. MatLab? No, there's no such track. [ Matlab users coming to R may produce wrong R code by using 0:n-1 instead of 0:(n-1) ; but I don't assume this would be the case ] MK> We use just a simple discretisation written in a for loop MK> and a variable (i.e. user-fed) time step. I don't think you should use your own code instead of "professional" ODE solvers, such as the one in R package 'odesolve' MK> Maybe, I'm too neurotic about this, but I guess I just want some comfort MK> after seeing a few particularly nasty orbits. As we know ``from Chaos theory'', there can be delicate inhereent and numerical problems in ODE solving.. Regards, Martin Maechler, ETH Zurich __ 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] select repositories under linux
See setRepositories() On 22/01/2008, Eleni Christodoulou <[EMAIL PROTECTED]> wrote: > Hi all, > > I am trying to install the package "GEOquery" in unix. I have downloaded the > standard version of R and this package is not contained in the default. I > know that I can select repositories under windows but I don't know how to do > it in unix. Does anyone have any idea on this? > > Thank you in advance, > Eleni > > [[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. > -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O __ 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 - linear regression
Hi, I am trying a linear regression model where the dependent variable is the size of the heart corrected for the patient's height and weight. This is labelled as LAVI. The independent variables are race (european or non-eurpoean), age, sex (male or female) of the patient and whether they have diabetes and high blood pressure. sample size 2000 patients selected from a community. when I model model1<-lm(lavi~age+sex+race+diabetes+hypertension, data=tb1) and model2<-lm(lavi~age+sex+age*race+diabetes+hypertension, data=tb1) in the first model race comes out as a significant predictor (p<0.005) where as in the second model race is not a significant predictor of lavi (p=.076) in my dataset mean age is 55.2 years in the non-europeans and 56.7 years in the europeans (p <0.0001 by t.test). should I or should I not include the interaction (age*race) in the model. Is it an acceptable rule to put in interactions if there is a significant relation between the indepenedent variables in univariate analyses. Many thanks bragadeesh _ Helping your favorite cause is as easy as instant messaging. You IM, we give. [[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] Reading Genepop files
Which is the output format of file? On 22/01/2008, H. Skaug <[EMAIL PROTECTED]> wrote: > Thanks, but I think this function (in the the ARES package) reads > a dataset in genepop input format, not the result file > from genepop.exe. > > hans > > > > On 1/21/08, Henrique Dallazuanna <[EMAIL PROTECTED]> wrote: > > Perhaps: > > > > > http://finzi.psych.upenn.edu/R/library/ARES/html/read.genepop.html > > > > On 21/01/2008, H. Skaug <[EMAIL PROTECTED]> wrote: > > > Dear list, > > > > > > Does there exist R routines for reading output files from Genepop? > > > > > > (GENEPOP is a population genetics software package by Raymond & Rousset; > > > http://genepop.curtin.edu.au/ ) > > > > > > I find several R packages that contain function for writing Genepop > input > > > files, but > > > non that does the reverse. > > > > > > Regards, > > > > > > hans > > > > > > [[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. > > > > > > > > > -- > > Henrique Dallazuanna > > Curitiba-Paraná-Brasil > > 25° 25' 40" S 49° 16' 22" O > > > > -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40" S 49° 16' 22" O __ 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] image/area plot
Perhaps you can do this:
On 21/01/2008, Marta Rufino <[EMAIL PROTECTED]> wrote:
>
> Thank you very much for the help.
>
>
>
> kk=data.frame(fact=letters[1:10],
> freq=c(5,1,10,2,10,7,5,10,30,20))
> res <- rep(kk[[1]], kk[[2]])
> resmat <- matrix(c(res), 10)
> image(1:10, 1:10, resmat, col=rainbow(20))
> grid(ncol(resmat), nrow(resmat))
>
>
> Great! that is much better :-)
> Still,... any idea about how to rearrange the matrix, in a way that the
> area of each letter is together (for example, in the fig. area 'f' and 'e'
> were split into two lines :-( )?
res1 <- do.call('rbind', lapply(split(c(res), c(res)),
function(x)append(x, rep(NA, max(table(res))-length(x)
image(t(res1), col=rainbow(20))
grid(30,10)
>
>
> ##1
> text(expand.grid(seq_len(ncol(resmat)), seq_len(nrow(resmat))),
> as.character(res))
>
> Excelent, this is very interesting code. Still, I wanted to have only one
> legend in each area.
pos1 <- t(sapply(unique(resmat), function(x)which(resmat==x, arr.ind=T)[1,]))
text(apply(pos1[!duplicated(pos1),][,-3], 2, as.numeric), labels=unique(res))
>
> ##2
> pos <- lapply(apply(apply(resmat, 2, duplicated), 2,
> function(x)which(!x)), append, 11)
> for(j in 1:length(pos)){
> rect(pos[[j]]-.5, j-.5, pos[[j]]-.5, j+.5, lwd=2)
> }
> abline(h=c(seq(1.5, 5.5, by=1), 8.5), lwd=2)
>
>
> This is exactly it!!!
>
>
> ##3
> plot(0, xlim=c(0,10), ylim=c(1, max(table(resmat))), type="n", xaxt="n")
> tb <- table(resmat)
> dis <- 0
> for(i in 1:10){
> rect(dis, seq(par("usr")[1], tb[i], by=1), dis+.8, seq(par("usr")[1],
> tb[i], by=1)+1)
> dis <- dis + 1
> }
> axis(1, at=0.5:9.5, labels=LETTERS[1:10])
image(1:10, 1:10, resmat, col=rainbow(20))
grid(ncol(resmat), nrow(resmat))
pos <- lapply(apply(apply(resmat, 2, duplicated), 2,
function(x)which(!x)), append, 11)
for(j in 1:length(pos)){
rect(pos[[j]]-.5, j-.5, pos[[j]]-.5, j+.5, lwd=7, col="white",
border=T, density=100)
}
abline(h=c(seq(1.5, 5.5, by=1), 8.5), lwd=7, col="white")
>
> What I meant was using the image plot (or something similar). Maybe it is
> easier to show some examples in the net:... here is an example:
>
> http://grammarpolice.net/archives/001387.php
>
> I guess this could be accomplished by re-ordering the matrix values, so
> that the values are not in rows but clustered into boxes, I guess... but how
> to do this?
>
>
> ##4
> I think that symbols function should be useful
>
> points(expand.grid(seq_len(ncol(resmat)), seq_len(nrow(resmat))), c(res))
> #using your excelent code, I think this makes the job :-)
>
> Thank you very much,
> Best wishes,
> Marta
>
>
> On 18/01/2008, Marta Rufino <[EMAIL PROTECTED]> wrote:
>
>
> Yes, that is it, a square pie chart :-) I did not knew the name... sorry...
>
> Does anyone knows about it?
> Thank you very much,
> Best wishes,
> Marta
>
> hadley wickham wrote:
>
>
> Do you have an example graphic that shows what you're trying to
> create? I can't figure out if you want something like a square pie
> chart (aka waffle chart), a stacked barchart, a levelplot, or
> something else.
>
> Hadley
>
> On Jan 18, 2008 6:06 AM, Marta Rufino <[EMAIL PROTECTED]> wrote:
>
>
>
> Dear R users,
>
> I am trying to produce an image plot, that represents the proportions of
> a factor (z variable), so that the number of squares of each colour
> represents each factor level, with the respective label inside (sorry
> for the crap English).
>
> # Something like this:
>
> kk=data.frame(fact=letters[1:10],
> freq=c(5,1,10,2,10,7,5,10,30,20)) #
> factor and respective frequecies
> res="a" # transform into a matrix (is there an easier way to do this?...
> for the image plot
> for(ii in 1:dim(kk)[1]){
> res=c(res, rep(as.character(kk[ii,1]), l=kk[ii, 2]))
> }
> res=res[-1]
> res
> res=matrix(c(factor(res)), nc=10)
>
> image(x=1:10,y=1:10, res[,order(colSums(res))], col=rainbow(20))
> abline(h=seq(0.5,10.5,1), col=8, lty=3); abline(v=seq(0.5,10.5,1),
> col=8, lty=3)#add some gridlines
>
> #Problems:
> #1. How to add the labels in each area
> text(1,1,paste("Factor level",kk[1,1]), pos=4)
>
> #2. How to separate the areas of each factor level (for BW printing),
> with lines (instead of colours as it is)
> segments(.5,1.5,5.5,1.5, lwd=2);segments(5.5,.5,5.5,1.5, lwd=2) #
> something like this, but automatically :-(
>
> #3. How to keep the areas together (contiguous) and not allow split over
> to lines?
>
> #4. Could I replace the col. by a symbol, for example? I think I would
> need to use plot instead of image.
> Any help will be much apretiated,
>
> Thank you very much in advance,
> Best wishes,
> Marta
> PS: This type of graphs are used in community ecology analysis, for
> example-...
>
> --
> ...
> Marta M. Rufino (PhD)
>
> __
> 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.h
Re: [R] select repositories under linux
On Tue, 22 Jan 2008, Eleni Christodoulou wrote: > Hi all, > > I am trying to install the package "GEOquery" in unix. I have downloaded the > standard version of R and this package is not contained in the default. I > know that I can select repositories under windows but I don't know how to do > it in unix. Does anyone have any idea on this? ?setRepositories (for both Windows and Unix). > > Thank you in advance, > Eleni > > [[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. > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Multivariable barplot
Hi, is it possible to do a multivariable barplot with ggplot2? I have something like that: > df LENGTH LAT 091639 10.002 42.26282 091640 30.808 42.26834 091641 21.591 42.31689 091642 22.030 41.53246 091643 22.744 42.01954 091644 12.702 42.67751 091645 39.728 42.06479 091647 63.057 41.25283 091648 19.523 41.01925 091649 13.336 42.46904 0916508.935 42.80971 09165125.275 42.50678 0916529.983 42.89345 0916539.416 41.15288 > p <- ggplot(df) > p <- p + geom_bar(aes(x=rownames(df), y=LENGTH), position="dodge", fill="red") > p <- p + geom_bar(aes(x=rownames(df), y=LAT), position="dodge", fill="green") > p but the result graphics are overlapping. Thank for your 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] Stationarity of a Time Series
On Tue, 22 Jan 2008, Pfaff, Bernhard Dr. wrote:
> Hello Stephen,
>
> stationarity tests as well as unit root tests have been implemented in a
> couple of packages. For instance, as already mentioned: tseries, but
> also uroot, fUnitRoots and urca. See the annotated task view
> "Econemtrics" and "Finance" for further information.
But note that these tests apply to just a few ways in which a series might
be non-stationary: they all seem an econmetrician's view of possible
non-stationarity.
In the end stationarity is a modelling assumption: it depends on what
might have happened but did not. E.g. a sine wave process is stationary
if and only if it has a random (uniform) phase, and you cannot tell that
from a single realization.
'Anna Karenina applies'[*] (as to most pure significance tests).
[*] Google it if you need elucidation.
>
> Best,
> Bernhard
>
>>
>> kpss.test in the tsereis package should do the trick
>>
>> On Jan 21, 2008 12:36 PM, stephen sefick <[EMAIL PROTECTED]> wrote:
>>
>>> Does anyone know of a test for stationarity of a time series, or like
>>> all ordination techniques it is a qualitative assessment of a
>>> quantitative result. Books, papers, etc. suggestions welcome.
>>> thanks
>>>
>>> Stephen
>>>
>>> --
>>> Let's not spend our time and resources thinking about things that are
>>> so little or so large that all they really do for us is puff
>> us up and
>>> make us feel like gods. We are mammals, and have not exhausted the
>>> annoying little problems of being mammals.
>>>
>>>
>> -K. Mullis
>>>
>>> __
>>> 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.
>>
> *
> Confidentiality Note: The information contained in this ...{{dropped:10}}
>
> __
> 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.
[R] Communicating with R through a named pipe: display refresh problem
Hello, On a linux system I'm trying to send commands to R through a named pipe and am *nearly* successful. I can send R commands and can plot graphs. The only problem I have is getting the x11 display to refresh - it appears to hang because of the pipe. The R server: $ mkfifo R_pipe $ R --no-save < R_pipe The R client: $ cat>> R_pipe Now, I can send R commands down the pipe: Client side: x <- seq(1,10) x Server side: > x <- seq(1:10) > x [1] 1 2 3 4 5 6 7 8 9 10 This is perfect. Now if I try to create a plot, e.g. plot(1:100), the server shows > plot(1:100) and the plot appears. However, if a window briefly obscures the graphical output, the x11 device won't refresh the display. It would appear the pipe is blocking the refresh. Can anyone else confirm this happens and any suggestions how to get the display to refresh? Thanks in advance, PJ __ 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] ODE's in R
Markku Karhunen wrote:
> Thanks, Dr. Maechler.
>
>> No, there's no such track.
>> [ Matlab users coming to R may produce wrong R code
>> by using 0:n-1 instead of 0:(n-1) ; but I don't assume this
>> would be the case ]
>>
>>
>>
> Been there, done that!
>
>> MK> We use just a simple discretisation written in a for loop
>> MK> and a variable (i.e. user-fed) time step.
>>
>> I don't think you should use your own code instead of "professional"
>> ODE solvers, such as the one in R package 'odesolve'
>>
>>
>>
> We must look into that. The problem, maybe, is that in fact half of the
> equations are, in fact, simple PDE's and I don't know, if you can put
> them into odesolve.
>
Usually, you can convert them to a system of ODE's ("the method of
lines" if i remember correctly).
One slight caveat with the high-end ODE solvers is that sometimes they
are too smart for their own good when used in connection with parameter
estimation. Because of things like adaptive stepsizing, you might end up
with sums of squared residuals that are non-smooth functions of the
parameters. This happens especially easily if the system itself is not
quite smooth (e.g. if your input to the system is a step function).
>> MK> Maybe, I'm too neurotic about this, but I guess I just want some
>> comfort
>> MK> after seeing a few particularly nasty orbits.
>>
>> As we know ``from Chaos theory'', there can be delicate
>> inhereent and numerical problems in ODE solving..
>>
>>
> But - to our best knowledge - they should not be any more acute in R,
> than on any other platform...
>
> BR,
> Markku
>
> __
> 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.
>
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] ODE's in R
Thanks, Dr. Maechler. > No, there's no such track. > [ Matlab users coming to R may produce wrong R code > by using 0:n-1 instead of 0:(n-1) ; but I don't assume this > would be the case ] > > Been there, done that! > MK> We use just a simple discretisation written in a for loop > MK> and a variable (i.e. user-fed) time step. > > I don't think you should use your own code instead of "professional" > ODE solvers, such as the one in R package 'odesolve' > > We must look into that. The problem, maybe, is that in fact half of the equations are, in fact, simple PDE's and I don't know, if you can put them into odesolve. > MK> Maybe, I'm too neurotic about this, but I guess I just want some > comfort > MK> after seeing a few particularly nasty orbits. > > As we know ``from Chaos theory'', there can be delicate > inhereent and numerical problems in ODE solving.. > But - to our best knowledge - they should not be any more acute in R, than on any other platform... BR, Markku __ 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] error bar position setting
Hi, I am using R on Windows XP. I am using 'arrows' funtion to plot the variance as error bar, BUT error bar goes only one side of the data point, I need to plot the error bar on both side of the data point (plot is attached), I am using following commands to plot, plot(file3$lat,file3$STotwoKm,pch=21,cex=2.5,ylim=c(-0.2,2.5),xlim=c(-50,50),xlab=NA,ylab=NA, col=1, xaxs="i",yaxs="i") arrows(file3$lat, file3$var1, file3$lat,file3$STotwoKm, col=1, code=3, angle=90, length=0.1) Here: lat=latitte (x-axis) STotwoKm = Data values (y-axis) Var1 = Variance Kindly help how I can plot error bar on both side of data point, Many thanks, Regards, Yogesh -- Yogesh K. Tiwari (Dr.rer.nat), Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) (Ext.250) Fax: 0091-20-258 93 825 __ 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 object as a function
On 22/01/2008 5:30 AM, Thomas Steiner wrote:
> I want to use a function as an argument to ingtegrate it twice.
> See the following (senseless) example of a double integration:
>
> test<-function(sf,lo,up,rest) {
> innerFkn<-function(sf,lo) {
> inte=integrate(f=sf,lower=lo,upper=4)
> return( inte$value )
> }
> integral=integrate(f=innerFkn,lower=1,upper=2,sf=sf,lo=lo,up=up)
> return( integral$vlaue+rest )
> }
> test(sf=stepfun(c(0,1),c(2,-1,3)),lo=0,up=2,rest=12)
>
> Why isn't it possible to define the "innerFkn" inside "test"?
It is possible, but it needs to take arguments in the order that
integrate expects, i.e. the first argument needs to be the values at
which it will be evaluated. You don't specify any "x" value.
The other problem is that integrate is not vectorized, it can only take
scalar values for lower and upper, so you'll need a loop within innerFkn
to do the integral over the values being passed in.
Duncan Murdoch
> "sf" is a stepfun, but it should possibly be any function.
> How can I define some R object like a stepfun (depending on variables)
> which can be evaluated like a function at some "lo"?
> Thanks for help,
> Thomas
>
> __
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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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Re: [R] R object as a function
On 22/01/2008 6:51 AM, Thomas Steiner wrote:
> Okay, let me try to better say what I meant:
>
> myfun1<-function(x=5,pa) {
> return(pa[1]*x^2+pa[2]*x+pa[3])
> }
> myfun2<-function(x=5,param,myfunk1) {
> return(param[1]*myfunk1(x)+param[2]*myfunk1(x))
> }
> test<-function(pars1,pars2,lo,up){
> mf=myfun1(x=2,pa=8*pars1)
> integ=integrate(f=myfun2,lower=lo,upper=up,param=pars2,myfunk1=mf)
> return( 2*integ$value )
> }
> test(pars1=c(1,2,3),pars2=c(-1,1),lo=2,up=7)
>
> So the function myfun2 will be integrated and has a function (myfunk1)
> itself as an argument.
You're not passing a function as myfunk1, you're passing mf, which is
the result of evaluating myfun1, so it's a numeric vector.
Duncan Murdoch
> Why is this not possible?
> Thanks,
> Thomas
>
> PS: the "x=5" and "pa=8*" has no influence...
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Re: [R] R object as a function
Okay, let me try to better say what I meant:
myfun1<-function(x=5,pa) {
return(pa[1]*x^2+pa[2]*x+pa[3])
}
myfun2<-function(x=5,param,myfunk1) {
return(param[1]*myfunk1(x)+param[2]*myfunk1(x))
}
test<-function(pars1,pars2,lo,up){
mf=myfun1(x=2,pa=8*pars1)
integ=integrate(f=myfun2,lower=lo,upper=up,param=pars2,myfunk1=mf)
return( 2*integ$value )
}
test(pars1=c(1,2,3),pars2=c(-1,1),lo=2,up=7)
So the function myfun2 will be integrated and has a function (myfunk1)
itself as an argument.
Why is this not possible?
Thanks,
Thomas
PS: the "x=5" and "pa=8*" has no influence...
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Re: [R] Multivariable barplot
Pilar Loren wrote: > Hi, is it possible to do a multivariable barplot with ggplot2? > > I have something like that: > > >> df >> >LENGTH LAT > 091639 10.002 42.26282 > 091640 30.808 42.26834 > 091641 21.591 42.31689 > 091642 22.030 41.53246 > 091643 22.744 42.01954 > 091644 12.702 42.67751 > 091645 39.728 42.06479 > 091647 63.057 41.25283 > 091648 19.523 41.01925 > 091649 13.336 42.46904 > 0916508.935 42.80971 > 09165125.275 42.50678 > 0916529.983 42.89345 > 0916539.416 41.15288 > > >> p <- ggplot(df) >> p <- p + geom_bar(aes(x=rownames(df), y=LENGTH), position="dodge", >> > fill="red") > >> p <- p + geom_bar(aes(x=rownames(df), y=LAT), position="dodge", >> > fill="green") > >> p >> df2=melt(id="idrow", df) qplot(data=df2, x=idrow, y=value, fill=variable,stat="identity",geom="bar", position="dodge") Ciao, domenico > > but the result graphics are overlapping. > > Thank for your 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. > > __ 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: determinants and inverses
hello Charilaos thank you for your reply. i know how to use R to calculate the results. i want to simplify the results mathematically. i found a reference that helps. see mardia, kent, bibby, "multivariate analysis", (2003) pg 457,458 for the correct simplifiations. (for those interested) |A+BC|=|A||I(p)+inv(A)BC|=|A||I(n)+Cinv(A)B| for B (p by n) , C (n by p), A (p by p) and non singular. regards Allan Clark Lecturer in Statistical Sciences Department University of Cape Town 7701 Rondebosch South Africa TEL (Office): +27-21-650-3228 FAX: +27-21-650-4773 http://web.uct.ac.za/depts/stats/aclark.htm >>> Charilaos Skiadas <[EMAIL PROTECTED]> 2008/01/22 01:24 PM >>> Can you just multiply the matrices with %*% ( ?"%*%" ), form the identity through diag ( ?diag ), and then use "det" to get the determinant? (though read the note in ?qr ). Haris Skiadas Department of Mathematics and Computer Science Hanover College On Jan 22, 2008, at 5:02 AM, Allan Clark wrote: > hello all > > sorry for the following "none" R related question. > > > > does anyone know of a reference to calculate the following identity: > > |I + ABC| > > where I is an identity matrix and A, B,C may not have to be square > matrices? > > > you help will be greatly appreciated. > > > > H. V. Henderson; S. R. Searle > SIAM Review, Vol. 23, No. 1. (Jan., 1981), pp. 53-60. > > provides a result to calculate the inverse of I + ABC. (for those > interested!!!) > > thanking you in advance > > > Allan Clark > > Lecturer in Statistical Sciences Department > University of Cape Town > 7701 Rondebosch > South Africa > TEL (Office): +27-21-650-3228 > FAX: +27-21-650-4773 > http://web.uct.ac.za/depts/stats/aclark.htm > > > [[alternative HTML version deleted]] [[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] Multivariable barplot
Domenico Vistocco wrote: > Pilar Loren wrote: > >> Hi, is it possible to do a multivariable barplot with ggplot2? >> >> I have something like that: >> >> >> >>> df >>> >>> >>LENGTH LAT >> 091639 10.002 42.26282 >> 091640 30.808 42.26834 >> 091641 21.591 42.31689 >> 091642 22.030 41.53246 >> 091643 22.744 42.01954 >> 091644 12.702 42.67751 >> 091645 39.728 42.06479 >> 091647 63.057 41.25283 >> 091648 19.523 41.01925 >> 091649 13.336 42.46904 >> 0916508.935 42.80971 >> 09165125.275 42.50678 >> 0916529.983 42.89345 >> 0916539.416 41.15288 >> >> >> >>> p <- ggplot(df) >>> p <- p + geom_bar(aes(x=rownames(df), y=LENGTH), position="dodge", >>> >>> >> fill="red") >> >> >>> p <- p + geom_bar(aes(x=rownames(df), y=LAT), position="dodge", >>> >>> >> fill="green") >> >> >>> p >>> >>> Sorry (I missed to past a command before the melt command): df=data.frame(idrow=rownames(df), df) > df2=melt(id="idrow", df) > qplot(data=df2, x=idrow, y=value, > fill=variable,stat="identity",geom="bar", position="dodge") > > Ciao, > domenico > >> but the result graphics are overlapping. >> >> Thank for your 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. >> >> >> > > __ > 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] contingency table on data frame
I am sorry if this is a faq or tutorial somewhere, but I am unable to
solve this one.
What I am looking for is a count of how many different
categories(numbers in this case) that appears for a given factor.
Example:
> l <- c("Yes", "No", "Perhaps")
> x <- factor( sample(l, 10, replace=T), levels=l )
> m <- c(1:5)
> y <- factor( sample(m, 10, replace=T), levels=m )
> z = c(1:10)
> my_df = data.frame("Z" = z, "Y"= y, "X" = x)
> my_df
Z Y X
1 1 4 Yes
2 2 1 No
3 3 2 Perhaps
4 4 3 Yes
5 5 4 No
6 6 5 No
7 7 1 Yes
8 8 4 Perhaps
9 9 4 Yes
10 10 2 Perhaps
>
I am now looking for a table that will give me this:
Yes 3 # Yes has these ys: 4,3,1,4, two are the same, ergo 3
No 3 # No has these ys: 1,4,5
Perhaps 2 # Perhaps has these ys: 2,4,2
My dataframe has lots of other colums too, but I only want this
information out.
Thankyou for your help!
Karin
--
Karin Lagesen, PhD student
[EMAIL PROTECTED]
http://folk.uio.no/karinlag
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Re: [R] error bar position setting
> I am using 'arrows' funtion to plot the variance as error bar, BUT error
> bar goes only one side of the data point, I need to plot the error bar
on
> both side of the data point (plot is attached), I am using following
> commands to plot,
>
> plot(file3$lat,file3$STotwoKm,pch=21,cex=2.5,ylim=c(-0.2,2.5),
> xlim=c(-50,50),xlab=NA,ylab=NA,
> col=1, xaxs="i",yaxs="i")
>
> arrows(file3$lat, file3$var1, file3$lat,file3$STotwoKm, col=1, code=3,
> angle=90, length=0.1)
Try using the arrows function with y0 as the lower error bound, y1 as the
upper error bound and code=3, so that arrowheads are drawn at both ends of
the arrow.
You should double check the y coordinates of the arrows. If the y values
are normally distributed, then a 95% confidence interval will give lower
bounds at yvalues + qnorm(0.025)*sqrt(variance), and an upper bound at
yvalues + qnorm(0.975)*sqrt(variance).
Regards,
Richie.
Mathematical Sciences Unit
HSL
"Statistics are like a lamp-post to a drunken man - more for leaning on
than illumination."
David Brent, The Office.
ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
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Re: [R] R object as a function
Thank you very much Duncan for your quick answers.
> You're not passing a function as myfunk1, you're passing mf, which is
> the result of evaluating myfun1, so it's a numeric vector.
Yes, this is exacty my problem.
If I leave it away, the problem will not be resolved (it needs pa or not)
myfun1<-function(x,pa) {
return(pa[1]*x^2+pa[2]*x+pa[3])
}
myfun2<-function(x,param,myfunk1) {
return(param[1]*myfunk1(x)+param[2]*myfunk1(x))
}
test<-function(pars1,pars2,lo,up){
integ=integrate(f=myfun2,lower=lo,upper=up,param=pars2,myfunk1=myfun1)#pa=pars1
return( 2*integ$value )
}
test(pars1=c(1,2,3),pars2=c(-1,1),lo=2,up=7)
Which gives an error:
Once the "argument pa" is missing and if you add the "pa=pars1" in
the comment, it says that the argument pa is redundant.
Thanks for help,
Thomas
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Re: [R] contingency table on data frame
Karin Lagesen wrote:
> I am sorry if this is a faq or tutorial somewhere, but I am unable to
> solve this one.
>
> What I am looking for is a count of how many different
> categories(numbers in this case) that appears for a given factor.
>
> Example:
>
>
>> l <- c("Yes", "No", "Perhaps")
>> x <- factor( sample(l, 10, replace=T), levels=l )
>> m <- c(1:5)
>> y <- factor( sample(m, 10, replace=T), levels=m )
>> z = c(1:10)
>> my_df = data.frame("Z" = z, "Y"= y, "X" = x)
>> my_df
>>
> Z Y X
> 1 1 4 Yes
> 2 2 1 No
> 3 3 2 Perhaps
> 4 4 3 Yes
> 5 5 4 No
> 6 6 5 No
> 7 7 1 Yes
> 8 8 4 Perhaps
> 9 9 4 Yes
> 10 10 2 Perhaps
>
>
> I am now looking for a table that will give me this:
>
> Yes 3 # Yes has these ys: 4,3,1,4, two are the same, ergo 3
> No 3 # No has these ys: 1,4,5
> Perhaps 2 # Perhaps has these ys: 2,4,2
>
Maybe:
apply(table(my_df$X,my_df$Y),1,function(x) sum(x!=0))
domenico
> My dataframe has lots of other colums too, but I only want this
> information out.
>
>
> Thankyou for your help!
>
> Karin
>
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Re: [R] Need suggestions about GUI
Thanks, John,
Here is some code to show what I want to do. BTW, it seems there is a
bug in svalue in gWidgetstcltk for gtext when using the drop=T
argument.
getsel <- function(obj, toolkit, ...) {
### get the selected text from gtext
getWidget <- gWidgetstcltk:::getWidget
if(tclvalue(tktag.ranges(getWidget(obj),"sel")) != "")
### notice
### gWidgetstcltk's _svalue(drop=T)_ has bug. should add tclvalue to
the above line.
{val = tclvalue(tkget(getWidget(obj),"sel.first","sel.last"))}
else val =""#tclvalue(tkget(getWidget(obj),"0.0","end"))
val = unlist(strsplit(val,"\n"))
return(val)
}
get_index <- function(obj, toolkit, ...) {
### get the selected text from gtext, return the index instead of text.
getWidget <- gWidgetstcltk:::getWidget
if(tclvalue(tktag.ranges(getWidget(obj),"sel")) != ""){
val = strsplit(tclvalue(tktag.ranges(getWidget(obj),
"sel")), " ")[[1]]}
else val =c(0,0)
return(as.numeric(val))
}
require(gWidgets)
#initial parameters, storing the relavant information
freecodes <- c("node1","node2")
n_coding <- 0
node <- character(1)
chunk <- character(1)
begin <- numeric(1)
end <- numeric(1)
imported_file <- readLines(file.path(R.home(),"COPYING"))
codepanel <- gpanedgroup(container=gwindow("Code bar"), horizontal = FALSE)
addcode = gdroplist(freecodes,0,container=codepanel,editable=TRUE)
addcodebutton <- gbutton("Add new
code",container=codepanel,handler=function(...) {
if(svalue(addcode)!="")
addcode[length(addcode)+1]<-svalue(addcode)
}
)
## allow the user to change the extant codes -- related to "freecodes" parameter
updatecodes <- gbutton("Update
Codes",container=codepanel,handler=function(...)
assign("freecodes",addcode[seq_len(length(addcode))],pos=1))
## get the items in gdroplist, and push it to variable "freecodes"
coding <- gbutton(" Coding ",container=codepanel,handler=
function(...){
if (svalue(addcode)!="" && sel!=""){
sel <<- paste(getsel(ed),collapse="\n")
sel_index <<- get_index(ed)
n_coding <<- n_coding + 1
node[n_coding] <<- svalue(addcode)
chunk[n_coding] <<- sel
begin[n_coding] <<- sel_index[1]
end[n_coding] <<- sel_index[2]
}}
)
## coding: get seleted text from gtext and link it to specific code/node.
ed <- gtext(con=T,width=500) # gtext
svalue(ed) <- imported_file # push it file to gtext
# steps to using this "toy":
1, enter new code names into the droplist box, for example node3, then
click "add new code"
2, select specific code, for example node2.
3, select text chunk in the gtext, and click coding. repeat step 3 in
coding process.
4, We can see what's been coded by inpecting variable of "node","chunk".
What I don't know how to do:
1, When I select specific code, and click some button (for example
highligh), all the text chunk related to that code will be highlighted
(through color or font style etc.)
2, I would like to arganize the codes like a tree. The code tree and
reorganized by drag and drop.
3, In the coding buttong, how can I avoid using <<- in handler function.
2008/1/22, j verzani <[EMAIL PROTECTED]>:
> ronggui gmail.com> writes:
>
> > Thanks.
> >
> > gWidgets is quite good. However, I want to get the selection text chunk as
> > well as the index, but the index arguments does not work for gtext.
> >
> > > obj<-gtext(cont=T)
> > > svalue(obj,drop=T)
> > [1] "cde"
> > > svalue(obj,drop=T,index=T)
> > [1] "cde"
> >
>
>
>
> The svalue method has the index argument for the widgets where you might want
> to
> return the index or value such with a radio button group or combobox. For
> gtext, the drop argument when TRUE returns just the text selected by the
> mouse,
> otherwise the entire text buffer is returned.
>
> library(gWidgets)
> options("guiToolkit"="RGtk2")
> obj = gtext("sadfsad",cont=T)
> svalue(obj) ## returns: "sadfsad\n"
> svalue(obj,drop=TRUE) ## returns ""
> ## now highlight some text
> svalue(obj,drop=TRUE) ## returns "dfsa"
>
> If you want to email me a bit more detail as to what you are trying to do, I
> can
> let you know if gWidgets can work for you.
>
> --John
> >
>
> > 2008/1/21, Gabor Grothendieck gmail.com>:
> > >
> > > You can find examples of using tcltk here:
> > >
> > > http://www.sciviews.org/_rgui/tcltk/
> > >
> > > Also the gwidgets package is a toolkit independent
> > > layer that can run on top of tcltk or RGtk and it is described
> > > with many examples here:
> > >
> > > http://wiener.math.csi.cuny.edu/pmg/gWidgets
> > >
> > > On Jan 21, 2008 4:02 AM, ronggui gmail.com> wrote:
> > > > What I want to do is:
> > > > 1, creat a text box, insert text into that box.
> > > > 2, select chunk of of the text by mouse, and link it to a lable. so I
> > > would
> > > > like a way to get that chunk of text.
> > > >
> > > > Can I do such job with tcltk? Any relavant tutorial materials?
> > > >
> > > > Thanks
> > > >
> > > > --
> > > > HUANG Ronggui
> > > >
> > > > Bachelor of S
[R] CRAN down?
I am having problems to access the r-project.org homepage, someone else as well? (I know there are CRAN mirrors but they link back on the main page if I search something) Stefan __ 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] CRAN down?
On 1/22/2008 8:04 AM, Stefan Grosse wrote: > I am having problems to access the r-project.org homepage, someone else as > well? > > (I know there are CRAN mirrors but they link back on the main page if I > search > something) They look fine from here. (By the way, the r-project.org homepage is different from CRAN. I had trouble with www.r-project.org on the weekend, but haven't seen any cran.r-project.org problems in a while.) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding an Sweave Vignette to a package
Thanks, Uwe. Before I modify this path, I want to make sure of one
thing. My path is set according to the specifications in the document
prescribed by Duncan Murdoch (at link below). Indeed, my path includes
the proper location of my MikTex and pdflatex.exe files. Here is my path
from the command you gave below:
"c:\\Rtools\\bin;C:\\Perl\\bin\\;c:\\Rtools\\MinGW\\bin;c:\\texmf\\mikte
k\\bin;c:\\cygwin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System3
2\\Wbem;C:\\subversion\\Subversion\\bin;C:\\Program
Files\\R\\R-2.2.0\\bin; "
http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset
AFAIK, the path indeed is set according to the Murdoch prescription for
building R packages, my pdflatex.exe lives in the directory pointed to
in this path, yet R cannot see it when doing Rcmd build.
I can successfully build and use the package at this point (again as my
other problem now solved). However, I am not sure what I should work on
to resolve the issue of building the vignette.
There are so many steps in building a package, I may have missed
something somewhere. So, if you see an error I appreciate any advice.
Harold
> -Original Message-
> From: Uwe Ligges [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, January 22, 2008 4:15 AM
> To: Doran, Harold
> Cc: James W. MacDonald; R Help
> Subject: Re: [R] Adding an Sweave Vignette to a package
>
> In R, type
> Sys.getenv("PATH")
> and you will probably find that the PATH does not include the
> path of the pdflatex executable of the mikTeX distribution.
>
> Uwe
>
>
> Doran, Harold wrote:
> > Jim
> >
> > First thanks for your patience. I use MikTex as well. I do
> have both
> > (texti2dvi and pdflatex) on my local machine. I copied and
> pasted the
> > code below and stepped through it. I think this break down with the
> > following error. Indeed, I think there is a path problem.
> >
> > However, I don't see a resolution in either Writing R Extensions or
> > the Leisch paper. So, I'm not quite sure what path to
> modify and/or how.
> >
> > Error in texi2dvi("TheVignette.tex", pdf = TRUE) :
> > unable to run pdflatex on 'TheVignette.tex'
> > In addition: Warning message:
> > In system(paste(shQuote(latex), "-interaction=nonstopmode",
> texfile)) :
> > "pdflatex" not found
> >
> >> -Original Message-
> >> From: James W. MacDonald [mailto:[EMAIL PROTECTED]
> >> Sent: Monday, January 21, 2008 4:53 PM
> >> To: Doran, Harold
> >> Cc: R Help
> >> Subject: Re: [R] Adding an Sweave Vignette to a package
> >>
> >> What TeX variant are you using? If texi2dvi() can't find
> texi2dvi, it
> >> tries to fall back on pdflatex which has to be in the path.
> >>
> >> I have always had good luck with MikTeX, which does have texi2dvi.
> >>
> >> You could always try
> >>
> >> library(tools)
> >> Sweave("TheVignette.Rnw")
> >> debug(texi2dvi)
> >> texi2dvi("TheVignette.tex", pdf=TRUE)
> >>
> >> and step through to see where it fails, although on the surface it
> >> looks like a path problem.
> >>
> >> Best,
> >>
> >> Jim
> >>
> >>
> >>
> >> Doran, Harold wrote:
> >>> There is now and it looks like I got through the first
> >> phase. But, now
> >>> I get the error below.
> >>>
> >>> * DONE (MiscPsycho)
> >>> * creating vignettes ... ERROR
> >>> Loading required package: statmod
> >>> Below is what alpha *would be* if the item were removed
> >>>
> >>> Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
> >>> quiet)
> >>> :
> >>> unable to run pdflatex on 'MP.tex'
> >>> Calls: buildVignettes -> texi2dvi
> >>> In addition: Warning messages:
> >>> 1: In readLines(f[1]) : incomplete final line found on 'MP.Rnw'
> >>> 2: In system(paste(shQuote(latex), "-interaction=nonstopmode",
> >>> texfile))
> >>> :
> >>> "pdflatex" not found
> >>> Execution halted
> >>>
> >>> I do have pdflatex, it's what I use all of the time.
> >> However, how do I
> >>> point to it for this build process?
> >>>
> -Original Message-
> From: James W. MacDonald [mailto:[EMAIL PROTECTED]
> Sent: Monday, January 21, 2008 4:09 PM
> To: Doran, Harold
> Cc: R Help
> Subject: Re: [R] Adding an Sweave Vignette to a package
>
> Hi Harold,
>
> Doran, Harold wrote:
> > I'm finalizing development of a package that will include a
> vignette.
> > Without the vignette, the package builds fine with no
> warnings and is
> > ready for distribution. Now, I am following the directions for
> > developing vignettes "Sweave, Part II: Package Vignettes"
> by Friedrich
> > Leisch.
> >
> > I am using a windows XP machine (other session info
> >> below). Here is
> > what I have done.
> >
> > 1) I add the 'inst/doc' directory to the package source tree.
> > 2) I have added the following information in the preamble
> of the .Rnw
> > file
> >
> > % \VignetteIndexEntry{An \texttt{R} Package for Miscellaneous
> > Psychometric Analyses} % \Vign
Re: [R] R object as a function
On 1/22/2008 7:52 AM, Thomas Steiner wrote:
> Thank you very much Duncan for your quick answers.
>
>> You're not passing a function as myfunk1, you're passing mf, which is
>> the result of evaluating myfun1, so it's a numeric vector.
>
> Yes, this is exacty my problem.
> If I leave it away, the problem will not be resolved (it needs pa or not)
>
> myfun1<-function(x,pa) {
> return(pa[1]*x^2+pa[2]*x+pa[3])
> }
> myfun2<-function(x,param,myfunk1) {
> return(param[1]*myfunk1(x)+param[2]*myfunk1(x))
> }
> test<-function(pars1,pars2,lo,up){
>
> integ=integrate(f=myfun2,lower=lo,upper=up,param=pars2,myfunk1=myfun1)#pa=pars1
> return( 2*integ$value )
> }
> test(pars1=c(1,2,3),pars2=c(-1,1),lo=2,up=7)
>
> Which gives an error:
> Once the "argument pa" is missing and if you add the "pa=pars1" in
> the comment, it says that the argument pa is redundant.
myfun2 has no pa argument, but it calls (through myfunk1) myfun1 which
does. Where is pa supposed to come from?
You need to think carefully about the requirements for arguments to each
of your functions. Look at every function call, and make sure the
arguments you are passing match the arguments in the header of the
function you call.
Duncan Murdoch
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[R] Can I StepAIC a ggwr object??
Hello everyone, I'm working on some ggwr model and I obtained a .ggwr object, now I'm ascking: Can I StepAIC the object to evaluate the best model and decide what variables, should get in??? Thanks Luca Moiana PhD Candidate - Environmental Science University of Milan - Bicocca _ [[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] CRAN down?
Stefan Grosse wrote: > I am having problems to access the r-project.org homepage, someone else as > well? > > (I know there are CRAN mirrors but they link back on the main page if I > search > something) > > Stefan > > It's up for me now, but I had rather slow access earlier in the day. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-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 an Sweave Vignette to a package
Actually, I'm running 2.6.1. The old version is in the path, but I am
working with the most recent version. I am working in DOS and am at the
prompt c:\program files\r\r-2.6.1\bin. From here I do all of the work in
building the package (build, check, install).
> -Original Message-
> From: Uwe Ligges [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, January 22, 2008 9:02 AM
> To: Doran, Harold
> Cc: R Help
> Subject: Re: [R] Adding an Sweave Vignette to a package
>
>
>
> Doran, Harold wrote:
> > Thanks, Uwe. Before I modify this path, I want to make sure of one
> > thing. My path is set according to the specifications in
> the document
> > prescribed by Duncan Murdoch (at link below). Indeed, my
> path includes
> > the proper location of my MikTex and pdflatex.exe files. Here is my
> > path from the command you gave below:
> >
> >
> "c:\\Rtools\\bin;C:\\Perl\\bin\\;c:\\Rtools\\MinGW\\bin;c:\\texmf\\mik
> > te
> >
> k\\bin;c:\\cygwin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\Syste
> > m3 2\\Wbem;C:\\subversion\\Subversion\\bin;C:\\Program
> > Files\\R\\R-2.2.0\\bin; "
> >
> >
> http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset
> >
> > AFAIK, the path indeed is set according to the Murdoch prescription
> > for building R packages, my pdflatex.exe lives in the directory
> > pointed to in this path, yet R cannot see it when doing Rcmd build.
> >
> > I can successfully build and use the package at this point
> (again as
> > my other problem now solved). However, I am not sure what I should
> > work on to resolve the issue of building the vignette.
> >
> > There are so many steps in building a package, I may have missed
> > something somewhere. So, if you see an error I appreciate
> any advice.
>
> Hmm, hard to tell, although I think it might make sense to
> upgrade your version of R, given I am correct that you are
> running R-2.2.0 (from the output you gave above).
>
> Uwe
>
>
> > Harold
> >
> >
> >> -Original Message-
> >> From: Uwe Ligges [mailto:[EMAIL PROTECTED]
> >> Sent: Tuesday, January 22, 2008 4:15 AM
> >> To: Doran, Harold
> >> Cc: James W. MacDonald; R Help
> >> Subject: Re: [R] Adding an Sweave Vignette to a package
> >>
> >> In R, type
> >> Sys.getenv("PATH")
> >> and you will probably find that the PATH does not include
> the path of
> >> the pdflatex executable of the mikTeX distribution.
> >>
> >> Uwe
> >>
> >>
> >> Doran, Harold wrote:
> >>> Jim
> >>>
> >>> First thanks for your patience. I use MikTex as well. I do
> >> have both
> >>> (texti2dvi and pdflatex) on my local machine. I copied and
> >> pasted the
> >>> code below and stepped through it. I think this break
> down with the
> >>> following error. Indeed, I think there is a path problem.
> >>>
> >>> However, I don't see a resolution in either Writing R
> Extensions or
> >>> the Leisch paper. So, I'm not quite sure what path to
> >> modify and/or how.
> >>> Error in texi2dvi("TheVignette.tex", pdf = TRUE) :
> >>> unable to run pdflatex on 'TheVignette.tex'
> >>> In addition: Warning message:
> >>> In system(paste(shQuote(latex), "-interaction=nonstopmode",
> >> texfile)) :
> >>> "pdflatex" not found
> >>>
> -Original Message-
> From: James W. MacDonald [mailto:[EMAIL PROTECTED]
> Sent: Monday, January 21, 2008 4:53 PM
> To: Doran, Harold
> Cc: R Help
> Subject: Re: [R] Adding an Sweave Vignette to a package
>
> What TeX variant are you using? If texi2dvi() can't find
> >> texi2dvi, it
> tries to fall back on pdflatex which has to be in the path.
>
> I have always had good luck with MikTeX, which does have
> texi2dvi.
>
> You could always try
>
> library(tools)
> Sweave("TheVignette.Rnw")
> debug(texi2dvi)
> texi2dvi("TheVignette.tex", pdf=TRUE)
>
> and step through to see where it fails, although on the
> surface it
> looks like a path problem.
>
> Best,
>
> Jim
>
>
>
> Doran, Harold wrote:
> > There is now and it looks like I got through the first
> phase. But, now
> > I get the error below.
> >
> > * DONE (MiscPsycho)
> > * creating vignettes ... ERROR
> > Loading required package: statmod
> > Below is what alpha *would be* if the item were removed
> >
> > Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
> > quiet)
> > :
> > unable to run pdflatex on 'MP.tex'
> > Calls: buildVignettes -> texi2dvi
> > In addition: Warning messages:
> > 1: In readLines(f[1]) : incomplete final line found on 'MP.Rnw'
> > 2: In system(paste(shQuote(latex), "-interaction=nonstopmode",
> > texfile))
> > :
> > "pdflatex" not found
> > Execution halted
> >
> > I do have pdflatex, it's what I use all of the time.
> However, how do I
> > point to it for this build process?
> >
> >> -Original Me
Re: [R] dendrogram - got it , just need to label :)
Hi!
To label your dendrogram edges with the path to each of them, execute the
following script (assuming that your dendrogram is 'dend', see last 2
lines).
dendrapplyGlobal <- function(dend,attrName,FUN,...,attrNameTo=NULL) {
if (is.null(attrNameTo)) {
attrNameTo <- attrName
}
funcGet <- function(x){
attr(x,attrName)
}
funcSet <- function(x,value){
attr(x,attrNameTo) <- value
return(x)
}
values <- dendrapplyToVector(dend,funcGet)
values <- FUN(values,...)
ret <- dendrapplyFromVector(dend,values,funcSet)
return(ret)
}
dendrapplyToVector <- function(X,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,path="") {
if (is.leaf(d)) {
ret <- c(FUN(d))
names(ret)[1] <- substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
ret <- vector()
for (j in seq_along(d)) {
addr <- paste(path,j,".",sep="")
ret <- append(ret,Napply(d[[j]],addr))
}
ret <- append(ret,FUN(d))
names(ret)[length(ret)] <-
substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
Napply(X)
}
dendrapplyFromVector <- function(X,theVector,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,v) {
if (is.leaf(d)) {
ret <- FUN(d,v)
return(ret)
} else {
ret <- d
if (!is.list(ret))
ret <- as.list(ret)
i <- 1
memsum <- 0
for (j in seq_along(d)) {
childrenCount <- getDendrogramNodeCount(d[[j]])
memsum <- memsum + childrenCount
indices <- i:(i+childrenCount-1)
ret[[j]] <- Napply(d[[j]],v[indices])
i <- i + childrenCount
}
ret <- FUN(ret,v[i])
}
return(ret)
}
Napply(X,theVector)
}
dend1 <- dendrapplyGlobal(dend,
"height",function(x){names(x)},attrNameTo="edgetext")
plot(dend1)
hth,
Florian
--
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] contingency table on data frame
It is not a good idea to use "sample' when building an
example like this! Running the code does not give the
example dataframe.
This is crude but it will do what you want.
x <- " Z Y X
1 4 Yes
2 1 No
3 2 Perhaps
4 3 Yes
5 4 No
6 5 No
7 1 Yes
8 4 Perhaps
9 4 Yes
10 2 Perhaps "
xx <- read.table(textConnection(x), header=TRUE,
as.is=TRUE); xx
df1 <- data.frame(xx[,3],xx[,2]) ; df1
df2 <- unique(df1)
table(df2[,1])
--- Karin Lagesen <[EMAIL PROTECTED]>
wrote:
>
> I am sorry if this is a faq or tutorial somewhere,
> but I am unable to
> solve this one.
>
> What I am looking for is a count of how many
> different
> categories(numbers in this case) that appears for a
> given factor.
>
> Example:
>
> > l <- c("Yes", "No", "Perhaps")
> > x <- factor( sample(l, 10, replace=T), levels=l )
> > m <- c(1:5)
> > y <- factor( sample(m, 10, replace=T), levels=m )
> > z = c(1:10)
> > my_df = data.frame("Z" = z, "Y"= y, "X" = x)
> > my_df
> Z Y X
> 1 1 4 Yes
> 2 2 1 No
> 3 3 2 Perhaps
> 4 4 3 Yes
> 5 5 4 No
> 6 6 5 No
> 7 7 1 Yes
> 8 8 4 Perhaps
> 9 9 4 Yes
> 10 10 2 Perhaps
> >
>
> I am now looking for a table that will give me this:
>
> Yes 3 # Yes has these ys: 4,3,1,4, two
> are the same, ergo 3
> No 3 # No has these ys: 1,4,5
> Perhaps 2 # Perhaps has these ys: 2,4,2
>
> My dataframe has lots of other colums too, but I
> only want this
> information out.
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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] Presenting results from multiple models in LaTeX table
Create a data frame from the coefficients of your summary.lm objects and use xtable.data.frame to latex that. At the R console this will display the relevant source code to see how to do it: xtable:::xtable.lm xtable:::xtable.summary.lm On Jan 22, 2008 9:02 AM, 宋时歌 <[EMAIL PROTECTED]> wrote: > Dear All, > > Is there a way to present results from multiple models in one LaTeX > table? I did some google search and found out that xtable cannot > automate this process > (https://stat.ethz.ch/pipermail/r-help/2006-August/74.html), are > there other alternatives? What about Design and Hmisc? Thanks. > > Best, > Shige > > __ > 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] Risk Management (Solvency or Basileia)
Dear Users, Anyone knows a good package to works with risk management? In particularly, if exist works in R about Solvency or Basileia projects? Best Regards Ana Patrícia Martins [[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] Adding an Sweave Vignette to a package
Doran, Harold wrote:
> Thanks, Uwe. Before I modify this path, I want to make sure of one
> thing. My path is set according to the specifications in the document
> prescribed by Duncan Murdoch (at link below). Indeed, my path includes
> the proper location of my MikTex and pdflatex.exe files. Here is my path
> from the command you gave below:
>
> "c:\\Rtools\\bin;C:\\Perl\\bin\\;c:\\Rtools\\MinGW\\bin;c:\\texmf\\mikte
> k\\bin;c:\\cygwin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System3
> 2\\Wbem;C:\\subversion\\Subversion\\bin;C:\\Program
> Files\\R\\R-2.2.0\\bin; "
>
> http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset
>
> AFAIK, the path indeed is set according to the Murdoch prescription for
> building R packages, my pdflatex.exe lives in the directory pointed to
> in this path, yet R cannot see it when doing Rcmd build.
>
> I can successfully build and use the package at this point (again as my
> other problem now solved). However, I am not sure what I should work on
> to resolve the issue of building the vignette.
>
> There are so many steps in building a package, I may have missed
> something somewhere. So, if you see an error I appreciate any advice.
Hmm, hard to tell, although I think it might make sense to upgrade your
version of R, given I am correct that you are running R-2.2.0 (from the
output you gave above).
Uwe
> Harold
>
>
>> -Original Message-
>> From: Uwe Ligges [mailto:[EMAIL PROTECTED]
>> Sent: Tuesday, January 22, 2008 4:15 AM
>> To: Doran, Harold
>> Cc: James W. MacDonald; R Help
>> Subject: Re: [R] Adding an Sweave Vignette to a package
>>
>> In R, type
>> Sys.getenv("PATH")
>> and you will probably find that the PATH does not include the
>> path of the pdflatex executable of the mikTeX distribution.
>>
>> Uwe
>>
>>
>> Doran, Harold wrote:
>>> Jim
>>>
>>> First thanks for your patience. I use MikTex as well. I do
>> have both
>>> (texti2dvi and pdflatex) on my local machine. I copied and
>> pasted the
>>> code below and stepped through it. I think this break down with the
>>> following error. Indeed, I think there is a path problem.
>>>
>>> However, I don't see a resolution in either Writing R Extensions or
>>> the Leisch paper. So, I'm not quite sure what path to
>> modify and/or how.
>>> Error in texi2dvi("TheVignette.tex", pdf = TRUE) :
>>> unable to run pdflatex on 'TheVignette.tex'
>>> In addition: Warning message:
>>> In system(paste(shQuote(latex), "-interaction=nonstopmode",
>> texfile)) :
>>> "pdflatex" not found
>>>
-Original Message-
From: James W. MacDonald [mailto:[EMAIL PROTECTED]
Sent: Monday, January 21, 2008 4:53 PM
To: Doran, Harold
Cc: R Help
Subject: Re: [R] Adding an Sweave Vignette to a package
What TeX variant are you using? If texi2dvi() can't find
>> texi2dvi, it
tries to fall back on pdflatex which has to be in the path.
I have always had good luck with MikTeX, which does have texi2dvi.
You could always try
library(tools)
Sweave("TheVignette.Rnw")
debug(texi2dvi)
texi2dvi("TheVignette.tex", pdf=TRUE)
and step through to see where it fails, although on the surface it
looks like a path problem.
Best,
Jim
Doran, Harold wrote:
> There is now and it looks like I got through the first
phase. But, now
> I get the error below.
>
> * DONE (MiscPsycho)
> * creating vignettes ... ERROR
> Loading required package: statmod
> Below is what alpha *would be* if the item were removed
>
> Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
> quiet)
> :
> unable to run pdflatex on 'MP.tex'
> Calls: buildVignettes -> texi2dvi
> In addition: Warning messages:
> 1: In readLines(f[1]) : incomplete final line found on 'MP.Rnw'
> 2: In system(paste(shQuote(latex), "-interaction=nonstopmode",
> texfile))
> :
> "pdflatex" not found
> Execution halted
>
> I do have pdflatex, it's what I use all of the time.
However, how do I
> point to it for this build process?
>
>> -Original Message-
>> From: James W. MacDonald [mailto:[EMAIL PROTECTED]
>> Sent: Monday, January 21, 2008 4:09 PM
>> To: Doran, Harold
>> Cc: R Help
>> Subject: Re: [R] Adding an Sweave Vignette to a package
>>
>> Hi Harold,
>>
>> Doran, Harold wrote:
>>> I'm finalizing development of a package that will include a
>> vignette.
>>> Without the vignette, the package builds fine with no
>> warnings and is
>>> ready for distribution. Now, I am following the directions for
>>> developing vignettes "Sweave, Part II: Package Vignettes"
>> by Friedrich
>>> Leisch.
>>>
>>> I am using a windows XP machine (other session info
below). Here is
>>> what I have done.
>>>
>>> 1) I add the 'in
[R] Presenting results from multiple models in LaTeX table
Dear All, Is there a way to present results from multiple models in one LaTeX table? I did some google search and found out that xtable cannot automate this process (https://stat.ethz.ch/pipermail/r-help/2006-August/74.html), are there other alternatives? What about Design and Hmisc? Thanks. Best, Shige __ 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] list.files sorted by date
xx<- file.info(dir()); xx xx[order(xx$mtime),] ? --- Alberto Monteiro <[EMAIL PROTECTED]> wrote: > Is there any (list.files)-like function that sorts > the files by > (modification) date? > > Alberto Monteiro > > __ > 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. > Looking for the perfect gift? Give the gift of Flickr! __ 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] accessing the "address" of items in a recursive list
j daniel wrote:
>
>
> I would like to print the "address" of the smaller dendrograms on the edge
> similar to this:
>
> addr <- function(n) {
> if(!is.leaf(n)) {
> attr(n, "edgetext") <- paste("height of",(attr(n,"height"))
> }
> n
> }
> labeledDends <- dendrapply(dend, addr)
>
> Where "i,j,k" is printed instead of "height". But I have not been able to
> figure out how to ask each dendrogram its address within the dendrapply
> function. Can anyone help me with this?
>
>
Hi!
Load the following four functions into R and execute this (assuming your
dendrogram is in variable 'dend')
newdend <- dendrapplyGlobal(dend,
"height",function(x){names(x)},attrNameTo="edgetext")
#From the specified dendrogram X a vector of all values of the specified
#node attribute is extracted, modified by the function FUN and a new
#dendrogram is created using the new values for the attribute. Optionally,
#a different attribute can be set using 'attrNameTo'
dendrapplyGlobal <- function(X,attrName,FUN,...,attrNameTo=NULL) {
if (is.null(attrNameTo)) {
attrNameTo <- attrName
}
funcGet <- function(x){
attr(x,attrName)
}
funcSet <- function(x,value){
attr(x,attrNameTo) <- value
return(x)
}
values <- dendrapplyToVector(X,funcGet)
values <- FUN(values,...)
ret <- dendrapplyFromVector(X,values,funcSet)
return(ret)
}
#Traverses the dendrogram in postorder and applies FUN to each node.
#The result of each evaluation is stored in the resulting array.
#Additional arguments to FUN can be passed as ...
#The names attribute of the resulting vector is the 'path' to each node.
#This implementation is based on dendrapply(graphics).
dendrapplyToVector <- function(X,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,path="") {
if (is.leaf(d)) {
ret <- c(FUN(d,...))
names(ret)[1] <- substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
ret <- vector()
for (j in seq_along(d)) {
addr <- paste(path,j,".",sep="")
ret <- append(ret,Napply(d[[j]],addr))
}
ret <- append(ret,FUN(d,...))
names(ret)[length(ret)] <-
substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
Napply(X)
}
#Traverses the dendrogram X in postorder and constructs a new dendrogram
using
#the specified function FUN and vector parVec. Each element of parVec must
#relate to a node in X, which is the case if parVec was created using
#dendrapplyToVector().
#Additional arguments to FUN can be passed as ...
#This implementation is based on dendrapply(graphics).
dendrapplyFromVector <- function(X,parVec,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,v) {
if (is.leaf(d)) {
ret <- FUN(d,v,...)
return(ret)
} else {
ret <- d
if (!is.list(ret))
ret <- as.list(ret)
i <- 1
for (j in seq_along(d)) {
childrenCount <- getDendrogramNodeCount(d[[j]])
indices <- i:(i+childrenCount-1)
ret[[j]] <- Napply(d[[j]],v[indices])
i <- i + childrenCount
}
ret <- FUN(ret,v[i],...)
}
return(ret)
}
Napply(X,parVec)
}
#Returns the number of nodes in a dendrogram.
getDendrogramNodeCount <- function(dend) {
if (!is.leaf(dend)){
childrenSum <- 0
for (child in dend) {
childrenSum <- childrenSum +
getDendrogramNodeCount(child)
}
return(childrenSum+1)
}
return(1)
}
--
View this message in context:
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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] predict from a multiple regression model
Hello how can I predict from a lm-object over a range of values of one explanatory variable without having to specify values for all the other explanatory variables? e.g. mod<-lm(y~x1+x2+x3+x4) x1.new<-seq(0, 100) predict(mod, new=list(x1=x1.new)) Here, predict() does not work, since values for x2, x3 and x4 are missing. Is there a function or argument that, in such a case, averages or weights over the other explanatory variables, how it is done in Genstat? Thanks Fränzi Dr. Fränzi Korner-Nievergelt oikostat - Statistische Analysen und Beratung Ausserdorf 43 CH - 6218 Ettiswil Tel.: +41 (0) 41 980 49 22 www.oikostat.ch * Schweizerische Vogelwarte CH - 6204 Sempach www.vogelwarte.ch * [[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] select repositories under linux
Agreed, i had no idea that this is a Bioconductor package.
G.
On Tue, Jan 22, 2008 at 09:49:50AM -0500, James W. MacDonald wrote:
> This is questionable advice for many CRAN packages, and horrible advice
> for a Bioconductor package. If there are any dependencies (and BioC
> packages often have many, and their dependencies may have
> dependencies...) you can end up in download hell, all because you have
> ignored the functionality that exists in R to handle such things.
>
> As other posters have noted, you can use setRepositories(). You can also
> set this in your .Rprofile file with something like
>
> options(repos=(CRAN="http://ACloseRepository";))
>
> so you don't have to do anything interactively.
>
> Then use install.packages(), with dependencies=TRUE if you think there
> may be dependencies (although I don't think it hurts if there are none).
>
> For Bioconductor packages, use biocLite()
>
> source("http://www.bioconductor.org/biocLite.R";)
> biocLite("GEOquery")
>
> Best,
>
> Jim
>
>
> Gabor Csardi wrote:
> >Eleni, download the package (I assume you know where it is),
> >on Linux you will need the source package. Then from R type
> >
> >install.packages("", repos=NULL)
> >
> >Gabor
> >
> >On Tue, Jan 22, 2008 at 11:26:12AM +0200, Eleni Christodoulou wrote:
> >>Hi all,
> >>
> >>I am trying to install the package "GEOquery" in unix. I have downloaded
> >>the
> >>standard version of R and this package is not contained in the default. I
> >>know that I can select repositories under windows but I don't know how to
> >>do
> >>it in unix. Does anyone have any idea on this?
> >>
> >>Thank you in advance,
> >>Eleni
> >>
> >>[[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.
> >
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
--
Csardi Gabor <[EMAIL PROTECTED]>UNIL DGM
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Re: [R] accessing the "address" of items in a recursive list
j daniel wrote:
>
>
> I would like to print the "address" of the smaller dendrograms on the edge
> similar to this:
>
> addr <- function(n) {
> if(!is.leaf(n)) {
> attr(n, "edgetext") <- paste("height of",(attr(n,"height"))
> }
> n
> }
> labeledDends <- dendrapply(dend, addr)
>
> Where "i,j,k" is printed instead of "height". But I have not been able to
> figure out how to ask each dendrogram its address within the dendrapply
> function. Can anyone help me with this?
>
>
Hi!
Load the following four functions into R and execute this (assuming your
dendrogram is in variable 'dend')
newdend <- dendrapplyGlobal(dend,
"height",function(x){names(x)},attrNameTo="edgetext")
#From the specified dendrogram X a vector of all values of the specified
#node attribute is extracted, modified by the function FUN and a new
#dendrogram is created using the new values for the attribute. Optionally,
#a different attribute can be set using 'attrNameTo'
dendrapplyGlobal <- function(X,attrName,FUN,...,attrNameTo=NULL) {
if (is.null(attrNameTo)) {
attrNameTo <- attrName
}
funcGet <- function(x){
attr(x,attrName)
}
funcSet <- function(x,value){
attr(x,attrNameTo) <- value
return(x)
}
values <- dendrapplyToVector(X,funcGet)
values <- FUN(values,...)
ret <- dendrapplyFromVector(X,values,funcSet)
return(ret)
}
#Traverses the dendrogram in postorder and applies FUN to each node.
#The result of each evaluation is stored in the resulting array.
#Additional arguments to FUN can be passed as ...
#The names attribute of the resulting vector is the 'path' to each node.
#This implementation is based on dendrapply(graphics).
dendrapplyToVector <- function(X,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,path="") {
if (is.leaf(d)) {
ret <- c(FUN(d,...))
names(ret)[1] <- substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
ret <- vector()
for (j in seq_along(d)) {
addr <- paste(path,j,".",sep="")
ret <- append(ret,Napply(d[[j]],addr))
}
ret <- append(ret,FUN(d,...))
names(ret)[length(ret)] <-
substr(path,start=1,stop=nchar(path)-1)
return(ret)
}
Napply(X)
}
#Traverses the dendrogram X in postorder and constructs a new dendrogram
using
#the specified function FUN and vector parVec. Each element of parVec must
#relate to a node in X, which is the case if parVec was created using
#dendrapplyToVector().
#Additional arguments to FUN can be passed as ...
#This implementation is based on dendrapply(graphics).
dendrapplyFromVector <- function(X,parVec,FUN,...) {
FUN <- match.fun(FUN)
if (!inherits(X, "dendrogram"))
stop("'X' is not a dendrogram")
Napply <- function(d,v) {
if (is.leaf(d)) {
ret <- FUN(d,v,...)
return(ret)
} else {
ret <- d
if (!is.list(ret))
ret <- as.list(ret)
i <- 1
for (j in seq_along(d)) {
childrenCount <- getDendrogramNodeCount(d[[j]])
indices <- i:(i+childrenCount-1)
ret[[j]] <- Napply(d[[j]],v[indices])
i <- i + childrenCount
}
ret <- FUN(ret,v[i],...)
}
return(ret)
}
Napply(X,parVec)
}
#Returns the number of nodes in a dendrogram.
getDendrogramNodeCount <- function(dend) {
if (!is.leaf(dend)){
childrenSum <- 0
for (child in dend) {
childrenSum <- childrenSum +
getDendrogramNodeCount(child)
}
return(childrenSum+1)
}
return(1)
}
hth,
Florian
--
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[R] Lattice on FreeBSD
Hi list I tried to install package lattice on FreeBSD, but install.package() does not seem to find it in the repositories, even trying different mirrors. Could it be that lattice package is not available for FreeBSD? -- Armin Goralczyk, M.D. -- Universitätsmedizin Göttingen Abteilung Allgemein- und Viszeralchirurgie Rudolf-Koch-Str. 40 39099 Göttingen -- Dept. of General Surgery University of Göttingen Göttingen, Germany -- http://www.gwdg.de/~agoralc __ 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] Lattice on FreeBSD
It is definitely on CRAN: http://cran.at.r-project.org/src/contrib/Descriptions/lattice.html You can download and install it "by hand", but if you want to make install.packages work, please give us at least an error message or something. G. On Tue, Jan 22, 2008 at 03:29:19PM +0100, Armin Goralczyk wrote: > Hi list > I tried to install package lattice on FreeBSD, but install.package() > does not seem to find it in the repositories, even trying different > mirrors. Could it be that lattice package is not available for > FreeBSD? > > -- > Armin Goralczyk, M.D. > -- > Universitätsmedizin Göttingen > Abteilung Allgemein- und Viszeralchirurgie > Rudolf-Koch-Str. 40 > 39099 Göttingen > -- > Dept. of General Surgery > University of Göttingen > Göttingen, Germany > -- > http://www.gwdg.de/~agoralc > __ > 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. -- Csardi Gabor <[EMAIL PROTECTED]>UNIL DGM __ 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] select repositories under linux
This is questionable advice for many CRAN packages, and horrible advice
for a Bioconductor package. If there are any dependencies (and BioC
packages often have many, and their dependencies may have
dependencies...) you can end up in download hell, all because you have
ignored the functionality that exists in R to handle such things.
As other posters have noted, you can use setRepositories(). You can also
set this in your .Rprofile file with something like
options(repos=(CRAN="http://ACloseRepository";))
so you don't have to do anything interactively.
Then use install.packages(), with dependencies=TRUE if you think there
may be dependencies (although I don't think it hurts if there are none).
For Bioconductor packages, use biocLite()
source("http://www.bioconductor.org/biocLite.R";)
biocLite("GEOquery")
Best,
Jim
Gabor Csardi wrote:
> Eleni, download the package (I assume you know where it is),
> on Linux you will need the source package. Then from R type
>
> install.packages("", repos=NULL)
>
> Gabor
>
> On Tue, Jan 22, 2008 at 11:26:12AM +0200, Eleni Christodoulou wrote:
>> Hi all,
>>
>> I am trying to install the package "GEOquery" in unix. I have downloaded the
>> standard version of R and this package is not contained in the default. I
>> know that I can select repositories under windows but I don't know how to do
>> it in unix. Does anyone have any idea on this?
>>
>> Thank you in advance,
>> Eleni
>>
>> [[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.
>
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
__
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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] 2 Rprofile.site files???
Dear R users, I have been having a problem with my file Rprofile.site. I did already ask the list some suggestions which have been well taken into account but unfortunately have not completely resolved my problem. I seem to have 2 files of Rprofile.site on my computer. If I open the file through " programm files/R/etc/rprofile.site" on my editor I get a different file than if I go on "Display file(s)" on the File option of the menu bar on R. Anyone has an idea why this is happening? Where is R going to find this file? Thank you very much for the attention, Marcia Rocha __ 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] Communicating with R through a named pipe: display refresh problem
Rather, non-interactive R does not run an event loop. The usual way around this is to use a pty, as R run from a pty is considered to be interactive. (Whether a fifo and a named pipe are the same concept is moot: some OSes have one and not the other.) The plan is to use threads in due course to handle X11 events. On Tue, 22 Jan 2008, Parker Jones wrote: > > Hello, > > On a linux system I'm trying to send commands to R through a named pipe and > am *nearly* successful. I can send R commands and can plot graphs. The only > problem I have is getting the x11 display to refresh - it appears to hang > because of the pipe. > > The R server: > $ mkfifo R_pipe > $ R --no-save < R_pipe > > The R client: > $ cat>> R_pipe > > Now, I can send R commands down the pipe: > > Client side: > x <- seq(1,10) > x > > Server side: >> x <- seq(1:10) >> x > [1] 1 2 3 4 5 6 7 8 9 10 > > This is perfect. > > Now if I try to create a plot, e.g. plot(1:100), the server shows >> plot(1:100) > and the plot appears. However, if a window briefly obscures the graphical > output, the x11 device won't refresh the display. It would appear the pipe > is blocking the refresh. > > Can anyone else confirm this happens and any suggestions how to get the > display to refresh? > > Thanks in advance, > PJ -- 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] predict from a multiple regression model
On 1/22/2008 9:50 AM, Fränzi Korner wrote:
> Hello
>
>
>
> how can I predict from a lm-object over a range of values of one explanatory
> variable without having to specify values for all the other explanatory
> variables?
>
>
>
> e.g.
>
>
>
> mod<-lm(y~x1+x2+x3+x4)
>
>
>
> x1.new<-seq(0, 100)
>
> predict(mod, new=list(x1=x1.new))
>
>
>
>
>
> Here, predict() does not work, since values for x2, x3 and x4 are missing.
> Is there a function or argument that, in such a case, averages or weights
> over the other explanatory variables, how it is done in Genstat?
You might consider effect() in the effects package by John Fox. For
example:
library(effects)
mod.pres <- lm(prestige ~ log(income, 10) + poly(education, 3) +
poly(women, 2), data=Prestige)
effect("poly(women,2)", mod.pres, xlevels=list(women = seq(0,100,20)))
poly(women,2) effect
women
0 20 40 60 80 100
47.71028 45.12385 44.53749 45.95121 49.36499 54.77883
> Thanks
>
> Fränzi
>
>
>
>
>
>
>
> Dr. Fränzi Korner-Nievergelt
>
> oikostat - Statistische Analysen und Beratung
>
> Ausserdorf 43
>
> CH - 6218 Ettiswil
>
> Tel.: +41 (0) 41 980 49 22
>
> www.oikostat.ch
>
>
>
> *
>
>
>
> Schweizerische Vogelwarte
>
> CH - 6204 Sempach
>
>
>
> www.vogelwarte.ch
>
> *
>
>
>
>
> [[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.
--
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894
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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] CRAN down?
I was told that they had a UPS failure on one of the servers at the weekend. It has been up and down for parts of each of the last three days, with many down periods (both short and long). On Tue, 22 Jan 2008, Peter Dalgaard wrote: Stefan Grosse wrote: I am having problems to access the r-project.org homepage, someone else as well? (I know there are CRAN mirrors but they link back on the main page if I search something) Stefan It's up for me now, but I had rather slow access earlier in the day. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-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] Communicating with R through a named pipe: display refresh problem
> Rather, non-interactive R does not run an event loop. The usual way
> around this is to use a pty, as R run from a pty is considered to be
> interactive.
>
> (Whether a fifo and a named pipe are the same concept is moot: some OSes
> have one and not the other.)
>
> The plan is to use threads in due course to handle X11 events.
>
I agree threads is the way to go.
In the meantime, I also tried a looping server which doesn't block on reads to
a pipe. This still doesn't refresh the display but if R has a command to
refresh the display then that will probably solve the problem.
# based on http://tolstoy.newcastle.edu.au/R/help/01c/2886.html
stream <- fifo("R_pipe", "r", blocking=FALSE,)
repeat
{
a <- readLines(stream)
if(length(a) != 0)
{
e <- try(eval(parse(text = a)))
if (inherits(e, "try-error"))
{
# error handling code here
cat("Error", "\n")
}
}
}
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[R] Duncan's MRT: limitations to qtukey() function?
Dear all, I'm using R to perform multiple comparison testing on agriculture genotype trials. To perform the Duncan's MRT, I use the qtukey() function with the following syntax: qtukey(p = ((1 - 0.05) ^ (pos - 1)), nmeans = pos, df = ni) I experience a strange behaviour when the number of means in the trial and the number of residual degrees of freedom (ni) becomes high (orientatively pos > 30 and ni > 60), i.e. the function returns NaN together with the following message: convergence failed in 'qtukey' Running the code below should reproduce a statistical table for Duncan's MRT, such those reported on old books of agricultural statistics (ex. Steel and Torrie, 1960). table <- matrix(0, 28, 14) pos <- c(10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 50, 100, 200) df <- c(2:20, seq(22, 30, by = 2), 40, 60, 100, 1000) for (i in 1:28) table [i, ] <- qtukey(p = ((1 - 0.05) ^ (pos - 1)), nmeans = pos, df = df[i]) colnames(table) <- pos rownames(table) <- df Indeed, I get several NaN and some odd figures. Am I doing something wrong or is there any intrinsic limit for the values of p, nmeans and df within the qtukey() function? Just in this latter case, is it possible to raise those limits? Some genotype trials can have more than thirty treatments under comparison. I thank you all for your attention. Andrea Onofri Department of Agriculture and Environmental Sciences University of Perugia (ITALY) __ 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] anova function to test the difference between two coefficients in nlme package
Dear Dr. Bates, and R-help, I've tried the anova function to test the difference between two coefficients, as shown on page 225 of your book "Mixed Effects Models in S and S-Plus (Statistics and Computing)". When I type: anova( fm2BW.lme, L = c(TimeDiet2 = 1, TimeDiet3 = -1) ) I got the following error message: Error: unexpected '=' in "anova( fm2BW.lme, L = c(Time:Diet2 =" Could you tell me whether I miss anything? > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] nlme_3.1-85 loaded via a namespace (and not attached): [1] grid_2.6.0 lattice_0.16-5 Thanks, Shirley __ 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 on a supercomputer?
If anyone gets R working with Rmpi and Grid Engine, please let me know. I will need to set up a compute farm with SGE. Thx, --Chi On Jan 21, 2008 8:19 PM, Mark Kimpel <[EMAIL PROTECTED]> wrote: > try Rmpi package > > On Jan 21, 2008 7:13 PM, markaoki <[EMAIL PROTECTED]> wrote: > > > hi, > > Does R have any built-in capabilities that allow one to use in a > > multi-node > > (supercomputer) environment? > > > > For example, MPI'ish commands allowing me to distribute specific R code to > > specific compute nodes? > > > > If not, well, I would have more programming to do. > > > > thanks for any information about this, > > -m.aoki > > > > __ > > 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. > > > > > > -- > -- > Mark W. Kimpel MD > Neuroinformatics > Department of Psychiatry > Indiana University School of Medicine > > [[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] Stationarity of a Time Series
the FinTS package includes in scripts\ch02.R a comparison of 4 different
AFD unit root functions with a published example.
it also includes a function plotArmaTrueacf that computes the roots from
the AR part of a theoretical or fitted model. From this, you can see if
any roots lie near the unit circle. You could wrap this in a Monte
Carlo to test for many nonstandard types of nonstationarity, e.g.
fractional differencing.
sg
Prof Brian Ripley wrote:
> On Tue, 22 Jan 2008, Pfaff, Bernhard Dr. wrote:
>
>
>> Hello Stephen,
>>
>> stationarity tests as well as unit root tests have been implemented in a
>> couple of packages. For instance, as already mentioned: tseries, but
>> also uroot, fUnitRoots and urca. See the annotated task view
>> "Econemtrics" and "Finance" for further information.
>>
>
> But note that these tests apply to just a few ways in which a series might
> be non-stationary: they all seem an econmetrician's view of possible
> non-stationarity.
>
> In the end stationarity is a modelling assumption: it depends on what
> might have happened but did not. E.g. a sine wave process is stationary
> if and only if it has a random (uniform) phase, and you cannot tell that
> from a single realization.
>
> 'Anna Karenina applies'[*] (as to most pure significance tests).
>
> [*] Google it if you need elucidation.
>
>
>> Best,
>> Bernhard
>>
>>
>>> kpss.test in the tsereis package should do the trick
>>>
>>> On Jan 21, 2008 12:36 PM, stephen sefick <[EMAIL PROTECTED]> wrote:
>>>
>>>
Does anyone know of a test for stationarity of a time series, or like
all ordination techniques it is a qualitative assessment of a
quantitative result. Books, papers, etc. suggestions welcome.
thanks
Stephen
--
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff
>>> us up and
>>>
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.
>>> -K. Mullis
>>>
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>>> [[alternative HTML version deleted]]
>>>
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>> *
>> Confidentiality Note: The information contained in this ...{{dropped:10}}
>>
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>
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Re: [R] Duncan's MRT: limitations to qtukey() function?
Andrea Onofri wrote: > Dear all, > > I'm using R to perform multiple comparison testing on agriculture > genotype trials. To perform the Duncan's MRT, I use the qtukey() > function with the following syntax: > > qtukey(p = ((1 - 0.05) ^ (pos - 1)), nmeans = pos, df = ni) > > I experience a strange behaviour when the number of means in the trial > and the number of residual degrees of freedom (ni) becomes high > (orientatively pos > 30 and ni > 60), i.e. the function returns NaN > together with the following message: > > convergence failed in 'qtukey' > > Running the code below should reproduce a statistical table for > Duncan's MRT, such those reported on old books of agricultural > statistics (ex. Steel and Torrie, 1960). > > table <- matrix(0, 28, 14) > pos <- c(10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 50, 100, 200) > df <- c(2:20, seq(22, 30, by = 2), 40, 60, 100, 1000) > for (i in 1:28) table [i, ] <- qtukey(p = ((1 - 0.05) ^ (pos - 1)), > nmeans = pos, df = df[i]) > colnames(table) <- pos > rownames(table) <- df > > Indeed, I get several NaN and some odd figures. > > Am I doing something wrong or is there any intrinsic limit for the > values of p, nmeans and df within the qtukey() function? Just in this > latter case, is it possible to raise those limits? Some genotype trials > can have more than thirty treatments under comparison. > > I thank you all for your attention. > > Andrea Onofri > Department of Agriculture and Environmental Sciences > University of Perugia (ITALY) > > __ > 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. > Yes, this looks a bit suspicious, especially the fact that it worsens with increasing df. The core of the matter seems to be this > qtukey(log(3.689754e-05),200,1000,log=T) [1] NaN Warning messages: 1: In qtukey(log(3.689754e-05), 200, 1000, log = T) : convergence failed in 'qtukey' 2: In qtukey(p, nranges, nmeans, df, lower.tail, log.p) : NaNs produced which presumably is from inverting ptukey, but > f <- Vectorize(function(x)ptukey(x,200,1000,log=T)-log(3.689754e-05)) > curve(f, from=3,to=5) > uniroot(f, c(3,5)) $root [1] 3.760707 $f.root [1] -5.756398e-05 $iter [1] 6 $estim.prec [1] 6.103516e-05 is looking perfectly nice. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-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] a Q about R in unix
Dear All, I finally have chance to have R install on our unix server. However, the system admin asked me if I prefer command-line or gui interface. I have experience with R on linux before but never use R on unix. Here are my questions that I need you guys help. 1) is there a good gui for R/unix like we do for windows and mac? 2) if the answer for 1) is yes, which one is better interms of computing performance and stability, cmd or gui? 3) do you have experience with ess+emacs on unix with R? Any insight? This will be an experimental use of R in our company. If I can make a successful case out of it, we might be able to use it in a larger scale. So your input and help are highly appreciated. === WenSui Liu Statistical Project Manager ChoicePoint Precision Marketing (http://spaces.msn.com/statcompute/blog) __ 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] ODE's in R
have you looked at lsoda{odesolve}?
have you looked at the scripts\CSTR subdirectory in the fda package? it
includes an example worked in both R and Matlab with slightly better
answers in R but with a much longer compute time.
sg
The fda package
Peter Dalgaard wrote:
> Markku Karhunen wrote:
>
>> Thanks, Dr. Maechler.
>>
>>
>>> No, there's no such track.
>>> [ Matlab users coming to R may produce wrong R code
>>> by using 0:n-1 instead of 0:(n-1) ; but I don't assume this
>>> would be the case ]
>>>
>>>
>>>
>>>
>> Been there, done that!
>>
>>
>>> MK> We use just a simple discretisation written in a for loop
>>> MK> and a variable (i.e. user-fed) time step.
>>>
>>> I don't think you should use your own code instead of "professional"
>>> ODE solvers, such as the one in R package 'odesolve'
>>>
>>>
>>>
>>>
>> We must look into that. The problem, maybe, is that in fact half of the
>> equations are, in fact, simple PDE's and I don't know, if you can put
>> them into odesolve.
>>
>>
> Usually, you can convert them to a system of ODE's ("the method of
> lines" if i remember correctly).
>
> One slight caveat with the high-end ODE solvers is that sometimes they
> are too smart for their own good when used in connection with parameter
> estimation. Because of things like adaptive stepsizing, you might end up
> with sums of squared residuals that are non-smooth functions of the
> parameters. This happens especially easily if the system itself is not
> quite smooth (e.g. if your input to the system is a step function).
>
>
>>> MK> Maybe, I'm too neurotic about this, but I guess I just want some
>>> comfort
>>> MK> after seeing a few particularly nasty orbits.
>>>
>>> As we know ``from Chaos theory'', there can be delicate
>>> inhereent and numerical problems in ODE solving..
>>>
>>>
>>>
>> But - to our best knowledge - they should not be any more acute in R,
>> than on any other platform...
>>
>> BR,
>> Markku
>>
>> __
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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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Re: [R] anova function to test the difference between two coefficients in nlme package
Dear Dr. Bates, and R-help,
I just found the reason I got the error message is because I copied
the code directly from the book. When I tried the code in
"~\library\nlme\scripts" under the R installation directory like the
following, I got the same answere as in the book.
anova(fm2BW.lme, L = c("Time:Diet2" = 1, "Time:Diet3" = -1))
Now my question is instead of test the difference between two
coefficients, can I use anova to test the significance of the sum of
two coefficients, like
anova(fm2BW.lme, L = c("Time:Diet2" = 1, "Time:Diet3" = 1))
Thanks,
Shirley
On Jan 22, 2008 10:38 AM, shirley zhang <[EMAIL PROTECTED]> wrote:
> Dear Dr. Bates, and R-help,
>
> I've tried the anova function to test the difference between two
> coefficients, as shown on page 225 of your book "Mixed Effects Models
> in S and S-Plus (Statistics and Computing)".
>
> When I type: anova( fm2BW.lme, L = c(TimeDiet2 = 1, TimeDiet3 = -1) )
>
> I got the following error message:
>
> Error: unexpected '=' in "anova( fm2BW.lme, L = c(Time:Diet2 ="
>
> Could you tell me whether I miss anything?
>
> > sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] nlme_3.1-85
>
> loaded via a namespace (and not attached):
> [1] grid_2.6.0 lattice_0.16-5
>
>
> Thanks,
> Shirley
>
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Re: [R] R object as a function
Dear Duncan,
thanks a lot for your answer. I was think a was distracted by the FED
rate cut ;)
Now it works.
Have a nice day
Thomas
myfun1<-function(x,pa) {
return(pa[1]*x^2+pa[2]*x+pa[3])
}
myfun2<-function(x,param,myfunk1,pa) {
return(param[1]*myfunk1(x,pa)+param[2]*myfunk1(-x,pa))
}
test<-function(pars1,pars2,lo,up){
integ=integrate(f=myfun2,lower=lo,upper=up,param=pars2,myfunk1=myfun1,pa=pars1)
return( integ$value )
}
test(pars1=c(1,2,3),pars2=c(-1,0),lo=1,up=7)
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[R] Recursive Function
It is possible to place two functions in a recursive function Main results so as to simultaneously? [[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] 2 Rprofile.site files???
On 1/22/2008 10:19 AM, [EMAIL PROTECTED] wrote: > Dear R users, > I have been having a problem with my file Rprofile.site. I did already ask > the list some suggestions which have been well taken into account but > unfortunately have not completely resolved my problem. I seem to have 2 files > of Rprofile.site on my computer. If I open the file through " programm > files/R/etc/rprofile.site" on my editor I get a different file than if I go > on "Display file(s)" on the File option of the menu bar on R. Anyone has an > idea why this is happening? Where is R going to find this file? > Thank you very much for the attention, The latter case generally looks in the current directory, which would be unlikely to be R_HOME/etc unless you had explicitly set it there. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R object as a function
On Tuesday 22 January 2008 13:52:29 Thomas Steiner wrote:
> Thank you very much Duncan for your quick answers.
>
> > You're not passing a function as myfunk1, you're passing mf, which is
> > the result of evaluating myfun1, so it's a numeric vector.
>
> Yes, this is exacty my problem.
> If I leave it away, the problem will not be resolved (it needs pa or not)
>
> myfun1<-function(x,pa) {
> return(pa[1]*x^2+pa[2]*x+pa[3])
> }
> myfun2<-function(x,param,myfunk1) {
> return(param[1]*myfunk1(x)+param[2]*myfunk1(x))
> }
> test<-function(pars1,pars2,lo,up){
>
> integ=integrate(f=myfun2,lower=lo,upper=up,param=pars2,myfunk1=myfun1)#pa=p
>ars1 return( 2*integ$value )
> }
> test(pars1=c(1,2,3),pars2=c(-1,1),lo=2,up=7)
>
> Which gives an error:
> Once the "argument pa" is missing and if you add the "pa=pars1" in
> the comment, it says that the argument pa is redundant.
>
If I understood your problem right (i don't know haw integrate() works) the
solution could be as follows
myfun1<-function(x=5,pa) {
return(function(x){pa[1]*x^2+pa[2]*x+pa[3]})
}
It's a substitution for your myfun1 and it gives back a closure (function with
bindings) instead of a numeric.
Hope it helps
Sebastian
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[R] MLE for censored distributions in R
Hi just wondering if there is a package that can get the maximum likelihood or method of moments estimator for distributions with censored data? The distributions I'm interested in are: Exponential, pareto, beta, gamma and lognormal. -- View this message in context: http://www.nabble.com/MLE-for-censored-distributions-in-R-tp15022863p15022863.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] recoding one variable into another - but differently for different cases
Hello, I have 2 variables in my sample Data: Data$A and Data$B Variable Data$A can assume values: 1, 2, 3, and 4. Variable Data$B identifies my cases and can assume values: 1 and 2. I need to recode my variable Data$A into a new variable Data$new such that: People who are Data[Data$B %in% 1, ] are recoded like this: Value on Data$AValue on Data$new 1 +1 2 -1 3 0 4 99 People who are Data[Data$B %in% 2, ] are recoded like this: Value on Data$AValue on Data$new 1 -1 2 +1 3 0 4 99 I am having hard time doing this. Any help would be greatly appreciated. Dimitri __ 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] select repositories under linux
On Tue, 22 Jan 2008, James W. MacDonald wrote:
> This is questionable advice for many CRAN packages, and horrible advice
> for a Bioconductor package. If there are any dependencies (and BioC
> packages often have many, and their dependencies may have
> dependencies...) you can end up in download hell, all because you have
> ignored the functionality that exists in R to handle such things.
But unfortunately the advice below is equally 'questionable'.
> As other posters have noted, you can use setRepositories(). You can also
> set this in your .Rprofile file with something like
>
> options(repos=(CRAN="http://ACloseRepository";))
>
> so you don't have to do anything interactively.
That is not what setRepositories() does: it is what chooseCRANmirror()
does and does not help here.
> Then use install.packages(), with dependencies=TRUE if you think there
> may be dependencies (although I don't think it hurts if there are none).
The default (dependencies=NA) was chosen for good reasons ... it selects
the dependencies you need to run the package, and not others needed to
e.g. check it.
> For Bioconductor packages, use biocLite()
>
> source("http://www.bioconductor.org/biocLite.R";)
> biocLite("GEOquery")
which advice should be clarified by noting that is just a wrapper to the R
facilities to handle multiple repositories, and if you are going to learn
to use those anyway for other repositories it is not necessary to do it
via the wrapper.
setRepositories(ind=c(1,3:6)) # Windows ind = c(1,2, 4:7)
... use install.packages for any CRAN or BioC package
*BUT* beware that some packages have incompatible versions on the two
repositories and that this will pick the largest version number for such.
> Best,
>
> Jim
>
>
> Gabor Csardi wrote:
>> Eleni, download the package (I assume you know where it is),
>> on Linux you will need the source package. Then from R type
>>
>> install.packages("", repos=NULL)
>>
>> Gabor
>>
>> On Tue, Jan 22, 2008 at 11:26:12AM +0200, Eleni Christodoulou wrote:
>>> Hi all,
>>>
>>> I am trying to install the package "GEOquery" in unix. I have downloaded the
>>> standard version of R and this package is not contained in the default. I
>>> know that I can select repositories under windows but I don't know how to do
>>> it in unix. Does anyone have any idea on this?
>>>
>>> Thank you in advance,
>>> Eleni
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> __
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>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
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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.
>
--
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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[R] extension to nlme self start SSmicmen?
Dear list, Has anyone created a version of SSmicmen that allows testing for group differences? The basic Michaelis-Menten equation is: (Bmax * X) / (Kd + X). The nlme package allows modeling of random effects for Bmax and Kd as needed, but I curious how I can build in group differences? I have receptor binding data for strains of mice, and following Pinheiro and Bates' lead in their book, a random effort for animal differences in Bmax seems reasonable, within strain. However, I'd like a self-start function, or even just the equation above, modified to allow testing for strain differences in Bmax and or Kd. Thank you. -Dave __ 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] Res: predict from a multiple regression model
Hi Franzi,
Up to I know you can´t predict values without you have x2,x3 and x4 parameters.
So you have three possible solution
1) set x2, x3 and x4 to Zero, *but* it will depend so much of what you want,
because if you set them to zero, it means that you are adjusting something like
mod<-lm(y~x1)
2) set x2,x3 and x4 to and mean value that you understand as rasonable for your
purpose]
and
3) build a set of for () looping, with the ranges of x2, x3 and x4, and see
what happens with the y, for each combination of x1-x2-x3-x4.
y<-runif(101)
x1<-sample(seq(0, 100))
x2<-seq(from=0,to=100,by=1)
x3<-seq(from=0,to=100,by=1)^2
x4<-exp(seq(from=0,to=100,by=1))
df<-data.frame(cbind(y,x1,x2,x3,x4))
mod<-lm(y~x1+x2+x3+x3,data=df)
df.complete<-NULL
for (x2 in seq(from=0,to=100,by=20)) {
for (x3 in seq(from=0,to=100,by=20)) {
for (x4 in seq(from=0,to=100,by=20)) {
x1<-seq(0, 100, by=10)
df.new<-data.frame(cbind(x1,x2,x3,x4))
df.new$pred<-predict(mod,new=df.new)
df.complete<-rbind(df.complete,df.new)
}}}
head(df.complete,50)
summary(df.complete)
But you have a problema. If you have four dimensions (x1-x4), it is so hard to
graph. In the case of two dimensions (like x1 and x2) you can use the function
interp() function of akima´s packge to generate a 3d plot of your response
variavel y-pred as a surface.
Good luck,
miltinho
Brazil
- Mensagem original
De: Fränzi Korner <[EMAIL PROTECTED]>
Para: r-help@r-project.org
Enviadas: Terça-feira, 22 de Janeiro de 2008 11:50:03
Assunto: [R] predict from a multiple regression model
Hello
how can I predict from a lm-object over a range of values of one explanatory
variable without having to specify values for all the other explanatory
variables?
e.g.
mod<-lm(y~x1+x2+x3+x4)
x1.new<-seq(0, 100)
predict(mod, new=list(x1=x1.new))
Here, predict() does not work, since values for x2, x3 and x4 are missing.
Is there a function or argument that, in such a case, averages or weights
over the other explanatory variables, how it is done in Genstat?
Thanks
Fränzi
Dr. Fränzi Korner-Nievergelt
oikostat - Statistische Analysen und Beratung
Ausserdorf 43
CH - 6218 Ettiswil
Tel.: +41 (0) 41 980 49 22
www.oikostat.ch
*
Schweizerische Vogelwarte
CH - 6204 Sempach
www.vogelwarte.ch
*
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armazenamento!
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Re: [R] recoding one variable into another - but differently for different cases
Dimitri Liakhovitski wrote:
> Hello,
> I have 2 variables in my sample Data: Data$A and Data$B
> Variable Data$A can assume values: 1, 2, 3, and 4.
> Variable Data$B identifies my cases and can assume values: 1 and 2.
>
> I need to recode my variable Data$A into a new variable Data$new such that:
>
> People who are Data[Data$B %in% 1, ] are recoded like this:
>
> Value on Data$AValue on Data$new
> 1 +1
> 2 -1
> 3 0
> 4 99
>
> People who are Data[Data$B %in% 2, ] are recoded like this:
>
> Value on Data$AValue on Data$new
> 1 -1
> 2 +1
> 3 0
> 4 99
>
> I am having hard time doing this. Any help would be greatly appreciated.
> Dimitri
How about this:
> Data
A B
14 2 2
12 4 2
6 2 1
10 2 2
15 3 2
9 1 2
8 4 1
3 3 1
4 4 1
11 3 2
16 4 2
5 1 1
2 2 1
7 3 1
13 1 2
1 1 1
# Create a vector of the codes, in sequence for each subset
Codes <- c("+1", "-1", "0", "99", "-1", "+1", "0", "99")
# Create 'new' using indices into 'Codes'
Data$new <- with(Data, Codes[((B - 1) * 4) + A])
> Data
A B new
14 2 2 +1
12 4 2 99
6 2 1 -1
10 2 2 +1
15 3 2 0
9 1 2 -1
8 4 1 99
3 3 1 0
4 4 1 99
11 3 2 0
16 4 2 99
5 1 1 +1
2 2 1 -1
7 3 1 0
13 1 2 -1
1 1 1 +1
HTH,
Marc Schwartz
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and provide commented, minimal, self-contained, reproducible code.
[R] stripchart
hi, I want to plot a dotplot graph but unfortunately R does not have it any more. It suggest to use either the stripchart or the dotchart and i prefer to play around with the stripchart graph. Sadly, the result is not like i want where I'm actually wants the plots/points were scattered around the x-axis. Plus, from the results shows that and the x-axis gave a very large scale, i.e 5.0e+0.7. How am i going to change this scale and to change the colour or symbols where i can show the difference of the sample data. Any suggestion?? two sample data: e [1] 17358865 17966995 21306539 27880531 34166504 36111044 36266288 [8] 36854306 43786190 44322336 45529444 46302360 53479132 58567262 [15] 60564442 72637088 79875476 93155112 94372260 96643396 103123936 [22] 116908456 131781664 132968364 135945080 141788832 149924864 156539568 [29] 157817896 162399496 168344072 173146584 176302744 182878168 183946152 [36] 185068720 190791232NA > f [1] 17906353 21295547 27880531 34118702 35395488 36132622 37916920 [8] 43786190 44322336 46302360 53494622 62105336 63817440 72637088 [15] 79875476 94545992 96506368 103123936 116908456 126190072 127446552 [22] 131781664 154658264 176302744 181670472 182625272 182878168 183946152 [29]NA R-command: stripchart(e,method="stack",col="green",add=F,at=0.0) stripchart(f,method="stack",col="blue",add=T,at=0.0) Thanks in advance. Cheers, Anisah - [[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] recoding one variable into another - but differently for different cases
You could create a lookup table or use recode in the car package. Another possibility is to use a logical/arithmetic expression. The following expression says that - if A is 1 then use the first term equals the coefficient, namely 1 if B ==1 and -1 if B == 2. Also, if A is not 1 then that term is zero and can be ignored. - if A is 2 or 99 then the second or third terms are used analogously - otherwise no terms are selected and the expression equals zero transform(Data, new = (A == 1) * ((B == 1) - (B == 2)) + (A == 2) * ((B == 2) - (B == 1)) + (A == 4) * 99) This could be reduced even more although at the expense of understandability, e.g. transform(Data, new = ifelse(A > 2, 99 * (A == 4), (A == B) - (A != B))) On Jan 22, 2008 12:25 PM, Dimitri Liakhovitski <[EMAIL PROTECTED]> wrote: > Hello, > I have 2 variables in my sample Data: Data$A and Data$B > Variable Data$A can assume values: 1, 2, 3, and 4. > Variable Data$B identifies my cases and can assume values: 1 and 2. > > I need to recode my variable Data$A into a new variable Data$new such that: > > People who are Data[Data$B %in% 1, ] are recoded like this: > > Value on Data$AValue on Data$new > 1 +1 > 2 -1 > 3 0 > 4 99 > > People who are Data[Data$B %in% 2, ] are recoded like this: > > Value on Data$AValue on Data$new > 1 -1 > 2 +1 > 3 0 > 4 99 > > I am having hard time doing this. Any help would be greatly appreciated. > Dimitri > > __ > 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] recoding one variable into another - but differently fordifferent cases
Try this: z1 <- c(1,-1,0,99)[Data$A] z2 <- c(-1,1,0,99)[Data$A] Data$new <- ifelse(Data$B == 1, z1,z2) (This does not generalize, however, and assumes that the values you gave are exact. Gabor's approach would work more generally) -- Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gabor Grothendieck Sent: Tuesday, January 22, 2008 11:09 AM To: Dimitri Liakhovitski Cc: R-Help List Subject: Re: [R] recoding one variable into another - but differently fordifferent cases You could create a lookup table or use recode in the car package. Another possibility is to use a logical/arithmetic expression. The following expression says that - if A is 1 then use the first term equals the coefficient, namely 1 if B ==1 and -1 if B == 2. Also, if A is not 1 then that term is zero and can be ignored. - if A is 2 or 99 then the second or third terms are used analogously - otherwise no terms are selected and the expression equals zero transform(Data, new = (A == 1) * ((B == 1) - (B == 2)) + (A == 2) * ((B == 2) - (B == 1)) + (A == 4) * 99) This could be reduced even more although at the expense of understandability, e.g. transform(Data, new = ifelse(A > 2, 99 * (A == 4), (A == B) - (A != B))) On Jan 22, 2008 12:25 PM, Dimitri Liakhovitski <[EMAIL PROTECTED]> wrote: > Hello, > I have 2 variables in my sample Data: Data$A and Data$B > Variable Data$A can assume values: 1, 2, 3, and 4. > Variable Data$B identifies my cases and can assume values: 1 and 2. > > I need to recode my variable Data$A into a new variable Data$new such that: > > People who are Data[Data$B %in% 1, ] are recoded like this: > > Value on Data$AValue on Data$new > 1 +1 > 2 -1 > 3 0 > 4 99 > > People who are Data[Data$B %in% 2, ] are recoded like this: > > Value on Data$AValue on Data$new > 1 -1 > 2 +1 > 3 0 > 4 99 > > I am having hard time doing this. Any help would be greatly appreciated. > Dimitri > > __ > 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] suppress some boxes drawn by legend(,fill)
Is there any way suppress box color and frame of a box drawn by
legend(,fill)? I am able to suppress the color, but not the frame (see
the example below). Many thanks! (This follows up from a question
asked on the list in 2006 by Florian Koller)
Tom
x1 <- rnorm(100)
x2 <- rnorm(100, 2)
hist(x1, main = "", col = "orange",ylab = "density", xlab = "x", freq
= F, density = 55,xlim = c(-2, 5), ylim = c(0, 0.5))
par(new = T)
hist(x2, main = "", col = "green", ylab = "", xlab = "",axes = F, xlim
= c(-2, 5), ylim = c(0, 0.5), density = 45, freq = F)
abline(v = mean(x1), col = "orange", lty = 2, lwd = 2.5)
abline(v = mean(x2), col = "green", lty = 2, lwd = 2.5)
legend(3, 0.45, legend = c("x1", "x2", "mean(x1)", "mean(x2)"),
col = c("orange", "green"), fill=c("orange","green", 0, 0),
lty = c(0, 0, 2, 2), merge = T)
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Re: [R] extension to nlme self start SSmicmen?
> Dear list, > > Has anyone created a version of SSmicmen that allows testing for > group differences? The basic Michaelis-Menten equation is: > > (Bmax * X) / (Kd + X). > > The nlme package allows modeling of random effects for Bmax and Kd > as needed, but I curious how I can build in group differences? I > have receptor binding data for strains of mice, and following > Pinheiro and Bates' lead in their book, a random effort for animal > differences in Bmax seems reasonable, within strain. However, I'd > like a self-start function, or even just the equation above, > modified to allow testing for strain differences in Bmax and or Kd. > > Thank you. > > -Dave Reading more closely, I now think I don't have to change the self start function SSmicmen to test for treatment group fixed effects. I just need to get the list of fixed effects right, to include the strain factor. Something like "fixed = list(bmax + kd ~ strain), random = list(bmax + kd ~ 1)". __ 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] stripchart
Have a look at stripplot in lattice. I think it may do
what you want if you cbind e & f and then create an
identifier to plot against.
e <- c(17358865 , 17966995 , 21306539 , 27880531,
34166504, 36111044, 36266288,
36854306 , 43786190 , 44322336 , 45529444, 46302360,
53479132, 58567262,
60564442 , 72637088 , 79875476 , 93155112, 94372260,
96643396, 103123936,
116908456, 131781664, 132968364, 135945080, 141788832,
149924864, 156539568,
157817896, 162399496, 168344072, 173146584, 176302744,
182878168, 183946152,
185068720, 190791232,NA )
f <- c(17906353, 21295547, 27880531, 34118702 ,
35395488, 36132622 , 37916920,
43786190, 44322336, 46302360, 53494622 , 62105336,
63817440 , 72637088 ,
79875476, 94545992 , 96506368, 103123936 ,116908456,
126190072, 127446552 ,
131781664, 154658264 ,176302744, 181670472, 182625272,
182878168, 183946152,
NA )
ec <- rep("ee", length(e))
fc <- rep("ff", length(f))
bb <- data.frame(c(ec,fc),c(e,f))
stripplot(bb[,2]~bb[,1])
--- mohamed nur anisah <[EMAIL PROTECTED]>
wrote:
> hi,
>
> I want to plot a dotplot graph but unfortunately R
> does not have it any more. It suggest to use either
> the stripchart or the dotchart and i prefer to play
> around with the stripchart graph. Sadly, the result
> is not like i want where I'm actually wants the
> plots/points were scattered around the x-axis. Plus,
> from the results shows that and the x-axis gave a
> very large scale, i.e 5.0e+0.7. How am i going to
> change this scale and to change the colour or
> symbols where i can show the difference of the
> sample data. Any suggestion??
>
>two sample data:
>e
> [1] 17358865 17966995 21306539 27880531
> 34166504 36111044 36266288
> [8] 36854306 43786190 44322336 45529444
> 46302360 53479132 58567262
> [15] 60564442 72637088 79875476 93155112
> 94372260 96643396 103123936
> [22] 116908456 131781664 132968364 135945080
> 141788832 149924864 156539568
> [29] 157817896 162399496 168344072 173146584
> 176302744 182878168 183946152
> [36] 185068720 190791232NA
> > f
> [1] 17906353 21295547 27880531 34118702
> 35395488 36132622 37916920
> [8] 43786190 44322336 46302360 53494622
> 62105336 63817440 72637088
> [15] 79875476 94545992 96506368 103123936
> 116908456 126190072 127446552
> [22] 131781664 154658264 176302744 181670472
> 182625272 182878168 183946152
> [29]NA
>
> R-command:
>
>
>
stripchart(e,method="stack",col="green",add=F,at=0.0)
>
> stripchart(f,method="stack",col="blue",add=T,at=0.0)
>
>
> Thanks in advance.
>
> Cheers,
> Anisah
>
>
> -
>
> [[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.
>
__
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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] suppress some boxes drawn by legend(,fill)
box.lty = 0
assuming I understand the question.
--- Tom Boonen <[EMAIL PROTECTED]> wrote:
> Is there any way suppress box color and frame of a
> box drawn by
> legend(,fill)? I am able to suppress the color, but
> not the frame (see
> the example below). Many thanks! (This follows up
> from a question
> asked on the list in 2006 by Florian Koller)
>
> Tom
>
> x1 <- rnorm(100)
> x2 <- rnorm(100, 2)
> hist(x1, main = "", col = "orange",ylab = "density",
> xlab = "x", freq
> = F, density = 55,xlim = c(-2, 5), ylim = c(0, 0.5))
> par(new = T)
> hist(x2, main = "", col = "green", ylab = "", xlab =
> "",axes = F, xlim
> = c(-2, 5), ylim = c(0, 0.5), density = 45, freq =
> F)
> abline(v = mean(x1), col = "orange", lty = 2, lwd =
> 2.5)
> abline(v = mean(x2), col = "green", lty = 2, lwd =
> 2.5)
> legend(3, 0.45, legend = c("x1", "x2", "mean(x1)",
> "mean(x2)"),
>col = c("orange", "green"),
> fill=c("orange","green", 0, 0),
>lty = c(0, 0, 2, 2), merge = T)
>
> __
> 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.
>
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and provide commented, minimal, self-contained, reproducible code.
[R] X11 font at size 6 could not be loaded
I recently upgraded my OS to Fedora 8 from Red Hat Enterprise Work Station 3.
Before I upgraded certain operations would produce a warning to the effect that
a desired font was not available so one had been substituted, which was okay.
After the upgrade to Fedora 8, the plotting operation halts midway through and I
get the following error message:
"X11 font at size 6 could not be loaded"
This is not okay, because plotting does not complete.
I've also gotten that message regarding size 8.
In R, if it do getOption("X11fonts") I get
[1] "-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
[2] "-adobe-symbol-medium-r-*-*-%d-*-*-*-*-*-*-*"
If from bash I do xlsfonts, I see that I have fonts that match, but the smallest
seem to be 11 points:
-adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso10646-1
-adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso8859-1
If I run the same program on my Fedora 8 system but use an X server on a Windows
PC (Hummingbird X server), I have no problem.
If I can't fix this, this is a disaster for me because some of the most common
things I do are afflicted by this problem.
Can anyone help me get adobe-helvetica 6 and 8 point fonts onto my system or
give any other advice?
Thanks very much.
-Ben
p.s., I also tried in R
options(X11fonts="-misc-fixed-%s-%s-*-*-%d-*-*-*-*-*-*-*")
but that resulted in
Error in X11(display, width, height, pointsize, if (is.null(gamma)) 1 else
gamma, :
invalid 'fonts' value
when I tried to plot.
p.p.s, here's my version information
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 6.1
year 2007
month 11
day26
svn rev43537
language R
version.string R version 2.6.1 (2007-11-26)
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Re: [R] suppress some boxes drawn by legend(,fill)
It occured to me afterwards that this was not what you
wanted. I think Jerome Asselin in
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/15483.html
has a solution that may do what you want
Try
legend(3, 0.45, legend = c("x1", "x2", "mean(x1)",
"mean(x2)"), pch=c(22,22,30,30),
col = c("orange", "green"),
pt.bg=c("orange","green","white","white"),
lty = c(0, 0, 2, 2), merge = T)
--- John Kane <[EMAIL PROTECTED]> wrote:
> box.lty = 0
>
> assuming I understand the question.
> --- Tom Boonen <[EMAIL PROTECTED]> wrote:
>
> > Is there any way suppress box color and frame of a
> > box drawn by
> > legend(,fill)? I am able to suppress the color,
> but
> > not the frame (see
> > the example below). Many thanks! (This follows up
> > from a question
> > asked on the list in 2006 by Florian Koller)
> >
> > Tom
> >
> > x1 <- rnorm(100)
> > x2 <- rnorm(100, 2)
> > hist(x1, main = "", col = "orange",ylab =
> "density",
> > xlab = "x", freq
> > = F, density = 55,xlim = c(-2, 5), ylim = c(0,
> 0.5))
> > par(new = T)
> > hist(x2, main = "", col = "green", ylab = "", xlab
> =
> > "",axes = F, xlim
> > = c(-2, 5), ylim = c(0, 0.5), density = 45, freq =
> > F)
> > abline(v = mean(x1), col = "orange", lty = 2, lwd
> =
> > 2.5)
> > abline(v = mean(x2), col = "green", lty = 2, lwd =
> > 2.5)
> > legend(3, 0.45, legend = c("x1", "x2", "mean(x1)",
> > "mean(x2)"),
> >col = c("orange", "green"),
> > fill=c("orange","green", 0, 0),
> >lty = c(0, 0, 2, 2), merge = T)
> >
> > __
> > 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.
> >
>
>
>
> Looking for the perfect gift? Give the gift of
> Flickr!
>
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>
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Re: [R] X11 font at size 6 could not be loaded
Wittner, Ben, Ph.D. wrote:
> I recently upgraded my OS to Fedora 8 from Red Hat Enterprise Work Station 3.
> Before I upgraded certain operations would produce a warning to the effect
> that
> a desired font was not available so one had been substituted, which was okay.
> After the upgrade to Fedora 8, the plotting operation halts midway through
> and I
> get the following error message:
> "X11 font at size 6 could not be loaded"
> This is not okay, because plotting does not complete.
>
> I've also gotten that message regarding size 8.
>
> In R, if it do getOption("X11fonts") I get
> [1] "-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
> [2] "-adobe-symbol-medium-r-*-*-%d-*-*-*-*-*-*-*"
>
> If from bash I do xlsfonts, I see that I have fonts that match, but the
> smallest
> seem to be 11 points:
> -adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso10646-1
> -adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso8859-1
>
> If I run the same program on my Fedora 8 system but use an X server on a
> Windows
> PC (Hummingbird X server), I have no problem.
>
> If I can't fix this, this is a disaster for me because some of the most common
> things I do are afflicted by this problem.
>
> Can anyone help me get adobe-helvetica 6 and 8 point fonts onto my system or
> give any other advice?
>
> Thanks very much.
> -Ben
>
> p.s., I also tried in R
> options(X11fonts="-misc-fixed-%s-%s-*-*-%d-*-*-*-*-*-*-*")
> but that resulted in
> Error in X11(display, width, height, pointsize, if (is.null(gamma)) 1 else
> gamma, :
> invalid 'fonts' value
> when I tried to plot.
>
> p.p.s, here's my version information
> platform i686-pc-linux-gnu
> arch i686
> os linux-gnu
> system i686, linux-gnu
> status
> major 2
> minor 6.1
> year 2007
> month 11
> day26
> svn rev43537
> language R
> version.string R version 2.6.1 (2007-11-26)
>
>
The usual suspect is that you do not have the unscalable fonts in both
75 and 100 dpi:
xorg-x11-fonts-100dpi-7.2-3.fc8
xorg-x11-fonts-ISO8859-1-75dpi-7.2-3.fc8
xorg-x11-fonts-ISO8859-1-100dpi-7.2-3.fc8
xorg-x11-fonts-75dpi-7.2-3.fc8
xorg-x11-fonts-ISO8859-2-75dpi-7.2-3.fc8
xorg-x11-fonts-ISO8859-2-100dpi-7.2-3.fc8
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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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] recoding one variable into another - but differently for different cases
Slight correction of the English: - if A is 1 then the first term equals the coefficient of (A == 1). That is the first term equals 1 if B==1 and equals -1 if B==2. If A does not equal 1 then the first term is zero and can be ignored. - terms 2 and 3 are interpreted analogously - if A==3 (or other value) then the (A==?) part of each term equals zero so the entire expression is zero. On Jan 22, 2008 2:08 PM, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > You could create a lookup table or use recode in the car package. > > Another possibility is to use a logical/arithmetic expression. The > following expression says that > > - if A is 1 then use the first term equals the coefficient, namely 1 > if B ==1 and -1 if B == 2. > Also, if A is not 1 then that term is zero and can be ignored. > - if A is 2 or 99 then the second or third terms are used analogously > - otherwise no terms are selected and the expression equals zero > > transform(Data, new = > (A == 1) * ((B == 1) - (B == 2)) + (A == 2) * ((B == 2) - (B == > 1)) + (A == 4) * 99) > > This could be reduced even more although at the expense of > understandability, e.g. > > transform(Data, new = ifelse(A > 2, 99 * (A == 4), (A == B) - (A != B))) > > > On Jan 22, 2008 12:25 PM, Dimitri Liakhovitski <[EMAIL PROTECTED]> wrote: > > Hello, > > I have 2 variables in my sample Data: Data$A and Data$B > > Variable Data$A can assume values: 1, 2, 3, and 4. > > Variable Data$B identifies my cases and can assume values: 1 and 2. > > > > I need to recode my variable Data$A into a new variable Data$new such that: > > > > People who are Data[Data$B %in% 1, ] are recoded like this: > > > > Value on Data$AValue on Data$new > > 1 +1 > > 2 -1 > > 3 0 > > 4 99 > > > > People who are Data[Data$B %in% 2, ] are recoded like this: > > > > Value on Data$AValue on Data$new > > 1 -1 > > 2 +1 > > 3 0 > > 4 99 > > > > I am having hard time doing this. Any help would be greatly appreciated. > > Dimitri > > > > __ > > 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] Reading .csv file under linux
I have encountered a problem with reading a .csv file on a linux box. I
can read the file on my windows machine (under XP) but on the linux box it
gives :
> patients <- read.csv("../Patients.csv", header = FALSE,
+ col.names = patientsNames)
Error in type.convert(data[[i]], as.is = as.is[i], dec = dec,
na.strings = character(0)) :
invalid multibyte string
Calls: read.csv -> read.table -> type.convert
Execution halted
I am running R 2.6.1 on both machines. I tried on another linux box
running 2.5.1 and got the same problem
I am guessing it is something to do with the character encoding. On the
linux box I have
LANG=en_US.UTF-8
Any advice would be welcome
David Scott
_
David Scott Department of Statistics, Tamaki Campus
The University of Auckland, PB 92019
Auckland 1142,NEW ZEALAND
Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000
Email: [EMAIL PROTECTED]
Graduate Officer, Department of Statistics
Director of Consulting, Department of Statistics
__
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] X11 font at size 6 could not be loaded
Have you also changed your locale? F8 defaults to UTF-8 locales, whereas
people usually set up RHEL3 with an 8-bit locale. That changes the font
selection, and you may find that running in en_US works whereas en_US.utf8
does not.
Note that the font you quote is an 8 point 100dpi font, at 11 pixels not
points. What you actually need depends on the dpi of your screen, and if
that is less than 100 dpi you need the 75dpi fonts.
Another idea is to install the scalable fonts in the urw-fonts package,
and use something like
foo <- getOption("X11fonts")
foo[1] <- "-urw-nimbus sans l-%s-%s-*-*-%d-*-*-*-*-*-*-*"
options(X11fonts=foo)
to select them.
On Tue, 22 Jan 2008, Wittner, Ben, Ph.D. wrote:
> I recently upgraded my OS to Fedora 8 from Red Hat Enterprise Work
> Station 3. Before I upgraded certain operations would produce a warning
> to the effect that a desired font was not available so one had been
> substituted, which was okay. After the upgrade to Fedora 8, the plotting
> operation halts midway through and I get the following error message:
> "X11 font at size 6 could not be loaded"
> This is not okay, because plotting does not complete.
>
> I've also gotten that message regarding size 8.
Showing the actual messages would have been helpful.
>
> In R, if it do getOption("X11fonts") I get
> [1] "-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
> [2] "-adobe-symbol-medium-r-*-*-%d-*-*-*-*-*-*-*"
>
> If from bash I do xlsfonts, I see that I have fonts that match, but the
> smallest
> seem to be 11 points:
> -adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso10646-1
> -adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso8859-1
Looks like you don't have the 75dpi fonts installed, so try installing
those (xorg-x11-fonts-75dpi, it seems).
> If I run the same program on my Fedora 8 system but use an X server on a
> Windows
> PC (Hummingbird X server), I have no problem.
That will have scalable fonts.
> If I can't fix this, this is a disaster for me because some of the most common
> things I do are afflicted by this problem.
>
> Can anyone help me get adobe-helvetica 6 and 8 point fonts onto my system or
> give any other advice?
>
> Thanks very much.
> -Ben
>
> p.s., I also tried in R
> options(X11fonts="-misc-fixed-%s-%s-*-*-%d-*-*-*-*-*-*-*")
> but that resulted in
> Error in X11(display, width, height, pointsize, if (is.null(gamma)) 1 else
> gamma, :
> invalid 'fonts' value
> when I tried to plot.
Yes, it does have to length 2.
>
> p.p.s, here's my version information
> platform i686-pc-linux-gnu
> arch i686
> os linux-gnu
> system i686, linux-gnu
> status
> major 2
> minor 6.1
> year 2007
> month 11
> day26
> svn rev43537
> language R
> version.string R version 2.6.1 (2007-11-26)
--
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] Reading .csv file under linux
On Wed, 23 Jan 2008, David Scott wrote:
>
> I have encountered a problem with reading a .csv file on a linux box. I
> can read the file on my windows machine (under XP) but on the linux box it
> gives :
>
>> patients <- read.csv("../Patients.csv", header = FALSE,
> + col.names = patientsNames)
> Error in type.convert(data[[i]], as.is = as.is[i], dec = dec,
> na.strings = character(0)) :
> invalid multibyte string
> Calls: read.csv -> read.table -> type.convert
> Execution halted
>
> I am running R 2.6.1 on both machines. I tried on another linux box
> running 2.5.1 and got the same problem
>
> I am guessing it is something to do with the character encoding. On the
> linux box I have
>
> LANG=en_US.UTF-8
So what encoding is the .csv file in? Consider the example at the end of
?file
## examples of use of encodings
cat(x, file = file("foo", "w", encoding="UTF-8"))
# read a 'Windows Unicode' file including names
A <- read.table(file("students", encoding="UCS-2LE"))
and adapt accordingly (encoding = "CP1252" is the most likely value if
this works in English-language Windows).
--
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] X11 font at size 6 could not be loaded
Thank you very much.
I found .noarch.rpm's for the first 4 of the 6 you listed below and installed
them and the problem went away.
Strangely, when I tried to intstall (using rpm -Uvh) the 100 dpi ones I got a
message saying that they were already installed. Nevertheless, when I restarted
the X server, xlsfonts showed more fonts for the 100 dpi case (in particular,
the small ones, 10 and 8) as well as the 75 dpis, which had not been there
before.
I don't understand that, but my problem is solved, so I am happy. Thanks again.
-Ben
> -Original Message-
> From: Peter Dalgaard [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, January 22, 2008 5:00 PM
> To: Wittner, Ben, Ph.D.
> Cc: r-help@r-project.org
> Subject: Re: [R] X11 font at size 6 could not be loaded
>
> Wittner, Ben, Ph.D. wrote:
> > I recently upgraded my OS to Fedora 8 from Red Hat Enterprise Work
> Station 3.
> > Before I upgraded certain operations would produce a warning to the
> effect that
> > a desired font was not available so one had been substituted, which was
> okay.
> > After the upgrade to Fedora 8, the plotting operation halts midway
> through and I
> > get the following error message:
> > "X11 font at size 6 could not be loaded"
> > This is not okay, because plotting does not complete.
> >
> > I've also gotten that message regarding size 8.
> >
> > In R, if it do getOption("X11fonts") I get
> > [1] "-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
> > [2] "-adobe-symbol-medium-r-*-*-%d-*-*-*-*-*-*-*"
> >
> > If from bash I do xlsfonts, I see that I have fonts that match, but the
> smallest
> > seem to be 11 points:
> > -adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso10646-1
> > -adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso8859-1
> >
> > If I run the same program on my Fedora 8 system but use an X server on a
> Windows
> > PC (Hummingbird X server), I have no problem.
> >
> > If I can't fix this, this is a disaster for me because some of the most
> common
> > things I do are afflicted by this problem.
> >
> > Can anyone help me get adobe-helvetica 6 and 8 point fonts onto my
> system or
> > give any other advice?
> >
> > Thanks very much.
> > -Ben
> >
> > p.s., I also tried in R
> > options(X11fonts="-misc-fixed-%s-%s-*-*-%d-*-*-*-*-*-*-*")
> > but that resulted in
> > Error in X11(display, width, height, pointsize, if (is.null(gamma)) 1
> else
> > gamma, :
> > invalid 'fonts' value
> > when I tried to plot.
> >
> > p.p.s, here's my version information
> > platform i686-pc-linux-gnu
> > arch i686
> > os linux-gnu
> > system i686, linux-gnu
> > status
> > major 2
> > minor 6.1
> > year 2007
> > month 11
> > day26
> > svn rev43537
> > language R
> > version.string R version 2.6.1 (2007-11-26)
> >
> >
> The usual suspect is that you do not have the unscalable fonts in both
> 75 and 100 dpi:
>
> xorg-x11-fonts-100dpi-7.2-3.fc8
> xorg-x11-fonts-ISO8859-1-75dpi-7.2-3.fc8
> xorg-x11-fonts-ISO8859-1-100dpi-7.2-3.fc8
> xorg-x11-fonts-75dpi-7.2-3.fc8
> xorg-x11-fonts-ISO8859-2-75dpi-7.2-3.fc8
> xorg-x11-fonts-ISO8859-2-100dpi-7.2-3.fc8
>
>
> --
>O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> (*) \(*) -- University of Copenhagen Denmark Ph: (+45)
> 35327918
> ~~ - ([EMAIL PROTECTED]) FAX: (+45)
> 35327907
The information transmitted in this electronic communication is intended only
for the person or entity to whom it is addressed and may contain confidential
and/or privileged material. Any review, retransmission, dissemination or other
use of or taking of any action in reliance upon this information by persons or
entities other than the intended recipient is prohibited. If you received this
information in error, please contact the Compliance HelpLine at 800-856-1983 and
properly dispose of this information.
__
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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] X11 font at size 6 could not be loaded
Dear Prof. Ripley,
Thanks very much.
Changing the locale did not help, but finding and installing (or re-installing)
xorg-x11-fonts for 75 and 100 dpi did the trick.
It's still a bit of a mystery to me, but my attempt to install xorg-x11-fonts
for 100 dpi appeared to fail, but nevertheless I found more 100 dpi
adobe-helvetica fonts available to the X server when I was done.
Thanks also for explaining why my attempt to change the X11fonts option was a
failure.
-Ben
> -Original Message-
> From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, January 22, 2008 5:16 PM
> To: Wittner, Ben, Ph.D.
> Cc: r-help@r-project.org
> Subject: Re: [R] X11 font at size 6 could not be loaded
>
> Have you also changed your locale? F8 defaults to UTF-8 locales, whereas
> people usually set up RHEL3 with an 8-bit locale. That changes the font
> selection, and you may find that running in en_US works whereas en_US.utf8
> does not.
>
> Note that the font you quote is an 8 point 100dpi font, at 11 pixels not
> points. What you actually need depends on the dpi of your screen, and if
> that is less than 100 dpi you need the 75dpi fonts.
>
> Another idea is to install the scalable fonts in the urw-fonts package,
> and use something like
>
> foo <- getOption("X11fonts")
> foo[1] <- "-urw-nimbus sans l-%s-%s-*-*-%d-*-*-*-*-*-*-*"
> options(X11fonts=foo)
>
> to select them.
>
>
> On Tue, 22 Jan 2008, Wittner, Ben, Ph.D. wrote:
>
> > I recently upgraded my OS to Fedora 8 from Red Hat Enterprise Work
> > Station 3. Before I upgraded certain operations would produce a warning
> > to the effect that a desired font was not available so one had been
> > substituted, which was okay. After the upgrade to Fedora 8, the plotting
> > operation halts midway through and I get the following error message:
> > "X11 font at size 6 could not be loaded"
> > This is not okay, because plotting does not complete.
> >
> > I've also gotten that message regarding size 8.
>
> Showing the actual messages would have been helpful.
>
> >
> > In R, if it do getOption("X11fonts") I get
> > [1] "-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
> > [2] "-adobe-symbol-medium-r-*-*-%d-*-*-*-*-*-*-*"
> >
> > If from bash I do xlsfonts, I see that I have fonts that match, but the
> smallest
> > seem to be 11 points:
> > -adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso10646-1
> > -adobe-helvetica-bold-o-normal--11-80-100-100-p-60-iso8859-1
>
> Looks like you don't have the 75dpi fonts installed, so try installing
> those (xorg-x11-fonts-75dpi, it seems).
>
> > If I run the same program on my Fedora 8 system but use an X server on a
> Windows
> > PC (Hummingbird X server), I have no problem.
>
> That will have scalable fonts.
>
> > If I can't fix this, this is a disaster for me because some of the most
> common
> > things I do are afflicted by this problem.
> >
> > Can anyone help me get adobe-helvetica 6 and 8 point fonts onto my
> system or
> > give any other advice?
> >
> > Thanks very much.
> > -Ben
> >
> > p.s., I also tried in R
> > options(X11fonts="-misc-fixed-%s-%s-*-*-%d-*-*-*-*-*-*-*")
> > but that resulted in
> > Error in X11(display, width, height, pointsize, if (is.null(gamma)) 1
> else
> > gamma, :
> > invalid 'fonts' value
> > when I tried to plot.
>
> Yes, it does have to length 2.
>
> >
> > p.p.s, here's my version information
> > platform i686-pc-linux-gnu
> > arch i686
> > os linux-gnu
> > system i686, linux-gnu
> > status
> > major 2
> > minor 6.1
> > year 2007
> > month 11
> > day26
> > svn rev43537
> > language R
> > version.string R version 2.6.1 (2007-11-26)
>
> --
> 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
The information transmitted in this electronic communication is intended only
for the person or entity to whom it is addressed and may contain confidential
and/or privileged material. Any review, retransmission, dissemination or other
use of or taking of any action in reliance upon this information by persons or
entities other than the intended recipient is prohibited. If you received this
information in error, please contact the Compliance HelpLine at 800-856-1983 and
properly dispose of this information.
__
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] Reading .csv file under linux
On Tue, 22 Jan 2008, Prof Brian Ripley wrote:
> On Wed, 23 Jan 2008, David Scott wrote:
>
>>
>> I have encountered a problem with reading a .csv file on a linux box. I
>> can read the file on my windows machine (under XP) but on the linux box it
>> gives :
>>
>>> patients <- read.csv("../Patients.csv", header = FALSE,
>> + col.names = patientsNames)
>> Error in type.convert(data[[i]], as.is = as.is[i], dec = dec,
>> na.strings = character(0)) :
>> invalid multibyte string
>> Calls: read.csv -> read.table -> type.convert
>> Execution halted
>>
>> I am running R 2.6.1 on both machines. I tried on another linux box
>> running 2.5.1 and got the same problem
>>
>> I am guessing it is something to do with the character encoding. On the
>> linux box I have
>>
>> LANG=en_US.UTF-8
>
> So what encoding is the .csv file in? Consider the example at the end of
> ?file
>
> ## examples of use of encodings
> cat(x, file = file("foo", "w", encoding="UTF-8"))
> # read a 'Windows Unicode' file including names
> A <- read.table(file("students", encoding="UCS-2LE"))
>
> and adapt accordingly (encoding = "CP1252" is the most likely value if this
> works in English-language Windows).
>
Thanks Brian for the super-quick, super-helpful reply. The encoding you
suggested worked.
I found a workaround myself too---I guessed that some plus/minus signs
might be the problem and replaced them and could read in the file.
That is just a kludge so I am using the encoding specification.
I am a total dunce when it comes to encodings though. How do you find the
encoding of a file?
David
_
David Scott Department of Statistics, Tamaki Campus
The University of Auckland, PB 92019
Auckland 1142,NEW ZEALAND
Phone: +64 9 373 7599 ext 86830 Fax: +64 9 373 7000
Email: [EMAIL PROTECTED]
Graduate Officer, Department of Statistics
Director of Consulting, Department of Statistics
__
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] Reading .csv file under linux
On Wed, 23 Jan 2008, David Scott wrote:
> On Tue, 22 Jan 2008, Prof Brian Ripley wrote:
>
>> On Wed, 23 Jan 2008, David Scott wrote:
>>
>>>
>>> I have encountered a problem with reading a .csv file on a linux box. I
>>> can read the file on my windows machine (under XP) but on the linux box it
>>> gives :
>>>
patients <- read.csv("../Patients.csv", header = FALSE,
>>> + col.names = patientsNames)
>>> Error in type.convert(data[[i]], as.is = as.is[i], dec = dec,
>>> na.strings = character(0)) :
>>> invalid multibyte string
>>> Calls: read.csv -> read.table -> type.convert
>>> Execution halted
>>>
>>> I am running R 2.6.1 on both machines. I tried on another linux box
>>> running 2.5.1 and got the same problem
>>>
>>> I am guessing it is something to do with the character encoding. On the
>>> linux box I have
>>>
>>> LANG=en_US.UTF-8
>>
>> So what encoding is the .csv file in? Consider the example at the end of
>> ?file
>>
>> ## examples of use of encodings
>> cat(x, file = file("foo", "w", encoding="UTF-8"))
>> # read a 'Windows Unicode' file including names
>> A <- read.table(file("students", encoding="UCS-2LE"))
>>
>> and adapt accordingly (encoding = "CP1252" is the most likely value if this
>> works in English-language Windows).
>>
>
>
> Thanks Brian for the super-quick, super-helpful reply. The encoding you
> suggested worked.
>
> I found a workaround myself too---I guessed that some plus/minus signs might
> be the problem and replaced them and could read in the file.
> That is just a kludge so I am using the encoding specification.
>
> I am a total dunce when it comes to encodings though. How do you find the
> encoding of a file?
You ask the person who gave it to you. You can't in general tell, and
e.g. ISO-8859-1 and ISO-8859-2 are only distinguishable by someone who can
read the contents (if it is a human language). If you have just the odd
symbol (e.g. degree sign or plus/minus) you can be completely stuck.
'file' on Linux can usually guess if a file is UTF-8 or ISO-8859-?, but
not of course what ? is. But guesses are based on statistical patterns
and are good for text but not so good for data.
--
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] recoding one variable into another - but differently for different cases
Thanks a lot, everyone! Dimitri On 1/22/08, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > Slight correction of the English: > > - if A is 1 then the first term equals the coefficient of (A == 1). > That is the first term equals 1 if B==1 and equals -1 if B==2. > If A does not equal 1 then the first term is zero and can be ignored. > - terms 2 and 3 are interpreted analogously > - if A==3 (or other value) then the (A==?) part of each term equals > zero so the entire expression is zero. > > On Jan 22, 2008 2:08 PM, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > > You could create a lookup table or use recode in the car package. > > > > Another possibility is to use a logical/arithmetic expression. The > > following expression says that > > > > - if A is 1 then use the first term equals the coefficient, namely 1 > > if B ==1 and -1 if B == 2. > > Also, if A is not 1 then that term is zero and can be ignored. > > - if A is 2 or 99 then the second or third terms are used analogously > > - otherwise no terms are selected and the expression equals zero > > > > transform(Data, new = > > (A == 1) * ((B == 1) - (B == 2)) + (A == 2) * ((B == 2) - (B == > > 1)) + (A == 4) * 99) > > > > This could be reduced even more although at the expense of > > understandability, e.g. > > > > transform(Data, new = ifelse(A > 2, 99 * (A == 4), (A == B) - (A != B))) > > > > > > On Jan 22, 2008 12:25 PM, Dimitri Liakhovitski <[EMAIL PROTECTED]> wrote: > > > Hello, > > > I have 2 variables in my sample Data: Data$A and Data$B > > > Variable Data$A can assume values: 1, 2, 3, and 4. > > > Variable Data$B identifies my cases and can assume values: 1 and 2. > > > > > > I need to recode my variable Data$A into a new variable Data$new such > > > that: > > > > > > People who are Data[Data$B %in% 1, ] are recoded like this: > > > > > > Value on Data$AValue on Data$new > > > 1 +1 > > > 2 -1 > > > 3 0 > > > 4 99 > > > > > > People who are Data[Data$B %in% 2, ] are recoded like this: > > > > > > Value on Data$AValue on Data$new > > > 1 -1 > > > 2 +1 > > > 3 0 > > > 4 99 > > > > > > I am having hard time doing this. Any help would be greatly appreciated. > > > Dimitri > > > > > > __ > > > 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.
