Re: [R] Standard errors of least squares adjusted means
Hi Bruno, Apropos of ls-means ... I have tried help.search and RSiteSearch with several terms including standard errors, least square means, adjusted means. And ls-means, which is what you call them? There are many threads on this, spanning many years. The following, RSiteSearch(ls-means) will get you to some, e.g.: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/103520.html Read through to the bottom. There are much better ways of examining/summarizing, your model. See, for instance, the effects package of Prof. Fox and functions in the Design package of Prof. Harrell. HTH, Mark. Bruno Estigarribia wrote: Hello, I have the following model: lm.7 - lm(Y ~ F + C1 + C2 , data = EM4) F is a 4-level factor, the rest are covariates centered at their mean (Y is a two-column matrix). I have tried to find functions to give the model-adjusted means (adjusted at the covariates'means) and their standard deviations for each. (That is, what I believe is called in SAS least square or LS-means, whose errors one obtains by STDERR) I have tried help.search and RSiteSearch with several terms including standard errors, least square means, adjusted means. I have found how to extract the SE from coefficients (se.coef from package arm), or the SE for contrasts (se.contrast from package stats), but not the SE for an adjusted mean. Thank you, -- Bruno Estigarribia Postdoctoral Fellow FPG Child Development Institute Neurodevelopmental Disorders Research Center University of North Carolina at Chapel Hill 105 Smith Level Rd Chapel Hill, NC 27599-8180 USA + 1 (919) 843-7685 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Standard-errors-of-least-squares-adjusted-means-tp21598897p21599542.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replacing dates with consecutive observations
Hi Alina,
You can always write a loop in R to do this:
# A function to shift values in an vector
shift = function(y) {
cnt = length(y) - 1
m=vector(mode = numeric,length = cnt)
for (j in 1:cnt) {
m[j] = y[j+1]}
m
}
Regards,
Indrajit
From: Alina Sheyman alina...@gmail.com
To: r-help@r-project.org
Sent: Thursday, January 22, 2009 2:48:42 AM
Subject: [R] Replacing dates with consecutive observations
I am working with a list of dates and I would like to replace each date with
the one that comes after, ie. 1/1/07 will become 1/5/07, 1/5/07 will become
1/7/07, etc. The number of days between my dates always varies, so I can't
just increase each one by 5 days or so. Does anyone know of a way I can do
this in R?
thank you
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[R] How to Run R Programs in a Scheduled Way
Hello R Experts, does anyone know how to run R programs automatically using the window scheduler? I want to run some R programs automatically and make the results available via web. Mit freundlichen GrüÃen / Best Regards / С наилÑÑÑими пожеланиÑми / üdvözlettel Thorsten [[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] problem with compating 2 strings
Hi all, I got one problem with compating charecterstrings with using == can anyone suggest if any other way to compare two charecterstrings thanks in advance [[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] reshape() problems
Hi I have a data frame with timeseries information like this: year cell Q1Q2 Q3 Q4 1940 1 1.2 1.4 1.41.9 1941 1 2.9 2.1 3.4 2.4 1942 1 2.7 3.2 1.52.6 1940 2 1.4 2.1 2.62.4 1941 2 2.4 1.4 1.43.4 1942 2 1.4 2.4 2.54.4 where the Qs mean 'quarter'. I want to extract from this a dataframe with a timeseries for each cell: year quarter cell1 cell2 1940 1 1.2 1.4 1940 2 1.4 2.1 1940 3 1.4 2.6 1940 4 1.9 2.4 1941 1 2.9 2.4 1941 2 2.1 1.4 1941 3 3.4 1.4 1942 4 2.4 3.4 1942 1 2.7 1.4 1942 2 3.2 2.4 1942 3 1.5 2.5 1942 4 2.6 4.4 Thus the third and fourth columns are the timeserieses for cell 1 and cell 2. Is there a nice vectorized way to do this? I can't quite make reshape() do what I want. [the real dataset is months, not quarters, has ~2000 cells and ~60 years] -- Robin K. S. Hankin Uncertainty Analyst University of Cambridge 19 Silver Street Cambridge CB3 9EP 01223-764877 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to Run R Programs in a Scheduled Way
Thorsten Muehge wrote: Hello R Experts, does anyone know how to run R programs automatically using the window scheduler? I want to run some R programs automatically and make the results available via web. Write some Windows command script (also referred to as batch file) that calls Rterm with some input file or R CMD BATCH. Then tell your scheduler to run that file as you like. For me this worked very well with Windows XP and Windows Server 2003. In Windows Server 2008 64-bit (and hence I guess the same in Vista) I found that the new scheduler runs R extremely slow (by a factor of roughly 10 if some relevant amount of CPU performance and IO traffic is requested) so that I decided to moved to a cron implementation. At least, I have not found any solution for the Windows 2008 task scheduler so far. Uwe Ligges Mit freundlichen Grüßen / Best Regards / С наилучшими пожелани�ми / üdvözlettel Thorsten [[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] problem with compating 2 strings
an example would be helpful ... PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. venkata kirankumar wrote: Hi all, I got one problem with compating charecterstrings with using == can anyone suggest if any other way to compare two charecterstrings thanks in advance [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] reshape() problems
Dear Robin, It is rather easy if you combine melt() and cast() from the reshape package. dataset - expand.grid(year = 1940:1942, cell = 1:2) dataset$Q1 - rnorm(nrow(dataset)) dataset$Q2 - rnorm(nrow(dataset)) dataset$Q3 - rnorm(nrow(dataset)) dataset$Q4 - rnorm(nrow(dataset)) library(reshape) datasetMelt - melt(dataset, id.var = c(year, cell)) cast(datasetMelt, year + variable ~ ...) HTH, Thierry 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 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Robin Hankin Verzonden: donderdag 22 januari 2009 10:52 Aan: r-help@r-project.org Onderwerp: [R] reshape() problems Hi I have a data frame with timeseries information like this: year cell Q1Q2 Q3 Q4 1940 1 1.2 1.4 1.41.9 1941 1 2.9 2.1 3.4 2.4 1942 1 2.7 3.2 1.52.6 1940 2 1.4 2.1 2.62.4 1941 2 2.4 1.4 1.43.4 1942 2 1.4 2.4 2.54.4 where the Qs mean 'quarter'. I want to extract from this a dataframe with a timeseries for each cell: year quarter cell1 cell2 1940 1 1.2 1.4 1940 2 1.4 2.1 1940 3 1.4 2.6 1940 4 1.9 2.4 1941 1 2.9 2.4 1941 2 2.1 1.4 1941 3 3.4 1.4 1942 4 2.4 3.4 1942 1 2.7 1.4 1942 2 3.2 2.4 1942 3 1.5 2.5 1942 4 2.6 4.4 Thus the third and fourth columns are the timeserieses for cell 1 and cell 2. Is there a nice vectorized way to do this? I can't quite make reshape() do what I want. [the real dataset is months, not quarters, has ~2000 cells and ~60 years] -- Robin K. S. Hankin Uncertainty Analyst University of Cambridge 19 Silver Street Cambridge CB3 9EP 01223-764877 __ 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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ 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] Replacing dates with consecutive observations
Try this also: x - seq(as.Date(2008-01-01), as.Date(2008-12-31), l = 10) as.Date(embed(matrix(x), 2)[,1], origin = 1970-01-01) On Wed, Jan 21, 2009 at 7:18 PM, Alina Sheyman alina...@gmail.com wrote: I am working with a list of dates and I would like to replace each date with the one that comes after, ie. 1/1/07 will become 1/5/07, 1/5/07 will become 1/7/07, etc. The number of days between my dates always varies, so I can't just increase each one by 5 days or so. Does anyone know of a way I can do this in R? thank you [[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] Odp: problem with compating 2 strings
Hi r-help-boun...@r-project.org napsal dne 22.01.2009 10:49:26: Hi all, I got one problem with compating charecterstrings with using == can anyone suggest if any other way to compare two charecterstrings Works for me a-letters b-letters[1:10] a==b [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [26] FALSE Warning message: In a == b : longer object length is not a multiple of shorter object length a%in%b [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [26] FALSE Regards Petr thanks in advance [[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] Sweave encoding problem
Hi Roland,
thanks for your answere. I actually tried out a different, smaller
Latex-header and the sweave-process suddenly worked. So I copied parts
of the old header into the new one, to check what part is causing the
trouble. In the end I had two documents with identical content. The new
document worked fine with Sweave the other still gave out the
error-message. If anybody has experienced that problem before, and knows
an answere, please let me know.
Unfortunaetly I also still have an encoding problem with the new documt,
that ran through Sweave. If I use ISO-8859-15 fontencoding in my
editor and latin1 for input encoding in my Latex-document everything
works fine. If I keep both in utf8, as I would like it, german mutated
vowels (Umlaute) aren't displayed correctly.
Rau, Roland schrieb:
Hi Gerrit,
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Gerrit Voigt
Sent: Monday, January 19, 2009 4:48 PM
To: r-help@r-project.org
Subject: [R] Sweave encoding problem
Hello,
Sweave seems to have trouble processing german letters in R.
For example, my noweb R-input looks like this.
=
Oberflächenfehler = c(4, 11, 6, 2, 7, 9)
@
If I send it through Sweave, I get the following error message.
error: chunk 1
Error in parse(text = chunk) : unexpected input in Oberflä
extra: Warning message:
In readLines(f[1]) :
underfull last line in C:\
(my R is in german, so I needed to translate the error
message myself.)
I got the impression, that this is an encoding issue of
Sweave, since
the input typed into R directly works just fine. The encoding
I use in
my noweb document is utf8.
I don't think it has something to do with German letters.
I saved the following text in a file 'sweavy.Snw':
\documentclass{article}
\begin{document}
Hello World!
=
1+1
@
=
Oberflächenfehler = c(4, 11, 6, 2, 7, 9)
@
\end{document}
This is what happened in R:
library(utils)
Sweave(sweavy.Snw)
Writing to file sweavy.tex
Processing code chunks ...
1 : echo term verbatim
2 : echo term verbatim
You can now run LaTeX on 'sweavy.tex'
sessionInfo()
R version 2.7.0 (2008-04-22)
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
And also the dvi looked fine after processing latex sweavy.tex
To make things sure, I did in my editor (GNU Emacs 22.1.50.1)
C-x RET f utf-8
to change
set-buffer-file-coding-system to utf-8.
Still works fine.
Maybe this helps you further to track down the reason for the problem?!?
Best,
Roland
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receive a mail that is apparently from a MPI user without this text
displayed, then the address has most likely been faked. If you are uncertain
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[R] addressing and summarizing columns of a dataframe in nlme package
Hi! Within the lm function I can address and summarize columns like that: lm1-lm(I(rowSums(spec[,5:81]))~pH) If I want to do the same in nlme package I get the following error: lme1-lme(I(rowSums(spec[,5:81]))~pH,random=~1|site) Error in model.frame.default(formula = ~spec + pH + site, data = environment, : invalid type (list) for variable 'spec' These kind of list seem to be not accepted by the lme function and my formula misinterpreted. Variables are pH and site, dataframe is spec and attached. How can I address and summarize any number of columns of a dataframe in the nlme package? Thanks a lot, cheers Eva -- Eva Remke work Biological Station, Biologenweg 15, 18565 Kloster/ Insel Hiddensee, Germany phone +49 (0)38300 50251 mobile +49 (0)171 478 3920 fax +49 (0)38300 60672 evare...@gmx.net __ 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 using heatmap :evaluation nested too deeply.....
Hi, I get following error when trying to plot a heatmap on a very large matrix (808 x5000). heatmap(ctab) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? Call to heatmap function is not contained within any other function or so. Upon searching the R mailing list, I found that someone had the same problem and the suggested solution was to set an option using options(expressions = 500). I tried it but even on small subset of the matrix, but it continues giving the same error. I use default distance matrix with row scaling. Please 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] text vector clustering
Hi, I am a new user of R using R 2.8.1 in windows 2003. I have a csv file with single column which contain the 30,000 students names. There were typo errors while entering this student names. The actual list of names is 1000. However we dont have that list for keyword search. I am interested in grouping/cluster these names as those which are similar letter to letter. Are there any text clustering algorithm in R which can group names of similar type in to segments of exactly matching , 90% matching, 80% matching,etc. thanks in advance, regards, srinivas statistical analyst. [[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] Standard errors of least squares adjusted means
Dear Bruno, See the effects package (on CRAN) for a generalization of adjusted means. I hope this helps, John -- John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Bruno Estigarribia Sent: January-22-09 12:32 AM To: r-help@r-project.org Subject: [R] Standard errors of least squares adjusted means Hello, I have the following model: lm.7 - lm(Y ~ F + C1 + C2 , data = EM4) F is a 4-level factor, the rest are covariates centered at their mean (Y is a two-column matrix). I have tried to find functions to give the model-adjusted means (adjusted at the covariates'means) and their standard deviations for each. (That is, what I believe is called in SAS least square or LS-means, whose errors one obtains by STDERR) I have tried help.search and RSiteSearch with several terms including standard errors, least square means, adjusted means. I have found how to extract the SE from coefficients (se.coef from package arm), or the SE for contrasts (se.contrast from package stats), but not the SE for an adjusted mean. Thank you, -- Bruno Estigarribia Postdoctoral Fellow FPG Child Development Institute Neurodevelopmental Disorders Research Center University of North Carolina at Chapel Hill 105 Smith Level Rd Chapel Hill, NC 27599-8180 USA + 1 (919) 843-7685 __ 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] pdf() and pch problems
Hi R-2.8.1, Suse 11.1 I'm having problems with pdf(). In the following transcript, file 'f.pdf' does not use the expected symbols for the plot. It uses a 'q' letter instead of the open circle I get when viewing the graphics window. I also get the same under r47678. Does anyone else get this? le112:~/scratch/R-2.8.1% R --vanilla --quiet pdf(file='~/f.pdf') plot(1:10 , pch=1) dev.off() null device 1 sessionInfo() R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base q() le112:~/scratch/R-2.8.1% -- Robin K. S. Hankin Uncertainty Analyst University of Cambridge 19 Silver Street Cambridge CB3 9EP 01223-764877 __ 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] Frequency and summary statistics table with different variables and categories
Hello helpers, This is probably quite simple, but I'm stuck. I want to create a summary statistics table with frequencies and summary statistics for a large number of variables. The problem here is that (1) there are two different classes of categories (sex, type of substance abuse and type of treatent) which overlap, (2) the data for different variables should be presented in different ways -- sometimes with relative frequencies, other times with mean values. The table would finally look something like: All Male Female Alcohol Drug ... Age (mean) (mean) ... Sex (% male)(freq) (freq) ... Alcohol CS (mean) (mean) ... ... ... Data is in a data frame with quite a lot of columns (variables) and each row represents a single case. I have found out that part of this can be done with tapply, for example tapply(age, sex, mean) and join it with tapply(age, abuse, mean). But how to do with frequencies? Or is there an even simpler way? /S [[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] Frequency and summary statistics table with different variables and categories
Since %male is basically the mean if you code male=1 and female=0, which is more informative than absolute frequency. So, you may want to have a glance at doBy package, especially the summaryBy function. All the best On Thu, Jan 22, 2009 at 7:17 PM, Stefan Björk stefan.bj...@gmail.com wrote: Hello helpers, This is probably quite simple, but I'm stuck. I want to create a summary statistics table with frequencies and summary statistics for a large number of variables. The problem here is that (1) there are two different classes of categories (sex, type of substance abuse and type of treatent) which overlap, (2) the data for different variables should be presented in different ways -- sometimes with relative frequencies, other times with mean values. The table would finally look something like: All Male Female Alcohol Drug ... Age (mean) (mean) ... Sex (% male)(freq) (freq) ... Alcohol CS (mean) (mean) ... ... ... Data is in a data frame with quite a lot of columns (variables) and each row represents a single case. I have found out that part of this can be done with tapply, for example tapply(age, sex, mean) and join it with tapply(age, abuse, mean). But how to do with frequencies? Or is there an even simpler way? /S [[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. -- HUANG Ronggui, Wincent Tel: (00852) 3442 3832 PhD Candidate Dept of Public and Social Administration City University of Hong Kong Homepage: http://ronggui.huang.googlepages.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] pdf() and pch problems
On Thu, 22 Jan 2009, Robin Hankin wrote: Hi R-2.8.1, Suse 11.1 I'm having problems with pdf(). In the following transcript, file 'f.pdf' does not use the expected symbols for the plot. It uses a 'q' letter instead of the open circle I get when viewing the graphics window. I also get the same under r47678. Does anyone else get this? Yes, if you use a broken PDF viewer (you have not told us yours). From ?pdf useDingbats: logical. Should small circles be rendered _via_ the Dingbats font? Defaults to true, which produces smaller and better output - this is provided for those who insist on using broken PDF viewers. I get the problem in evince but not acroread in F10. le112:~/scratch/R-2.8.1% R --vanilla --quiet pdf(file='~/f.pdf') plot(1:10 , pch=1) dev.off() null device 1 sessionInfo() R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base q() le112:~/scratch/R-2.8.1% -- Robin K. S. Hankin Uncertainty Analyst University of Cambridge 19 Silver Street Cambridge CB3 9EP 01223-764877 __ 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, rip...@stats.ox.ac.uk 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] Does anyone has this paper in pdf?
aiminy wrote: de Jong, S. (1993) SIMPLS: an alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18, 251263 Yes, the publishers do, you can purchase it from http://dx.doi.org/10.1016/0169-7439(93)85002-X Its a shame that not all journals make their back-catalogue available free of charge, but I don't see why you expect people on this list to breach copyright for you? Neil -- View this message in context: http://www.nabble.com/Does-anyone-has-this-paper-in-pdf--tp21594321p21602580.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave encoding problem
Gerrit Voigt wrote:
Hi Roland,
thanks for your answere. I actually tried out a different, smaller
Latex-header and the sweave-process suddenly worked. So I copied parts
of the old header into the new one, to check what part is causing the
trouble. In the end I had two documents with identical content. The new
document worked fine with Sweave the other still gave out the
error-message. If anybody has experienced that problem before, and knows
an answere, please let me know.
This sounds like you have discovered homeopathic properties in Sweave!
It will be serious if input files remember errors even after they have
been removed.
But I think it's more likely that the files just look the same in your
editor, but are actually different in some way you don't see. Candidates:
- the encoding: maybe your editor is recognizing the encoding, and
automatically displaying similar content from different input.
- non-printing characters: maybe your editor is skipping some.
I'd suggest doing a binary compare on the two files to see what the
differences are. I think you are on Windows (but I may be misreading
the quotes below); I recommend Beyond Compare (a shareware compare
utility). It has a hex viewer plug-in that could show you a detailed
comparison. I imagine diff on Unix has something similar.
Duncan Murdoch
Unfortunaetly I also still have an encoding problem with the new documt,
that ran through Sweave. If I use ISO-8859-15 fontencoding in my
editor and latin1 for input encoding in my Latex-document everything
works fine. If I keep both in utf8, as I would like it, german mutated
vowels (Umlaute) aren't displayed correctly.
Rau, Roland schrieb:
Hi Gerrit,
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Gerrit Voigt
Sent: Monday, January 19, 2009 4:48 PM
To: r-help@r-project.org
Subject: [R] Sweave encoding problem
Hello,
Sweave seems to have trouble processing german letters in R.
For example, my noweb R-input looks like this.
=
Oberflächenfehler = c(4, 11, 6, 2, 7, 9)
@
If I send it through Sweave, I get the following error message.
error: chunk 1
Error in parse(text = chunk) : unexpected input in Oberflä
extra: Warning message:
In readLines(f[1]) :
underfull last line in C:\
(my R is in german, so I needed to translate the error
message myself.)
I got the impression, that this is an encoding issue of
Sweave, since
the input typed into R directly works just fine. The encoding
I use in
my noweb document is utf8.
I don't think it has something to do with German letters.
I saved the following text in a file 'sweavy.Snw':
\documentclass{article}
\begin{document}
Hello World!
=
1+1
@
=
Oberflächenfehler = c(4, 11, 6, 2, 7, 9)
@
\end{document}
This is what happened in R:
library(utils)
Sweave(sweavy.Snw)
Writing to file sweavy.tex
Processing code chunks ...
1 : echo term verbatim
2 : echo term verbatim
You can now run LaTeX on 'sweavy.tex'
sessionInfo()
R version 2.7.0 (2008-04-22)
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
And also the dvi looked fine after processing latex sweavy.tex
To make things sure, I did in my editor (GNU Emacs 22.1.50.1)
C-x RET f utf-8
to change
set-buffer-file-coding-system to utf-8.
Still works fine.
Maybe this helps you further to track down the reason for the problem?!?
Best,
Roland
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then the address has most likely been faked. If you are uncertain about the
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Opening a script with the R editor via file association (on Windows)
pdewitt wrote: I read the posting about opening .R files in windows with the Rgui and was wondering if anything has changed for R-2.8.1 and Windows Vista? I have not yet been able to get the files to open in the Rgui, the association works enough to open R but that is about it. Thanks for the input. I don't recall anyone submitting code to do that. It's not easy to get it right: for example, if you click on a file while R is running, you probably want to open the file in the current R instance, not open a new R session: that means running a program to send a message to R to open the file. And since the R script editor isn't the greatest editor in the world, people who would write that sort of thing probably don't use it for most of their editing, and have little motivation to do all the work. So I'd recommend that you should investigate WinEdt, or Tinn-R, or Emacs, all of which are much more capable editors, with available connections to R. 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] Sweave encoding problem
Duncan Murdoch wrote: I'd suggest doing a binary compare on the two files to see what the differences are. I think you are on Windows (but I may be misreading the quotes below); I recommend Beyond Compare (a shareware compare utility). It has a hex viewer plug-in that could show you a detailed comparison. I imagine diff on Unix has something similar. diff -s vQ __ 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] Frequency and summary statistics table with different variables and categories
One of the various tabulation functions would seem to be the most appropriate for getting frequency summaries: ?table ?xtabs On Jan 22, 2009, at 6:17 AM, Stefan Björk wrote: Hello helpers, This is probably quite simple, but I'm stuck. I want to create a summary statistics table with frequencies and summary statistics for a large number of variables. The problem here is that (1) there are two different classes of categories (sex, type of substance abuse and type of treatent) which overlap, (2) the data for different variables should be presented in different ways -- sometimes with relative frequencies, other times with mean values. The table would finally look something like: All Male Female Alcohol Drug ... Age (mean) (mean) ... Sex (% male)(freq) (freq) ... Alcohol CS (mean) (mean) ... ... ... Data is in a data frame with quite a lot of columns (variables) and each row represents a single case. I have found out that part of this can be done with tapply, for example tapply(age, sex, mean) and join it with tapply(age, abuse, mean). But how to do with frequencies? Or is there an even simpler way? /S [[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] Error as.Date on Invalid Dates
-begin included message However, as.Date encounters an error when the string does not represent an actual date. eg: date1 - 2009-02-29 # Note: 2009 not a leap year as.Date(date1) Error in fromchar(x) : character string is not in a standard unambiguous format As I have many instances of date entries like this, date1, date2, date3, etc. , I'd like the script to error out gracefully and to be able to point the user to which date they need to correct, rather than Error in fromchar(x)..., which doesn't make it obvious what they need to do to fix the error. Ideally I'd love to send the user a message like: print(paste(date1, is an invalid date. Refer to calendar., sep= )) If anyone has any suggestions on catching this type of error and feedback which directs the user, it would be much appreciated. --- end inclusion - One idea is to use the as.date function, for the older (and less capable) 'date' class. This is currently loaded by default with library(survival). It returns NA for an invalid date rather than dying. as.date(c(2009-5-10, 2007/2/29, 1953/3/10), order='ymd') [1] 10May2009 NA10Mar53 The order argument in needed here since the default assumption is the US habit of month-day-year. You can then convert to the more modern format. temp - as.date(c(2009-5-10, 2007/2/29, 1953/3/10), order='ymd') as.Date(temp) [1] 2009-05-10 NA 1953-03-10 Terry Therneau Note: as.Date will return a string with NA's as well, AS LONG AS the first date in the sequence is legal. It uses the first to pick a format (I presume). __ 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] dimnames in pkg ipred
Hello List, I`m trying to make prediction using a bagged tree with the package ipred. I tried to follow the manual but I`m getting an error message. Also browsing through the list-archive I didn`t find any hint. Maybe someone can help me? selbag - bagging(SOIL_UNIT ~., data=traindat.bin, coob=TRUE) Error in dimnames(X) - list(dn[[1L]], unlist(collabs, use.names = FALSE)) : length of 'dimnames' [2] not equal to array extent I´m using R 2.7.2 on Win XP and the latest version of ipred. Thanks a lot. TIM --- Dipl.-Geogr. Tim Häring Sachgebiet Standort und Bodenschutz (SG 2.1) Bayerische Landesanstalt für Wald und Forstwirtschaft Am Hochanger 11 D-85354 Freising Tel.: +49-(0)8161/71-4769 E-Mail: tim.haer...@lwf.bayern.de http://www.lwf.bayern.de [[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] Error as.Date on Invalid Dates
On Thu, 22 Jan 2009, Terry Therneau wrote: -begin included message However, as.Date encounters an error when the string does not represent an actual date. eg: date1 - 2009-02-29 # Note: 2009 not a leap year as.Date(date1) Error in fromchar(x) : character string is not in a standard unambiguous format As I have many instances of date entries like this, date1, date2, date3, etc. , I'd like the script to error out gracefully and to be able to point the user to which date they need to correct, rather than Error in fromchar(x)..., which doesn't make it obvious what they need to do to fix the error. Ideally I'd love to send the user a message like: print(paste(date1, is an invalid date. Refer to calendar., sep= )) If anyone has any suggestions on catching this type of error and feedback which directs the user, it would be much appreciated. --- end inclusion - One idea is to use the as.date function, for the older (and less capable) 'date' class. This is currently loaded by default with library(survival). It returns NA for an invalid date rather than dying. So does as.Date *if you specify the format* (as you have to with your as.date: it has a default one): as.Date(date1, format=%Y-%m-%d) [1] NA as.date(c(2009-5-10, 2007/2/29, 1953/3/10), order='ymd') [1] 10May2009 NA10Mar53 The order argument in needed here since the default assumption is the US habit of month-day-year. You can then convert to the more modern format. temp - as.date(c(2009-5-10, 2007/2/29, 1953/3/10), order='ymd') as.Date(temp) [1] 2009-05-10 NA 1953-03-10 Terry Therneau Note: as.Date will return a string with NA's as well, AS LONG AS the first date in the sequence is legal. It uses the first to pick a format (I presume). -- Brian D. Ripley, rip...@stats.ox.ac.uk 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] pdf() and pch problems
Quoting Brian D Ripley rip...@stats.ox.ac.uk: On Thu, 22 Jan 2009, Robin Hankin wrote: Hi R-2.8.1, Suse 11.1 I'm having problems with pdf(). In the following transcript, file 'f.pdf' does not use the expected symbols for the plot. It uses a 'q' letter instead of the open circle I get when viewing the graphics window. I also get the same under r47678. Does anyone else get this? Yes, if you use a broken PDF viewer (you have not told us yours). From ?pdf useDingbats: logical. Should small circles be rendered _via_ the Dingbats font? Defaults to true, which produces smaller and better output - this is provided for those who insist on using broken PDF viewers. I get the problem in evince but not acroread in F10. The problem is caused by missing fontconfig rules in openSUSE 11.1 (that the PDF library poppler depends on). I reported the problem a while ago here http://bugs.freedesktop.org/show_bug.cgi?id=18002 (instructions on how to fix the issue are included) and filed a bug at the openSUSE bug database https://bugzilla.novell.com/show_bug.cgi?id=434676. The bug was closed, but I reopened it. le112:~/scratch/R-2.8.1% R --vanilla --quiet pdf(file='~/f.pdf') plot(1:10 , pch=1) dev.off() null device 1 sessionInfo() R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base q() le112:~/scratch/R-2.8.1% -- Robin K. S. Hankin Uncertainty Analyst University of Cambridge 19 Silver Street Cambridge CB3 9EP 01223-764877 __ 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, rip...@stats.ox.ac.uk 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-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] melt stumbles over deleted columns
I have a data frame that is the result of a cast (reshape) operation. I deleted the variable column and tried to melt the resulting data frame. Depending on which method I use to delete the column I get different error messages when melting: head(tinfos) vpn group trial_no item relation trial_type rt variable # 1 102 21 4351diag1 distractor 8471fix_d 27 2 102 22 1214 id target 4072fix_d 17 3 102 23 4213diag1 distractor 7040fix_d 27 4 102 24 1314 id target 4370fix_d 15 5 102 25 2655 vert distractor 4397fix_d 17 6 102 26 3322horiz distractor 6132fix_d 26 tinfos$variable - NULL melt(tinfos) Error: id variables not found in data: variable Or: tinfos2 - tinfos[,-match(variable,names(tinfos))] melt(tinfos2) Error in `rownames-`(`*tmp*`, value = character(0)) : attempt to set rownames on object with no dimensions In addition: Warning messages: 1: In `[-.factor`(`*tmp*`, ri, value = c(8471L, 4072L, 7040L, 4370L, : invalid factor level, NAs generated 2: In `[-.factor`(`*tmp*`, ri, value = c(0L, 0L, 1L, 0L, 0L, 0L, 0L, : invalid factor level, NAs generated I figure there must be some internal inconsistency in the data frame after deletion. Does anybody have an idea how to fix that? Thanks! Titus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] melt stumbles over deleted columns
On Thu, Jan 22, 2009 at 8:01 AM, Titus von der Malsburg malsb...@gmail.com wrote: I have a data frame that is the result of a cast (reshape) operation. I deleted the variable column and tried to melt the resulting data frame. Depending on which method I use to delete the column I get different error messages when melting: head(tinfos) vpn group trial_no item relation trial_type rt variable # 1 102 21 4351diag1 distractor 8471fix_d 27 2 102 22 1214 id target 4072fix_d 17 3 102 23 4213diag1 distractor 7040fix_d 27 4 102 24 1314 id target 4370fix_d 15 5 102 25 2655 vert distractor 4397fix_d 17 6 102 26 3322horiz distractor 6132fix_d 26 tinfos$variable - NULL melt(tinfos) Error: id variables not found in data: variable Cast stores some extra information in the data frame that makes future melting a bit easier, provided that you don't delete any of the columns. Since you have, you need to throw away the extra info with: tinfos - as.data.frame(tinfos) Regards, Hadley -- http://had.co.nz/ __ 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] pdf() and pch problems
TZ == T Zumbrunn t.zumbr...@unibas.ch on Thu, 22 Jan 2009 14:52:37 +0100 writes: TZ Quoting Brian D Ripley rip...@stats.ox.ac.uk: On Thu, 22 Jan 2009, Robin Hankin wrote: Hi R-2.8.1, Suse 11.1 I'm having problems with pdf(). In the following transcript, file 'f.pdf' does not use the expected symbols for the plot. It uses a 'q' letter instead of the open circle I get when viewing the graphics window. I also get the same under r47678. Does anyone else get this? Yes, if you use a broken PDF viewer (you have not told us yours). From ?pdf useDingbats: logical. Should small circles be rendered _via_ the Dingbats font? Defaults to true, which produces smaller and better output - this is provided for those who insist on using broken PDF viewers. I get the problem in evince but not acroread in F10. TZ The problem is caused by missing fontconfig rules in openSUSE 11.1 TZ (that the PDF library poppler depends on). I reported the problem a TZ while ago here http://bugs.freedesktop.org/show_bug.cgi?id=18002 TZ (instructions on how to fix the issue are included) and filed a bug at TZ the openSUSE bug database TZ https://bugzilla.novell.com/show_bug.cgi?id=434676. The bug was TZ closed, but I reopened it. That's interesting, thank you very much, Thomas, for the extra explanation! As you know (but your text above could be read differently) this bug ... quite long standing! ... seems to be much wider spread than just (Open)SuSE. I have seen and still see it on Redhat (RHEL 5) and many Ubuntu versions too. And indeed, the workaround recommended (somewhere) in the above URL is working for me too: Add the following (without the - lines) to your ~/.fonts.conf file (or create such a file) : --snip- alias binding=same familyZapfDingbats/family acceptfamilyDingbats/family/accept /alias --snip- Martin Maechler, ETH Zurich le112:~/scratch/R-2.8.1% R --vanilla --quiet pdf(file='~/f.pdf') plot(1:10 , pch=1) dev.off() null device 1 sessionInfo() R version 2.8.1 (2008-12-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base q() le112:~/scratch/R-2.8.1% -- Robin K. S. Hankin Uncertainty Analyst University of Cambridge 19 Silver Street Cambridge CB3 9EP 01223-764877 __ 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, rip...@stats.ox.ac.uk 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. TZ __ TZ R-help@r-project.org mailing list TZ https://stat.ethz.ch/mailman/listinfo/r-help TZ PLEASE do read the posting guide http://www.R-project.org/posting-guide.html TZ 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] infer haplotypes phasing trios tdthap
Dear R mailing list, I have a dataset with genotypes from trios and I would like to infer haplotypes for each mother, father and child. The package that I could find that can do this is tdthap. But when the mother is homozygous (e.g., 2/2) the haplotype is called as not possible to infer (0); I would prefer for it to call the genotype (2). From what I understand it is doing what I would like for the father (example below). Can anyone provide me with some information about this tdthap behaviour? And is there any other package that would do this? (Searched for it, couldn't find it) Thank you very much, Tiago Magalhães example (ped file with pedigrees) 9 100 102 101 1 2 1 1 2 1 2 2 1 2 9 101 0 0 2 1 1 1 2 1 2 2 2 2 9 102 0 0 1 1 2 1 2 1 2 2 1 1 data out: hap.transmit(example) pedidfathermother 9 100102 101 f.tr.1f.tr.2f.tr.3f.tr.4 1 0 2 1 m.tr.1m.tr.2m.tr.3m.tr.4 00 0 0 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to Run R Programs in a Scheduled Way
Hi Thorsten, the way i do this (on Windows Vista Ultimate, SP1) is to create a batch file and then have windows task scheduler call it at a specific time. For example, to create my batch file i open up Notepad and type the following single line into it: C:\Program Files\R\R-2.8.1\bin\R.exe CMD BATCH --vanilla --slave \ \PFO-SBS001\Redirected\tonyb\Desktop\myScript.R so this is basically: [location of R.exe] CMD BATCH --vanilla -- slave [location of your R script file] I then save this Notepad text file, and change the extension from '.txt' to '.bat'. If you double click on this .bat file, it will run your script. All you have to do now is have scheduler point to your new .bat file :-) HTH, Tony Breyal P.S. Be careful with windows scheduler (at least in Vista) if you want the same script to run several times a day (e.g. setting a daily trigger starting at 0900 and repeating every 2 hours for a duration of 12 hours). Instead of stopping when expected, it will just keep going every 2 hours regardless of the duration you set (the only way around this that i found was to programme in time constraints into my r script itself, such as only running the script if a condition like 9=current.hour current.hour=21 are met.) On 22 Jan, 09:10, Thorsten Muehge mue...@de.ibm.com wrote: Hello R Experts, does anyone know how to run R programs automatically using the window scheduler? I want to run some R programs automatically and make the results available via web. Mit freundlichen Grüßen / Best Regards / С наилучшими Ð¿Ð¾Ð¶ÐµÐ»Ð°Ð½Ð¸Ñ Ð¼Ð¸ / üdvözlettel Thorsten [[alternative HTML version deleted]] __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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] problem with geepack
Hi, I think in such cases you need to use the 'wave' parameter (wave = Date), but I must admit I found contradictory comments on how missing values are treated in geepack. Does someone know what geepack is doing with missing values? Popko Giacomo Santini wrote: Hi all I am analyzing a data set containing information about the behaviour of marine molluscs on a vertical wall. Since I have replicate observations on the same individuals I was thinking to use the geepack library. The data are organised in a dataframe with the following variables Date = date of sampling, Size = dimensions (mm) Activity duration of activity (min) Water = duration of splashing by waves Hgt = resting eight of each specimen before activity begin Individual = a code indicating the id of the specimen. I have up to 12 replicate observations for individual. Some observation are missing and I organized the data frame to have exactly 12 rows for each specimen, with NAs where there is a missing observation. The following model worked fine: gee1-geese(Activity~Water, id=Individual, data=dataF, family=gaussian) but when I use other variables e.g gee2-geese(Activity~Hgt+Size+Water, id=Individual, data=dataF, family=gaussian) I get the error message Error in geese.fit(x, y, id, offset, soffset, w, waves, zsca, zcor, corp, : nrow(zsca) and length(y) not match which I am not able to understand. The same problem has been reported in the list in 2006, but I have not found any response to it. Any suggestion? Giacomo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/problem-with--geepack-tp15851828p21601979.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] U R ready for R! Now deploy your R models via cloud computing!
Hi Michael, Can you also build the PMML model on the cloud with R, paying for the processor ,memory usage. Any plans to extend the abilty to model, or is it just deploy PMML models on the cloud servers. Regards, Ajay http://www.decisionstats.com On Thu, Jan 22, 2009 at 4:29 AM, MZ zeller.mich...@gmail.com wrote: Following the recent NYT article about R, I thought this group is not only ready for R but ready to take it one step further. Got models in R? Deploy and score them in ADAPA in minutes on the Amazon EC2 cloud computing infrastructure! Zementis ( http://www.zementis.com ) has been working with the R community, specifically to extend the support for the Predictive Model Markup Language (PMML) standard which allows model exchange among various statistical software tools ( http://adapasupport.zementis.com/2008/02/how-can-i-export-pmml-code-from-r.html ). If you develop your models in R, you can easily deploy and execute these models in the Zementis ADAPA scoring engine ( http://www.zementis.com/products.htm ) using the PMML standard. This not only eliminates potential memory constraints in R but also speeds execution and allows SOA-based integration. For the IT department, ADAPA delivers reliability and scalability needed for production-ready deployment and real-time predictive analytics. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot: abline() - define line length
Use either the 'clip' function from the graphics package, or the 'clipplot' function from the TeachingDemos package. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Jörg Groß Sent: Wednesday, January 21, 2009 5:02 PM To: r-help@r-project.org Subject: [R] plot: abline() - define line length Hi, is there a way to define, that a line drawn via abline() should only go from for example -2 to 1 on the x-axis (with something working similiar to xlim()) ? thanks for any help! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error as.Date on Invalid Dates
I am relatively new to R, so maybe I am miss something, but I now tried the as.Date now and have problems understanding how it works (or don't work as it seem). Brian D Ripley wrote: On Thu, 22 Jan 2009, Terry Therneau wrote: One idea is to use the as.date function, for the older (and less capable) 'date' class. This is currently loaded by default with library(survival). It returns NA for an invalid date rather than dying. So does as.Date **if you specify the format** (as you have to with your as.date: it has a default one): as.Date(2001/1/1) Works fine as.Date(1/1/2001) Prints 1-01-20 ??? as.Date(13/1/2001) Prints 13-01-20 ??? as.Date(1/13/2001) Prints error: not in standard unambigous format It seems that as if both 1/1/2001 and 13/1/2001 were considered by R to be in a standard unambiguous format (or otherwise an error be reported?) and yet they are parsed incorrectly according to what one could think is obvious. It is also surprizing that not only 13/1/2001 but also 1/2/2001 and 2/1/2001 are successful but incorrect parsed as if they are unambiguous, and yet 13/1/2001 is ambiguous, though there is really just one way to parse it meaningfully. I think the strings that are incorrectly parsed should raise errors, and the last example should be succesful parsed. What is the reason for the observed? Mvh. Marie [[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] Finding the distance between ordered integers
I'm stuck on how best to of find the distance between ordered integers (presented below as a birthday problem). Given the vector x, how do I most efficiently generate the vector x[i+1] - x[i]? Thanks. --Dale For example... set.seed(555) x - sample(1:365, 10, replace=TRUE) x - sort(x) x x[i+1]-x[i] ------ 14 14 0 75 61 136 61 197 61 236 39 253 17 310 57 323 13 355 32 __ 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] text vector clustering
Simply doing a tabulation and isolating the cases with only one entry might have been a possibility if the count discrepancy weren't so high. It appears you have a greater degree of corruption than would be expected just from typos. Have you looked at the packages referenced at: http://cran.r-project.org/web/views/NaturalLanguageProcessing.html The Soundex algorithm is an old programming chestnut which I have seen implemented in R, but I understand there are improved versions. How well they perform on persons' names may depend strongly on cultural origins of your population. -- David Winsemius On Jan 22, 2009, at 6:03 AM, srinivasa raghavan wrote: Hi, I am a new user of R using R 2.8.1 in windows 2003. I have a csv file with single column which contain the 30,000 students names. There were typo errors while entering this student names. The actual list of names is 1000. However we dont have that list for keyword search. I am interested in grouping/cluster these names as those which are similar letter to letter. Are there any text clustering algorithm in R which can group names of similar type in to segments of exactly matching , 90% matching, 80% matching,etc. thanks in advance, regards, srinivas statistical analyst. [[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] Finding the distance between ordered integers
Dear Dale, Try this: set.seed(555) x - sample(1:365, 10, replace=TRUE) x - sort(x) diff(x) HTH, Jorge On Thu, Jan 22, 2009 at 10:07 AM, Dale Steele dale.w.ste...@gmail.comwrote: I'm stuck on how best to of find the distance between ordered integers (presented below as a birthday problem). Given the vector x, how do I most efficiently generate the vector x[i+1] - x[i]? Thanks. --Dale For example... set.seed(555) x - sample(1:365, 10, replace=TRUE) x - sort(x) x x[i+1]-x[i] ------ 14 14 0 75 61 136 61 197 61 236 39 253 17 310 57 323 13 355 32 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-SIG-Finance] how to study the lead and lag relation of two time series?
Dear Michael, David Ruelle wrote a very interesting paper on Recurrence plots of dynamical Systems that you should read, and I remember of simples lead/lags methods to detect random or determinist systems. I think that you should take a look at this very interesting paper on Lead-lag cross-sectional structure and detection of correlated-anticorrelated regime shifts: http://tinyurl.com/b6cw5m Regards. Sylvain __ Sylvain Barthélémy Research Director, TAC Applied Economic Financial Research Tel: +33.(0).299.393.140 - Fax: +33.(0).299.393.189 E-mail: ba...@tac-financial.com www.tac-financial.com | www.sylbarth.com -Message d'origine- De : r-sig-finance-boun...@stat.math.ethz.ch [mailto:r-sig-finance-boun...@stat.math.ethz.ch] De la part de Michael Envoyé : jeudi 22 janvier 2009 02:18 À : r-help; r-sig-fina...@stat.math.ethz.ch Objet : [R-SIG-Finance] how to study the lead and lag relation of two time series? Hi all, Is there a way to study the lead and lag relation of two time series? Let's say I have two time series, At and Bt. Is there a systematic way of concluding whether it's A leading B or B leading A and by how much? Thanks! ___ r-sig-fina...@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-finance -- Subscriber-posting only. -- If you want to post, subscribe first. No virus found in this incoming message. Checked by AVG - http://www.avg.com 21/01/2009 21:15 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] trouble converting an array to a dataframe
On Thu, Jan 22, 2009 at 9:09 AM, Christopher W. Ryan cr...@binghamton.edu wrote: I probably did not explain my data clearly. I am starting with a dataframe with three columns: redlognumb radiologistbarrtotal where the entries in the variable radiologist are either 1 or 2, indicating which radiologist generated that barrtotal. All subjects had their X-ray read independently by both radiologists. So there are two rows for each subject. I want to convert it to this structure: redlognumbradiologist.1.barrtotalradiologist.2.barrtotal in which there is only one row for each subject. At any rate, in the meantime, I think I figured out that I was melting improperly, and I think I've got it now. Thanks. You should just be able to cast like: cast(m, redlognumb ~ radiologist + variable) If you haven't already, you might want to look at the introduction available at http://had.co.nz/reshape Regards, Hadley -- http://had.co.nz/ __ 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 using zeroinfl()
Hi all, I have been trying to use zeroinfl() with the pscl package with R version 2.1.1. and with the newest versions of the contrib packages compatible with R 2.1.1. I have read the examples, the vignette and all the posts relating to zeroinfl() but I am still confused as to how to structure the model. Here is a small example; the error message is the same for big data sets library(mvtnorm,lib.loc=C:/Documents and Settings/simonp/My Documents/R backup library) library(pscl,lib.loc=C:/Documents and Settings/simonp/My Documents/R backup library) y-c(0,0.2,0.4,0.7,0,0,0,0.8,0,0,0,0,0) x-c(3,4,5,2,3,6,3,7,4,8,5,8,3) m1-zeroinfl(y~x|x) Zero-Inflated Count Model Using logit to model zero vs non-zero Using Poisson for counts Error in terms.formula(formula, data = data) : argument is not a valid model Can anyone shed any light please? Simon. Dr. Simon Pickett Research Ecologist Land Use Department Terrestrial Unit British Trust for Ornithology The Nunnery Thetford Norfolk IP242PU 01842750050 [[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] Package installation failed
Hi folks, I am currently having the problem with using R 2.8.1 that I cannot install some of packages from CRAN or local drive and somebody may be able to help me. ex) faraway package and lme4 package. I have downloaded them in my hard drive as local, but still R was unable to find the package (message showed up as no such file). I could download most packages, but not all what I want. I showed my PC to R experts around and nobody had ideas. I've re-installed newest R and updated packages hundred times, but still same message came up. My working environment is: OS: XP Windows R2.8.1 Any suggestions would be appreciated. Thanks a lot, Odette [[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] robust regression
Dear Miss R, I have a large dataset that is skewed and would like to calculate confidence intervals for my regression line. Unfortunately I have trouble finding commands for rubust regression and in particular for the confidence intervals... Can you possibly give a hint? Thank you and best regards, Gerog. [[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] convergence problem gamm / lme
Hope one of you could help with the following question/problem:
We would like to explain the spatial
distribution of juvenile fish. We have 2135 records, from 75 vessels
(code_tripnr) and 7 to 39 observations for each vessel, hence the random effect
for code_tripnr. The offset (offsetter) accounts for the haul duration and
sub sampling factor. There are no extreme outliers in lat/lon. The model we try
to fit is:
gamm3-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family=poisson,
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
We tried several things. We added some
noise to lon and lat, modelled the density instead of using a count with model
offset, and we normalized the explanatory variables. We also changed several
settings (see models below).
Interestingly, we do manage to fit a more
complex model:
gamm2-gamm(count~offset(offsetter)+
s(lat,lon,year,dayofyear), random=list(code_tripnr=~1),family=poisson,
correlation = corGaus(0.1, form=~lat + lon))
The models are fitted using mgcv 1.4-1 and
R 2.7.1 on a 64Bits Debian OS.
So there seems to be a convergence problem, correct? And does someone have an
idea what
might cause this? Secondly are there some tricks/solutions. E.g. perhaps we
could use the results from the more complex model (gamm2 above), but I do not
know exactly how. All help/advice would be greatly appreciated.
Kind regards, Geert
gamm3-gamm(count~offset(offsetter)+s(lon,lat),
random=list(code_tripnr=~1),family=poisson, correlation = corExp(1,
form=~X + Y),nite
rPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in recalc.corSpatial(object[[i]],
conLin) :
NA/NaN/Inf in foreign function call (arg 1)
gamm3-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(code_tripnr=~1),family=poisson,
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in lme.formula(fixed = fixed, random
= random, data = data, correlation = correlation, :
nlminb
problem, convergence error code = 1
message = false convergence (8)
In addition: Warning messages:
1: In if (k M + 1) { :
the
condition has length 1 and only the first element will be used
.Options$mgcv.vc.logrange=0.001 # we also
tried higher settings
gamm3-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family=poisson,
niterPQL=200, control=lmeControl(opt=optim))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in optim(c(coef(lmeSt)),
function(lmePars) -logLik(lmeSt, lmePars),
:
initial value in 'vmmin' is not finite
gamm3-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family=poisson,
niterPQL=200,control=lmeControl(minAbsParApV
ar=0.1))
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in recalc.corSpatial(object[[i]],
conLin) :
NA/NaN/Inf in foreign function call (arg 1)
gamm3-gamm(count~offset(offsetter)+s(lon,lat),random=list(code_tripnr=~1),family=poisson,
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in MEestimate(lmeSt, grps) :
NA/NaN/Inf in foreign function call (arg 1)
gamm3-gamm(count~offset(offsetter)+s(lon,lat,k=c(1,1)),random=list(code_tripnr=~1),family=poisson,
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in lme.formula(fixed = fixed, random
= random, data = data, correlation = correlation, :
nlminb problem, convergence
error code = 1
message = false convergence (8)
In addition: Warning messages:
1: In if (k M + 1) { :
the
condition has length 1 and only the first element will be used
2: In smooth.construct.tp.smooth.spec(object,
dk$data, dk$knots) :
basis dimension, k, increased to minimum possible
gamm3-gamm(count~offset(offsetter)+s(lon,lat,k=c(8,8)),random=list(code_tripnr=~1),family=poisson,
niterPQL=200)
Maximum number of PQL iterations: 200
iteration 1
iteration 2
Error in lme.formula(fixed = fixed, random
= random, data = data, correlation = correlation, :
nlminb problem, convergence
error code = 1
message = false convergence (8)
In addition: Warning messages:
1: In if (k M + 1) { :
the
condition has length 1 and only the first element will be used
2: In 1:UZ.len : numerical expression has 2
elements: only the first used
3: In if (p.rank ncol(XZ)) p.rank
- ncol(XZ) :
the
condition has length 1 and only the first element will be used
4: In 1:p.rank : numerical expression has 2
elements: only the first used
5: In if (p.rank k - j) Xf - XZU[,
(p.rank + 1):(k - j), drop = FALSE] else Xf - matrix(0, :
the
condition has length 1 and only the first element will be used
6: In (p.rank + 1):(k - j) :
numerical expression has 2 elements: only the first used
7: In 1:p.rank : numerical
Re: [R] Frequency and summary statistics table with different variables and categories
You should look at how summary.data.frame does it. (You are, of course, re-inventing the wheel.) You probably ought to also look at the doBy package with its summaryBy function. The help page example uses the length function for counts. I often prefer the output of describe() in Hmisc. -- David Winsemius On Jan 22, 2009, at 8:32 AM, David Winsemius wrote: One of the various tabulation functions would seem to be the most appropriate for getting frequency summaries: ?table ?xtabs On Jan 22, 2009, at 6:17 AM, Stefan Björk wrote: Hello helpers, This is probably quite simple, but I'm stuck. I want to create a summary statistics table with frequencies and summary statistics for a large number of variables. The problem here is that (1) there are two different classes of categories (sex, type of substance abuse and type of treatent) which overlap, (2) the data for different variables should be presented in different ways -- sometimes with relative frequencies, other times with mean values. The table would finally look something like: All Male Female Alcohol Drug ... Age (mean) (mean) ... Sex (% male)(freq) (freq) ... Alcohol CS (mean) (mean) ... ... ... Data is in a data frame with quite a lot of columns (variables) and each row represents a single case. I have found out that part of this can be done with tapply, for example tapply(age, sex, mean) and join it with tapply(age, abuse, mean). But how to do with frequencies? Or is there an even simpler way? /S [[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] Simple package question
With respect to scripts in the tests directory of a package: Can they depend on data sets found in the 'data' directory of said package? -available by default - need to use a data() call - need to explicitly attach? This isn't clear to me from reading the documentation in section 1.1.3 of the Writing R Extensions document. Terry Therneau __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help using zeroinfl()
On Thu, 22 Jan 2009, Simon Pickett wrote: Hi all, I have been trying to use zeroinfl() with the pscl package with R version 2.1.1. That version is ancient, please upgrade. and with the newest versions of the contrib packages compatible with R 2.1.1. A version number for pscl would have been most helpful. I'm pretty sure that this is a version of pscl prior to the re-design of the count regression functionality, i.e., a version of the package which does not have the vignette you refer to. Surprisingly, the vignette applies to the version of the package which actually contains the vignette. In any case, please use the most recent version of pscl. I have read the examples, the vignette and all the posts relating to zeroinfl() but I am still confused as to how to structure the model. Here is a small example; the error message is the same for big data sets library(mvtnorm,lib.loc=C:/Documents and Settings/simonp/My Documents/R backup library) Not needed here. library(pscl,lib.loc=C:/Documents and Settings/simonp/My Documents/R backup library) y-c(0,0.2,0.4,0.7,0,0,0,0.8,0,0,0,0,0) Non-integer counts are not allowed. (If these stem from division by some offset, please do not divide and use the offset instead.) hth, Z x-c(3,4,5,2,3,6,3,7,4,8,5,8,3) m1-zeroinfl(y~x|x) Zero-Inflated Count Model Using logit to model zero vs non-zero Using Poisson for counts Error in terms.formula(formula, data = data) : argument is not a valid model Can anyone shed any light please? Simon. Dr. Simon Pickett Research Ecologist Land Use Department Terrestrial Unit British Trust for Ornithology The Nunnery Thetford Norfolk IP242PU 01842750050 [[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] Package installation failed
Odette Gaston wrote: Hi folks, I am currently having the problem with using R 2.8.1 that I cannot install some of packages from CRAN or local drive and somebody may be able to help me. ex) faraway package and lme4 package. I have downloaded them in my hard drive as local, but still R was unable to find the package (message showed up as no such file). I could download most packages, but not all what I want. I showed my PC to R experts around and nobody had ideas. I've re-installed newest R and updated packages hundred times, but still same message came up. So, what is the error message when you try, e.g. install.packages(lme4) ? Uwe Ligges My working environment is: OS: XP Windows R2.8.1 Any suggestions would be appreciated. Thanks a lot, Odette [[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] ggplot2, pretty=FALSE
The following code used to work on an earlier version of ggplot2. But it gives me an error now. qplot(Year,CDR,data=b3,colour=Phase,geom=c(point,line))-p p+scale_colour_gradient2(limits=c(1,3), midpoint=2,low=magenta, mid=darkgreen, high=blue)-p (print(p,pretty=F)-p) print(p,pretty=F)-p The error is: Error in ggplotGrob(x, ...) : unused argument(s) (pretty = FALSE) In fact, I get the same error when I run the following code from Hadley's site. p - qplot(wt, mpg, data=mtcars, colour=cyl) grid.newpage() pushViewport(viewport(height=0.4, width=0.4, x=0.4, y=0.8)) print(p, newpage=FALSE, pretty=FALSE) Is there some other way of doing pretty=FALSE in the new version of ggplot2? Vikas Rawal [[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] Simple package question
Terry Therneau wrote: With respect to scripts in the tests directory of a package: Can they depend on data sets found in the 'data' directory of said package? -available by default - need to use a data() call - need to explicitly attach? Terry, you need to load the package and then it depends on your package's settings. If you need to load the data by data() when your package is installed, you will also need a call to data() in your test scripts. So for short, it behaves like your regularly installed package. Best, Uwe This isn't clear to me from reading the documentation in section 1.1.3 of the Writing R Extensions document. Terry Therneau __ 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] Confused about behavior of an S4 object containing a ts object
I posted the question below about a month ago but received no response. I still have not been able to figure out what is happening. I also noticed another oddity. When the data part of the object is a multivariate time series, it doesn't show up in the structure, but it can be treated as a multivariate time series. Is this a bug in str? setClass(tsExtended, representation = representation(description + = character), contains = ts) [1] tsExtended tmp - new(tsExtended, matrix(1:20, ncol=2), description = My Time Series) tsp(tmp) - c(1, 5.5, 2) tmp Object of class tsExtended Time Series: Start = c(1, 1) End = c(5, 2) Frequency = 2 Series 1 Series 2 1.01 11 1.52 12 2.03 13 2.54 14 3.05 15 3.56 16 4.07 17 4.58 18 5.09 19 5.5 10 20 Slot description: [1] My Time Series str(tmp) Formal class 'tsExtended' [package .GlobalEnv] with 4 slots ..@ .Data : int [1:20] 1 2 3 4 5 6 7 8 9 10 ... ..@ description: chr My Time Series ..@ tsp: num [1:3] 1 5.5 2 ..@ .S3Class : chr ts tmp[,1] Time Series: Start = c(1, 1) End = c(5, 2) Frequency = 2 [1] 1 2 3 4 5 6 7 8 9 10 plot(tmp[,2]) Mark Lyman -Original Message- From: Lyman, Mark Sent: Thursday, December 18, 2008 1:02 PM To: 'r-help@r-project.org' Subject: Confused about behavior of an S4 object containing a ts object I am trying to define an S4 class that contains a ts class object, a simple example is shown in the code below. However, when I try to create a new object of this class the tsp part is ignored, see below. Am I doing something wrong, or is this just a peril of mixing S3 and S4 objects? setClass(tsExtended, representation = representation(description = character), contains = ts) [1] tsExtended new(tsExtended, ts(1:10, frequency = 2), description = My Time Series) Object of class tsExtended Time Series: Start = 1 End = 10 Frequency = 1 [1] 1 2 3 4 5 6 7 8 9 10 Slot description: [1] My Time Series # This however seems to work tmp - new(tsExtended, 1:10, description = My Time Series) tsp(tmp) - c(1, 5.5, 2) tmp Object of class tsExtended Time Series: Start = c(1, 1) End = c(5, 2) Frequency = 2 [1] 1 2 3 4 5 6 7 8 9 10 Slot description: [1] My Time Series Mark Lyman, Statistician Engineering Systems Integration, ATK __ 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] blowup portion of graph beside it
Hi, I'd like to blow up portions of my graph and put it in boxes beside the graph.Is there an addon to do this? -- Rajesh.J [[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] quantile question
Hi, A simple quantile question: I need to calculate the 95% and 5% quantiles (aka percentiles) for the following data: 67.12 64.51 62.06 55.45 51.41 43.78 10.74 10.14 if I use the formula: 95% quantile point= 95 (8+1)/100, I get the 8.55th point as the 95% quantile. Which does not make too much sense as I have only 8 data points. The other option is to use (95*8)/100 = 7.6th data point (which can be found by interpolation between the 7th and 8th data points). Reportedly, the second formula is not too accurate. However in my case the first formula does not make much sense. Any advice? TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[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] robust regression
On Jan 22, 2009, at 11:06 AM, Georg Ehret wrote: Dear Miss R, I have a large dataset that is skewed and would like to calculate confidence intervals for my regression line. Unfortunately I have trouble finding commands for rubust regression and in particular for the confidence intervals... Can you possibly give a hint? Such difficulty is inexplicable. Search with Google for robust regression and add r-project to your search string for narrowing. (First hit is John Fox's 4 page addendum to CAR with worked examples. Many hundreds of hits but with high chance that the count is inflated. Further addition of confidence intervals still produces hundreds of results.) Search r-site-search for robust regression http://search.r-project.org/nmz.html (roughly 300 hits) See also the CRAN TAsk View on Robust Statistical Methods: http://cran.r-project.org/web/views/Robust.html (I have had very satisfactory results with Koenker's quantreg package functions, but you have provided insufficient description of a) the data, b) the domain of analysis, or c) your goals to allow any comment on the need or applicability of methods to your tasks.) -- David Winsemius Thank you and best regards, Gerog. [[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] ggplot2
I have been struggling to get the legends in ggplot2 right or do away with them altogether (on which I have already sent a post). In the following code, the labels argument in the scale_colour_gradient2 does not give me the desired labels in the legend. Could someone explain? qplot(Year,CDR,data=b3,colour=Phase,geom=c(point,line),legend.position=bottom)-p p+scale_colour_gradient2(limits=c(1,2), midpoint=1,low=magenta, mid=magenta, high=darkblue,breaks=c(1,2),labels=c(a,b)-p p Vikas [[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] blowup portion of graph beside it
Here is one way:
tmpmat - cbind( c(1,1), c(1,1), c(2,3) )
layout(tmpmat)
with(iris, plot(Sepal.Width, Sepal.Length,
col=c('red','green','blue')[Species]))
with(iris, plot(Sepal.Width, Sepal.Length, col=c('red','green','blue')[Species],
xlim=c(2.5,3), ylim=c(6,6.5)))
with(iris, plot(Sepal.Width, Sepal.Length, col=c('red','green','blue')[Species],
xlim=c(2.5,3.5), ylim=c(4.5,5.5)))
If that is not what you want, then give more detail so we can help better.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of rajesh j
Sent: Thursday, January 22, 2009 9:51 AM
To: r-help@r-project.org
Subject: [R] blowup portion of graph beside it
Hi,
I'd like to blow up portions of my graph and put it in boxes beside the
graph.Is there an addon to do this?
--
Rajesh.J
[[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] quantile question
Read the help page for the quantile function (the whole page, there is a lot of good detail in there), the 2nd reference on the page should also be a helpful read. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of ANJAN PURKAYASTHA Sent: Thursday, January 22, 2009 9:52 AM To: r-help@r-project.org Subject: [R] quantile question Hi, A simple quantile question: I need to calculate the 95% and 5% quantiles (aka percentiles) for the following data: 67.12 64.51 62.06 55.45 51.41 43.78 10.74 10.14 if I use the formula: 95% quantile point= 95 (8+1)/100, I get the 8.55th point as the 95% quantile. Which does not make too much sense as I have only 8 data points. The other option is to use (95*8)/100 = 7.6th data point (which can be found by interpolation between the 7th and 8th data points). Reportedly, the second formula is not too accurate. However in my case the first formula does not make much sense. Any advice? TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[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] quantile question
have a look at the online help file of ?quantile(); check also: x - c(67.12, 64.51, 62.06, 55.45, 51.41, 43.78, 10.74, 10.14) sapply(1:9, function (i) quantile(x, c(0.05, 0.95), type = i)) I hope it helps. Best, Dimitris ANJAN PURKAYASTHA wrote: Hi, A simple quantile question: I need to calculate the 95% and 5% quantiles (aka percentiles) for the following data: 67.12 64.51 62.06 55.45 51.41 43.78 10.74 10.14 if I use the formula: 95% quantile point= 95 (8+1)/100, I get the 8.55th point as the 95% quantile. Which does not make too much sense as I have only 8 data points. The other option is to use (95*8)/100 = 7.6th data point (which can be found by interpolation between the 7th and 8th data points). Reportedly, the second formula is not too accurate. However in my case the first formula does not make much sense. Any advice? TIA, Anjan -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] Loess fitting with bisquare
Hi, It seems there is no straightforward way to carry out in R the loess fitting with bisquare, as given by William Cleveland in his Visualizing Data. Am I right? Thanks in advance, Marcin -- Build up your weaknesses until they become your strong points -- Knute Rockne __ 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] write.fasta (seqinr package)
Hi I would like to use 'write.fasta(sequences, names, nbchar = 60, file.out, open = w)' to convert a DNA sequence in a text file to fasta format. How do I read the the text file to prepare the argument 'sequences' of the function. The DNA sequence in the text file is one line as below: ATCACACAACGACACTCACCCTGGACGCTCATC. Thank you [[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] quantile question
Thanks all for your prompt and helpful replies! Anjan On Thu, Jan 22, 2009 at 11:52 AM, ANJAN PURKAYASTHA anjan.purkayas...@gmail.com wrote: Hi, A simple quantile question: I need to calculate the 95% and 5% quantiles (aka percentiles) for the following data: 67.12 64.51 62.06 55.45 51.41 43.78 10.74 10.14 if I use the formula: 95% quantile point= 95 (8+1)/100, I get the 8.55th point as the 95% quantile. Which does not make too much sense as I have only 8 data points. The other option is to use (95*8)/100 = 7.6th data point (which can be found by interpolation between the 7th and 8th data points). Reportedly, the second formula is not too accurate. However in my case the first formula does not make much sense. Any advice? TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[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] maintaining variable types in data frames
Suppose X and Y are two data frames with the same structures, variable names and dimensions but with different data and different patterns of missing. I want to replace missing values in Y with corresponding values from X. I'll construct a simple two-by-two case: X - as.data.frame(matrix(c(a,b,1,2),2,2), stringsAsFactors=FALSE) X[,2] - as.integer(X[,2]) str(X) 'data.frame': 2 obs. of 2 variables: $ V1: chr a b $ V2: int 1 2 Y - as.data.frame(matrix(c(c,d,NA,4),2,2), stringsAsFactors=FALSE) Y[,2] - as.integer(Y[,2]) str(Y) 'data.frame': 2 obs. of 2 variables: $ V1: chr c d $ V2: int NA 4 This seems to be what I want to do... Y[is.na(Y)] - X[is.na(Y)] ...and it works except that the structure of Y is changed so that Y$V2 is now of type chr instead of type int: str(Y) 'data.frame': 2 obs. of 2 variables: $ V1: chr c d $ V2: chr 1 4 This behavior makes sense because the vector X[is.na(Y)] is of the character type: is.character(X[is.na(Y)]) [1] TRUE str(X[is.na(Y)]) chr 1 X[is.na(Y)] [1] 1 The last couple of results seem weird at first. The 1 was originally an integer but now it is a character. This *must* be because the typing is done at an earlier stage in the process, back when R decides which elements of X have to be checked against the logical matrix is.na(Y). It then decides the type for the vector and only afterward does it find that only one of the four elements of X will be selected, but it was prepared from that early stage for any of the four, even all four of them, to be selected. Suppose there were no NA elements in Y, what should we expect to see if we repeat what we did above? Y - as.data.frame(matrix(c(c,d,3,4),2,2), stringsAsFactors=FALSE) Y[,2] - as.integer(Y[,2]) str(Y) 'data.frame': 2 obs. of 2 variables: $ V1: chr c d $ V2: int 3 4 Even though there are no elements in X[is.na(Y)], the null element is of type chr: is.vector(X[is.na(Y)]) [1] TRUE is.character(X[is.na(Y)]) [1] TRUE str(X[is.na(Y)]) chr(0) X[is.na(Y)] character(0) So what happens if we do this... Y[is.na(Y)] - X[is.na(Y)] ...will it change the structure of Y so that Y$V2 becomes type chr? str(Y) 'data.frame': 2 obs. of 2 variables: $ V1: chr c d $ V2: int 3 4 No. I think there is an obvious reason for that: Y was not changed, and more specifically, Y$V2 was not changed, so no change was made to the variable types. It all makes sense, but I want an easy way to maintain the structure of a data frame when I do this kind of operation. I ought to be able to do something like this: Ytypes - get_types(Y) Y[is.na(Y)] - X[is.na(Y)] use_types(Y, Ytypes) That kind of system would ensure that the basic structure of the data frame can be maintained. I don't want to have to check by hand, and sometimes it would be impossible to do so. So what's the trick? Is there a trick? Mike __ 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] Loess fitting with bisquare
The loess function in R uses the tricube weights that are described in my copy of Cleveland, so that may do what you want. If you really want to do the same general idea but with a different weight function, then it is not that hard to write your own function to do the estimating (but I doubt that you will see much improvement over the standard loess function). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Marcin Kozak Sent: Thursday, January 22, 2009 10:08 AM To: r-help@r-project.org Subject: [R] Loess fitting with bisquare Hi, It seems there is no straightforward way to carry out in R the loess fitting with bisquare, as given by William Cleveland in his Visualizing Data. Am I right? Thanks in advance, Marcin -- Build up your weaknesses until they become your strong points -- Knute Rockne __ 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] Loess fitting with bisquare
Hi, doing a search in R gives help.search(loess) ?loess Look out for the family argument in the help page. Christian __ 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] title: words in different colors?
Here's my version of the technicolor title function:
multiTitle - function(...){
###
### multi-coloured title
###
### examples:
### multiTitle(color=red,Traffic,
### color=orange, light ,
### color=green,signal)
###
### - note triple backslashes needed for embedding quotes:
###
### multiTitle(color=orange,Hello ,
### color=red, \\\world\\\!)
###
### Barry Rowlingson b.rowling...@lancaster.ac.uk
###
l = list(...)
ic = names(l)=='color'
colors = unique(unlist(l[ic]))
for(i in colors){
color=par()$col.main
strings=c()
for(il in 1:length(l)){
p = l[[il]]
if(ic[il]){ # if this is a color:
if(p==i){ # if it's the current color
current=TRUE
}else{
current=FALSE
}
}else{ # it's some text
if(current){
# set as text
strings = c(strings,paste('',p,'',sep=))
}else{
# set as phantom
strings = c(strings,paste(phantom(\,p,\),sep=))
}
}
} # next item
## now plot this color
prod=paste(strings,collapse=*)
express = paste(expression(,prod,),sep=)
e=eval(parse(text=express))
title(e,col.main=i)
} # next color
return()
}
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Re: [R] dimnames in pkg ipred
Häring, Tim (LWF) wrote: Hello List, I`m trying to make prediction using a bagged tree with the package ipred. I tried to follow the manual but I`m getting an error message. Also browsing through the list-archive I didn`t find any hint. Maybe someone can help me? selbag - bagging(SOIL_UNIT ~., data=traindat.bin, coob=TRUE) Error in dimnames(X) - list(dn[[1L]], unlist(collabs, use.names = FALSE)) : length of 'dimnames' [2] not equal to array extent I´m using R 2.7.2 on Win XP and the latest version of ipred. Please do read the posting guide. - We do not have traindat.bin, hence cannot reproduce your problem - Does it happen with recent versions of R and ipred? Best, Uwe Ligges Thanks a lot. TIM --- Dipl.-Geogr. Tim Häring Sachgebiet Standort und Bodenschutz (SG 2.1) Bayerische Landesanstalt für Wald und Forstwirtschaft Am Hochanger 11 D-85354 Freising Tel.: +49-(0)8161/71-4769 E-Mail: tim.haer...@lwf.bayern.de http://www.lwf.bayern.de [[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] infer haplotypes phasing trios tdthap
Dear Tiago, I received this message from r-help. I should say I have limited experiences with tdthap so David should have the final say about it? Alternatively, you may wish to use independent programs as listed in the linkage server at Rockefeller? I would of course find out if I have miscopied David's original code! Many thanks, Jing Hua -Original Message- From: Tiago R Magalhães [mailto:tiag...@gmail.com] Sent: 22 January 2009 11:10 To: r-help@R-project.org Subject: infer haplotypes phasing trios tdthap Dear R mailing list, I have a dataset with genotypes from trios and I would like to infer haplotypes for each mother, father and child. The package that I could find that can do this is tdthap. But when the mother is homozygous (e.g., 2/2) the haplotype is called as not possible to infer (0); I would prefer for it to call the genotype (2). From what I understand it is doing what I would like for the father (example below). Can anyone provide me with some information about this tdthap behaviour? And is there any other package that would do this? (Searched for it, couldn't find it) Thank you very much, Tiago Magalhães example (ped file with pedigrees) 9 100 102 101 1 2 1 1 2 1 2 2 1 2 9 101 0 0 2 1 1 1 2 1 2 2 2 2 9 102 0 0 1 1 2 1 2 1 2 2 1 1 data out: hap.transmit(example) pedidfathermother 9 100102 101 f.tr.1f.tr.2f.tr.3f.tr.4 1 0 2 1 m.tr.1m.tr.2m.tr.3m.tr.4 00 0 0 __ 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] Converting ddf/dct/sas data definition file to R
Dear all, I was wondering whether anyone knows about a program which converts (part of) a data definition file (such as a .dct file for stata, or .sas file for sas) into an R-script. Here is an example with a .sas file: -- snipp VALUE HTYPE (default=32) 0 = Not in household 1 = Married couple family household 2 = Male householder family 3 = Female householder family 4 = Male householder nonfamily 5 = Female householder nonfamily 6 = Group quarters ; snapp -- This entry defines the variable HTYPE as a factor and assigns levels and labels. Ideally, it would be transformed into the following entry in R: data.frame$HTYPE - factor(data.frame$HTYPE, levels=c(0,1,2,3,4,5,6), labels=c(Not in household, Married couple family household, Male householder family, Female householder family, Male householder nonfamily, Female householder nonfamily, Group quarters ) ) Of course, this can be done by hand and isn't too bad with a good text editor. The reason why I am looking for a program is because I have a bunch of datasets (about 100) and there are about 200 variables defined per dataset. My goal is to provide R-scripts for these datasets such that the data files can be read in with R, making them accessible for R users. Thanks! Stephan -- --- Stephan Lindner University of Michigan __ 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] Unexpected behaviour of the as.Date (was: Error as.Date on Invalid Dates)
Dear Brian, I dont understand what you mean. The thread was about the as.Date which you suggested to be used instead of the as.date. Following your advice I tried the as.Date and have questions about the observed behaviour, which was surprising to me. Is this what you call hijacking? Do you mean I ought start a new thread instead? I thought my question were relevant to the threads' subject. I am sorry if it were not. So here is the questions once again: why do the as.Date behave as in my examples below, is this intended? On Thu, Jan 22, 2009 at 3:55 PM, Brian D Ripley rip...@stats.ox.ac.ukwrote: You've hijacked a thread here. On Thu, 22 Jan 2009, Marie Sivertsen wrote: I am relatively new to R, so maybe I am miss something, but I now tried the a s.Date now and have problems understanding how it works (or don't work as it seem). Brian D Ripley wrote: On Thu, 22 Jan 2009, Terry Therneau wrote: One idea is to use the as.date function, for the older (and less capable) 'date' class. This is currently loaded by default with library(survival). It re turns NA for an invalid date rather than dying. So does as.Date *if you specify the format* (as you have to with your as.da te: it has a default one): My examples: as.Date(2001/1/1) Works fine as.Date(1/1/2001) Prints 1-01-20 ??? as.Date(13/1/2001) Prints 13-01-20 ??? as.Date(1/13/2001) Prints error: not in standard unambigous format It seems that as if both 1/1/2001 and 13/1/2001 were considered by R to b e in a standard unambiguous format (or otherwise an error be reported?) and yet they are parsed incorrectly according to what one could think is obvious. It is a lso surprizing that not only 13/1/2001 but also 1/2/2001 and 2/1/2001 are successful but incorrect parsed as if they are unambiguous, and yet 13/1/2001 is ambiguous, though there is really just one way to parse it meaningfully. I think the strings that are incorrectly parsed should raise errors, and the last example should be succesful parsed. What is the reason for the observed ? Mvh. Marie -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/http://www.stats.ox.ac.uk/%7Eripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[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] Converting ddf/dct/sas data definition file to R
The sas.get function in the Hmisc package, or the sasxport.get function, will do what you want by a different approach. Frank Stephan Lindner wrote: Dear all, I was wondering whether anyone knows about a program which converts (part of) a data definition file (such as a .dct file for stata, or .sas file for sas) into an R-script. Here is an example with a .sas file: -- snipp VALUE HTYPE (default=32) 0 = Not in household 1 = Married couple family household 2 = Male householder family 3 = Female householder family 4 = Male householder nonfamily 5 = Female householder nonfamily 6 = Group quarters ; snapp -- This entry defines the variable HTYPE as a factor and assigns levels and labels. Ideally, it would be transformed into the following entry in R: data.frame$HTYPE - factor(data.frame$HTYPE, levels=c(0,1,2,3,4,5,6), labels=c(Not in household, Married couple family household, Male householder family, Female householder family, Male householder nonfamily, Female householder nonfamily, Group quarters ) ) Of course, this can be done by hand and isn't too bad with a good text editor. The reason why I am looking for a program is because I have a bunch of datasets (about 100) and there are about 200 variables defined per dataset. My goal is to provide R-scripts for these datasets such that the data files can be read in with R, making them accessible for R users. Thanks! Stephan -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] Loess fitting with bisquare
If you you use robust fitting (family = symmetric), there are (at least) two sets of weights used (and documented in the Help file): tricube weights are used to weight the points by their distances from the current point being estimated; bisquare weights are used in the robust fit to weight by scaled residual size. -- Bert Gunter Genentech -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Greg Snow Sent: Thursday, January 22, 2009 9:38 AM To: Marcin Kozak; r-help@r-project.org Subject: Re: [R] Loess fitting with bisquare The loess function in R uses the tricube weights that are described in my copy of Cleveland, so that may do what you want. If you really want to do the same general idea but with a different weight function, then it is not that hard to write your own function to do the estimating (but I doubt that you will see much improvement over the standard loess function). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Marcin Kozak Sent: Thursday, January 22, 2009 10:08 AM To: r-help@r-project.org Subject: [R] Loess fitting with bisquare Hi, It seems there is no straightforward way to carry out in R the loess fitting with bisquare, as given by William Cleveland in his Visualizing Data. Am I right? Thanks in advance, Marcin -- Build up your weaknesses until they become your strong points -- Knute Rockne __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting ddf/dct/sas data definition file to R
Hi Stephan, Does the foreign package help? HTH, (another) Stephan Stephan Lindner schrieb: Dear all, I was wondering whether anyone knows about a program which converts (part of) a data definition file (such as a .dct file for stata, or .sas file for sas) into an R-script. Here is an example with a .sas file: -- snipp VALUE HTYPE (default=32) 0 = Not in household 1 = Married couple family household 2 = Male householder family 3 = Female householder family 4 = Male householder nonfamily 5 = Female householder nonfamily 6 = Group quarters ; snapp -- This entry defines the variable HTYPE as a factor and assigns levels and labels. Ideally, it would be transformed into the following entry in R: data.frame$HTYPE - factor(data.frame$HTYPE, levels=c(0,1,2,3,4,5,6), labels=c(Not in household, Married couple family household, Male householder family, Female householder family, Male householder nonfamily, Female householder nonfamily, Group quarters ) ) Of course, this can be done by hand and isn't too bad with a good text editor. The reason why I am looking for a program is because I have a bunch of datasets (about 100) and there are about 200 variables defined per dataset. My goal is to provide R-scripts for these datasets such that the data files can be read in with R, making them accessible for R users. Thanks! Stephan __ 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] Unexpected behaviour of the as.Date (was: Error as.Date on Invalid Dates)
The first number is the year, the second is the month and the third is the day. It ignores trailing characters. library(chron) f - function(x) str(month.day.year(as.Date(x))) f(2001/1/1) List of 3 $ month: num 1 $ day : num 1 $ year : num 2001 f(1/1/2001) List of 3 $ month: num 1 $ day : num 20 $ year : num 1 # trailing 01 ignored. f(13/1/2001) List of 3 $ month: num 1 $ day : num 20 $ year : num 13 # no 13th month as.Date(1/13/2001) Error in fromchar(x) : character string is not in a standard unambiguous format On Thu, Jan 22, 2009 at 1:54 PM, Marie Sivertsen mariesiv...@gmail.com wrote: Dear Brian, I dont understand what you mean. The thread was about the as.Date which you suggested to be used instead of the as.date. Following your advice I tried the as.Date and have questions about the observed behaviour, which was surprising to me. Is this what you call hijacking? Do you mean I ought start a new thread instead? I thought my question were relevant to the threads' subject. I am sorry if it were not. So here is the questions once again: why do the as.Date behave as in my examples below, is this intended? On Thu, Jan 22, 2009 at 3:55 PM, Brian D Ripley rip...@stats.ox.ac.ukwrote: You've hijacked a thread here. On Thu, 22 Jan 2009, Marie Sivertsen wrote: I am relatively new to R, so maybe I am miss something, but I now tried the a s.Date now and have problems understanding how it works (or don't work as it seem). Brian D Ripley wrote: On Thu, 22 Jan 2009, Terry Therneau wrote: One idea is to use the as.date function, for the older (and less capable) 'date' class. This is currently loaded by default with library(survival). It re turns NA for an invalid date rather than dying. So does as.Date *if you specify the format* (as you have to with your as.da te: it has a default one): My examples: as.Date(2001/1/1) Works fine as.Date(1/1/2001) Prints 1-01-20 ??? as.Date(13/1/2001) Prints 13-01-20 ??? as.Date(1/13/2001) Prints error: not in standard unambigous format It seems that as if both 1/1/2001 and 13/1/2001 were considered by R to b e in a standard unambiguous format (or otherwise an error be reported?) and yet they are parsed incorrectly according to what one could think is obvious. It is a lso surprizing that not only 13/1/2001 but also 1/2/2001 and 2/1/2001 are successful but incorrect parsed as if they are unambiguous, and yet 13/1/2001 is ambiguous, though there is really just one way to parse it meaningfully. I think the strings that are incorrectly parsed should raise errors, and the last example should be succesful parsed. What is the reason for the observed ? Mvh. Marie -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/http://www.stats.ox.ac.uk/%7Eripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[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] Unexpected behaviour of the as.Date (was: Error as.Date on Invalid Dates)
I believe the original thread was about whether the function returns NA or stops with an error when given an invalid date (such as Feb 29 in a non-leap year). Your question was about how as.Date returned something different from what you expected. Related, but different enough that it probably would have been better to start a new thread. For your question, the help page for as.Date includes: format: A character string. The default is '%Y-%m-%d'. For details see 'strftime'. And Character strings are processed as far as necessary for the format specified: any trailing characters are ignored. I don't see anything in your examples that runs counter to the above. Remember that computers do exactly what you tell them to do, not what you think that they should do. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Marie Sivertsen Sent: Thursday, January 22, 2009 11:55 AM To: Brian D Ripley; r-h...@stat.math.ethz.ch Subject: [R] Unexpected behaviour of the as.Date (was: Error as.Date on Invalid Dates) Dear Brian, I dont understand what you mean. The thread was about the as.Date which you suggested to be used instead of the as.date. Following your advice I tried the as.Date and have questions about the observed behaviour, which was surprising to me. Is this what you call hijacking? Do you mean I ought start a new thread instead? I thought my question were relevant to the threads' subject. I am sorry if it were not. So here is the questions once again: why do the as.Date behave as in my examples below, is this intended? On Thu, Jan 22, 2009 at 3:55 PM, Brian D Ripley rip...@stats.ox.ac.ukwrote: You've hijacked a thread here. On Thu, 22 Jan 2009, Marie Sivertsen wrote: I am relatively new to R, so maybe I am miss something, but I now tried the a s.Date now and have problems understanding how it works (or don't work as it seem). Brian D Ripley wrote: On Thu, 22 Jan 2009, Terry Therneau wrote: One idea is to use the as.date function, for the older (and less capable) 'date' class. This is currently loaded by default with library(survival). It re turns NA for an invalid date rather than dying. So does as.Date *if you specify the format* (as you have to with your as.da te: it has a default one): My examples: as.Date(2001/1/1) Works fine as.Date(1/1/2001) Prints 1-01-20 ??? as.Date(13/1/2001) Prints 13-01-20 ??? as.Date(1/13/2001) Prints error: not in standard unambigous format It seems that as if both 1/1/2001 and 13/1/2001 were considered by R to b e in a standard unambiguous format (or otherwise an error be reported?) and yet they are parsed incorrectly according to what one could think is obvious. It is a lso surprizing that not only 13/1/2001 but also 1/2/2001 and 2/1/2001 are successful but incorrect parsed as if they are unambiguous, and yet 13/1/2001 is ambiguous, though there is really just one way to parse it meaningfully. I think the strings that are incorrectly parsed should raise errors, and the last example should be succesful parsed. What is the reason for the observed ? Mvh. Marie -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/http://www.stats.ox.ac.uk/%7Eripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[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] looping over a string
Hi list,
I'm using R 2.8.1 under Windows vista. I have the following problem:
First of all I create a string-vector. Then I convert these strings
into variables and assign a vector of numeric values. So far
everything's fine.
Now I want to do nearly the same again: I create another string-vector
and I want to assign the variance. So I have to loop over the first
string-vector.
But this does not work unfortunately. I looked in the R-list-search but
I cannot find the right answer.
Please find enclosed the pseudo-code:
#Tage zwischen berechnung und 31.03.2009
Berechnung-as.Date(22.01.2009,%d.%m.%Y)
Enddatum-as.Date(31.03.2009,%d.%m.%Y)
Tage-difftime(Enddatum, Berechnung)
Tage-as.numeric(substr(format(Tage),1,2))
#maximal interessierend sind 100 Tage (4 Monate)-Differenzen
max_int-82
Tage-max_int
max_bob-82
varnames-paste(st_rendite_,seq(max_int),sep=)
analyse-rnorm(1)
for(i in 1:min(max_bob,max_int)){
assign(varnames[i],diff(log(analyse),i)*100)
}
#Wurzel_t - Approximation überprüfen
varianzen-paste(var_,seq(Tage),sep=)
for(i in 1:Tage){
#in this line is the error I cannot handle (st_rendite_i):
assign(varianzen[i],var(st_rendite_i)/100^2)
}
Thanks for your help,
Thomas
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[R] (no subject)
ggplot2 should make legends automatically if the data is in the correct format. If you could send a reproducible example, that would help detect the error. Take the following two plots. The first one produces a broken line. In the second one, the variable Phase is numeric and therefore it does not break the line between two Phases. That is why I am trying to do it by assigning a number to the Phase and then use different labels in the legend. If I put the text of those labels in the variable Phase itself, as done in the first example, it gives me a broken line. # Plot 1 data.frame(Year=c(1:20),CDR=rnorm(20))-b3 c(rep(a,10),rep(b,10))-b3$Phase qplot(Year,CDR,data=b3,colour=Phase,geom=c(point,line),gpar(legend.position=bottom))-p p #Plot 2 data.frame(Year=c(1:20),CDR=rnorm(20))-b3 c(rep(1,10),rep(2,10))-b3$Phase qplot(Year,CDR,data=b3,colour=Phase,geom=c(point,line),gpar(legend.position=bottom))-p p+scale_colour_gradient2(limits=c(1,2), midpoint=1.5,low=magenta,high=darkblue,breaks=c(1,2),labels=c(a,b))-p p Also, legend.position does not work. I am sure I am not doing it the right way. I appreciate your help. Vikas [[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] how to get a primitive function object
Hi, I want to create an alias for the - function and then later overwrite it. Any idea how I can get the - function object? I know for other functions it's easy, something like f - seq will do; how really no clue for this one. Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get a primitive function object
Is there many functions: See: grep(-, ls(package:base), value = TRUE) For 'substring-': type `substring-` in R On Thu, Jan 22, 2009 at 5:41 PM, Yi Zhang yizhan...@gmail.com wrote: Hi, I want to create an alias for the - function and then later overwrite it. Any idea how I can get the - function object? I know for other functions it's easy, something like f - seq will do; how really no clue for this one. Thanks! __ 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.
Re: [R] how to get a primitive function object
On 1/22/2009 2:41 PM, Yi Zhang wrote: Hi, I want to create an alias for the - function and then later overwrite it. Any idea how I can get the - function object? I know for other functions it's easy, something like f - seq will do; how really no clue for this one. Thanks! get(-) will give it to you, and `-` - function(x, y) cat(x=, x, y=, y, \n) will change it -- and will probably be the last effective thing you do in that session, unless you're really careful: x - 1 x [1] 1 `-` - function(x, y) cat(x=, x, y=, y, \n) x - 3 x= 1 y= 3 x [1] 1 # now what?? %#* q(no) 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] looping over a string
I don't see right off why the one works and the other doesn't, but this looks
like one of those cases that would be better done using a list rather than
global variables.
Instead of assigning the variables in the global workspace, create a list and
assign them there. Then you can use lapply instead of a loop and you avoid the
potential pitfalls associated with globals.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Thomas Schwander
Sent: Thursday, January 22, 2009 12:38 PM
To: r-help@r-project.org
Subject: [R] looping over a string
Hi list,
I'm using R 2.8.1 under Windows vista. I have the following problem:
First of all I create a string-vector. Then I convert these strings
into variables and assign a vector of numeric values. So far
everything's fine.
Now I want to do nearly the same again: I create another string-vector
and I want to assign the variance. So I have to loop over the first
string-vector.
But this does not work unfortunately. I looked in the R-list-search but
I cannot find the right answer.
Please find enclosed the pseudo-code:
#Tage zwischen berechnung und 31.03.2009
Berechnung-as.Date(22.01.2009,%d.%m.%Y)
Enddatum-as.Date(31.03.2009,%d.%m.%Y)
Tage-difftime(Enddatum, Berechnung)
Tage-as.numeric(substr(format(Tage),1,2))
#maximal interessierend sind 100 Tage (4 Monate)-Differenzen
max_int-82
Tage-max_int
max_bob-82
varnames-paste(st_rendite_,seq(max_int),sep=)
analyse-rnorm(1)
for(i in 1:min(max_bob,max_int)){
assign(varnames[i],diff(log(analyse),i)*100)
}
#Wurzel_t - Approximation überprüfen
varianzen-paste(var_,seq(Tage),sep=)
for(i in 1:Tage){
#in this line is the error I cannot handle (st_rendite_i):
assign(varianzen[i],var(st_rendite_i)/100^2)
}
Thanks for your help,
Thomas
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Re: [R] Does anyone has this paper in pdf?
On 23/01/2009, at 12:49 AM, Neil Shephard wrote: aiminy wrote: de Jong, S. (1993) SIMPLS: an alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18, 251263 Yes, the publishers do, you can purchase it from http://dx.doi.org/10.1016/0169-7439(93)85002-X Its a shame that not all journals make their back-catalogue available free of charge, but I don't see why you expect people on this list to breach copyright for you? Is this really a violation of copyright? If I have a copy of a journal I believe it is within the compass of ``fair practice'' (or some such jargon) to make a photocopy of a particular article and give this copy to a colleague or student for research purposes. Likewise I believe it is ``fair practice'' for me to send a copy of a pdf file (that I have legitimately acquired) to a colleague or student for research purposes. It always gets fussy and fiddly whenever legal issues arise. It would be nice if there were no such thing as ``intellectual property'' (which has always seemed to me to be an oymoron) and no such thing as lawyers. cheers, Rolf ## Attention: This e-mail message is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This e-mail has been scanned and cleared by MailMarshal www.marshalsoftware.com ## __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unexpected behaviour of the as.Date (was: Error as.Date on Invalid Dates)
Thank you Greg and Gabor for explanations. I have some further question below. On Thu, Jan 22, 2009 at 8:16 PM, Greg Snow greg.s...@imail.org wrote: I believe the original thread was about whether the function returns NA or stops with an error when given an invalid date (such as Feb 29 in a non-leap year). Your question was about how as.Date returned something different from what you expected. Related, but different enough that it probably would have been better to start a new thread. I hope it was then okay I started a new thread. For your question, the help page for as.Date includes: format: A character string. The default is '%Y-%m-%d'. For details see 'strftime'. To be strict, neither 1/13/2001 nor 13/1/2001 match the format, so both should raise error, I think. Since the behaviour seem not to apply the default strictly, why ought one think 13/1/2001 will not be parsed the only reasonable way? And Character strings are processed as far as necessary for the format specified: any trailing characters are ignored. I don't see anything in your examples that runs counter to the above. Yes they do. None of them match the format, but some parse correctly, some produce rubbish, and some raise error. Maybe you want to improve the help page fo the as.Date to say something like The default is a sequence of numerical representations of the year, then the month, then the day, separated by one of '-', '/', ..., which make it clearer. Remember that computers do exactly what you tell them to do, not what you think that they should do. Computers do exactly what they were programmed to do, and what they will do depends on what the developer told them to do when they are given certain input. I expect them to do exactly what I tell them to do, and it is to parse 1/13/2001 the only reasonable way. It seems that someone told them to do something else... Mvh. Marie [[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] looping over a string
Greg Snow schrieb: I don't see right off why the one works and the other doesn't, but this looks like one of those cases that would be better done using a list rather than global variables. Instead of assigning the variables in the global workspace, create a list and assign them there. Then you can use lapply instead of a loop and you avoid the potential pitfalls associated with globals. Hope this helps, Greg, thanks for the answer. The difference is, that in the first case I assign a value to a string, but afterwards I want to read the value of the string. Trying to get it with lists. Cheers, Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get a primitive function object
On Thu, Jan 22, 2009 at 3:06 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
get(-) will give it to you, and
`-` - function(x, y) cat(x=, x, y=, y, \n)
will change it -- and will probably be the last effective thing you do in
that session, unless you're really careful:
x - 1
x
[1] 1
`-` - function(x, y) cat(x=, x, y=, y, \n)
x - 3
x= 1 y= 3
x
[1] 1
# now what?? %#*
q(no)
Duncan Murdoch
Thanks for the replies! Actually I have thought about this; what I
plan to do is:
oldAssign - `-`
oldAssign(`-`, function(x,value){if (...) do_something; oldAssign(x,value)})
x-1
x # object not found!!
So the problem now is the effect of oldAssign(x,value) is only
local--within that anonymous function. Is there a way to do
assignInNamespace (or how to get the namespace where the overridden -
is called)?
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[R] How to handle NA in C#, RDCOM
I am using RDCOM as a data-transfer between R and C#.net. I got a question on datasets with missing data. For instance, if list = c(1,2,3,NA,5), in R, typeof(list) is integer but, in C#, I did not see a suitable data type for (1,2,3,NA,5). Of course, one can use is.na to transfer (1,2,3,NA,5) into string[] in C#. So, how to handle NA in this case? Please help. Thank, -james __ 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] Does anyone has this paper in pdf?
Rolf Turner wrote: On 23/01/2009, at 12:49 AM, Neil Shephard wrote: s Is this really a violation of copyright? If I have a copy of a journal I believe it is within the compass of ``fair practice'' (or some such jargon) to make a photocopy of a particular article and give this copy to a colleague or student for research purposes. Likewise I believe it is ``fair practice'' for me to send a copy of a pdf file (that I have legitimately acquired) to a colleague or student for research purposes. one message that is pervasive on this list is 'what you believe is not necessarily what really is'. it seems to be applicable here, rolf. many scientific journals restrict your rights to distribute your own articles published with them, and you can buy printed copies for redistribution or rights to make pdfs available for a limited number of downloads, etc. see, e.g., [1]. it may be ``fair practice'' to distribute your papers without asking the publisher for permision, and it is quite common and indeed very useful, yet it may still be a violation of copyright. 'legitimately acquired' is underspecified, as in many circumstances you acquire a pdf of your article or book for your own use only, not for redistribution. otherwise, a 'legitimately acquired' article sent to another person is surely 'legitimately acquired' by that person, and thus, by induction, can be further distributed for 'legitimate acquisition', with no limitations in sight. that said, i support the view that scientific work should be redistributable without restrictions. on this occasion, i inform the person who once asked about anyone sharing a pdf copy of Prof Brian Ripley's book on spatial statistics that one of my colleagues happens to have such a pdf and will probably be happy to redistribute it. vQ (one of *the trolls*, i guess) [1] http://www.nature.com/reprints/author-reprints.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] User input in batch mode
Dear R-users, [Sorry to have to send this again but my former posts were trimmed because of some embedded HTML code] readline is a nice function to get user input when one is working with the terminal. This function does not allow any interaction with the user when a script in batch mode (I guess by design)... Unfortunately, that is exactly what I am trying to do. I would greatly appreciate if any R-user could: - tell me if this is possible - indicate a function I could look at, that would allow this type of interaction during a batch run. Thank you in advance, Version: R 2.8.1 installed on a Solaris system -- *Sebastien Bihorel, PharmD, PhD* PKPD Scientist Cognigen Corp Email: sebastien.biho...@cognigencorp.com mailto:sebastien.biho...@cognigencorp.com Phone: (716) 633-3463 ext. 323 __ 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] Apology for Multiple Posts
Dear R-Users I sincerely apologise for the multiple posts yesterday afternoon. Apparently there was an error in the server here at work which resulted in the message being sent eight times. I am new to R, as you can probably tell from the majority of my posts, and I really appreciate all the help I get from this forum. The last thing I want to do is offend anyone. Anyway, please accept my apology, I will ensure It doesn’t happen again. Kind Regards, James Dare -- View this message in context: http://www.nabble.com/Apology-for-Multiple-Posts-tp21612723p21612723.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get a primitive function object
Duncan Murdoch wrote: On 1/22/2009 2:41 PM, Yi Zhang wrote: Hi, I want to create an alias for the - function and then later overwrite it. Any idea how I can get the - function object? I know for other functions it's easy, something like f - seq will do; how really no clue for this one. Thanks! get(-) will give it to you, and `-` - function(x, y) cat(x=, x, y=, y, \n) will change it -- and will probably be the last effective thing you do in that session, unless you're really careful: x - 1 x [1] 1 `-` - function(x, y) cat(x=, x, y=, y, \n) x - 3 x= 1 y= 3 x [1] 1 # now what?? %#* now you are really motivated to use '=' instead of '-': x = 3 x # 3 vQ __ 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] Unexpected behaviour of the as.Date (was: Error as.Date on Invalid Dates)
Comments interspersed below From: Marie Sivertsen [mailto:mariesiv...@gmail.com] Sent: Thursday, January 22, 2009 1:17 PM To: Greg Snow Cc: r-h...@stat.math.ethz.ch Subject: Re: [R] Unexpected behaviour of the as.Date (was: Error as.Date on Invalid Dates) [snip] For your question, the help page for as.Date includes: format: A character string. The default is '%Y-%m-%d'. For details see 'strftime'. To be strict, neither 1/13/2001 nor 13/1/2001 match the format, so both should raise error, I think. Since the behaviour seem not to apply the default strictly, why ought one think 13/1/2001 will not be parsed the only reasonable way? The help page for as.Date refers to the help page for strptime which says that details are system specific. So there may be some systems where you would get an error from '/' not being '-', but apparently on your system they are treated the same. Personally I see a big difference between interpreting an obvious separator as such and changing the order of values. The fact that it sometimes gets the one correct does not imply to me that the other should happen automatically. Dealing with the separators can be done on an individual basis as each character string is processed. Guessing the order of the entries could require looking at the entire vector/file/dataset, which I expect would slow things down quite a bit. (and how long would it be before someone complained that it processed file A correctly, but file B should have been treated like A, but since it only included days less than 13, the program did not realize this). And Character strings are processed as far as necessary for the format specified: any trailing characters are ignored. I don't see anything in your examples that runs counter to the above. Yes they do. None of them match the format, but some parse correctly, some produce rubbish, and some raise error. Maybe you want to improve the help page fo the as.Date to say something like The default is a sequence of numerical representations of the year, then the month, then the day, separated by one of '-', '/', ..., which make it clearer. But is it correct? It may be system dependent (or all systems may do the exact same now). How about if the help page tells you to find out for your system (easy fix, it already does). Remember that computers do exactly what you tell them to do, not what you think that they should do. Computers do exactly what they were programmed to do, and what they will do depends on what the developer told them to do when they are given certain input. I expect them to do exactly what I tell them to do, and it is to parse 1/13/2001 the only reasonable way. It seems that someone told them to do something else... I was using the general 'you' above that includes the programmer as well as the user, since you (singular) did not specify the format, the computer used the default format that the programmer (part of the collective 'you') specified which says the order is year, month, day. Many problems come as a result of users forgetting that they are smarter than the computer. I see 3 ways to remedy the problem: 1. Make computers that are as smart or smarter than people. 2. Make the programmers anticipate every way that someone may use a particular function and make them implement all of the functionality even if they don't think it is worth the time/effort since there is an easy work around for many of the less likely used features. 3. Don't expect the computer to guess correctly and tell it exactly what you want it to do. I don't think that number 1 will ever happen, and there are plenty of science fiction stories that suggest problems with even trying. Option 2 stinks of hubris, and even if it were possible, I personally would not want to wait until they were finished before being able to use the functions/programs. Which leaves option 3, which I think is the best approach even without arguments against the others. I think the moral of this story is: program defensively, always specify a date format! Mvh. Marie -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problems with statistics
Hello, I have the following csv file n, n_red 1, 0 1, 1 2, 1 2, 1 3, 0 4, 1 4, 2 4, 3 I would like to plot this data. On the x-axis there should be n and on the y-axis the mean of all n_red where n is the according value on the x-axis. The plot should look like plotting the following data: n, n_red 1, 0.5 2, 1 3, 0 4, 2 Is there any simple way to do this? Greetings odif __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get a primitive function object
On Thu, Jan 22, 2009 at 4:17 PM, Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: Duncan Murdoch wrote: On 1/22/2009 2:41 PM, Yi Zhang wrote: Hi, I want to create an alias for the - function and then later overwrite it. Any idea how I can get the - function object? I know for other functions it's easy, something like f - seq will do; how really no clue for this one. Thanks! get(-) will give it to you, and `-` - function(x, y) cat(x=, x, y=, y, \n) will change it -- and will probably be the last effective thing you do in that session, unless you're really careful: x - 1 x [1] 1 `-` - function(x, y) cat(x=, x, y=, y, \n) x - 3 x= 1 y= 3 x [1] 1 # now what?? %#* now you are really motivated to use '=' instead of '-': x = 3 x # 3 vQ Thanks. That certainly is an option. But I want to preserve `-`'s functionality because I'm writing a package and I don't want to limit the package user's freedom to use `-`... -- Yi __ 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] looping over a string
Ah, I missed that. You can get the value from the string by using paste to create the name of the variable (as you already did), then use the 'get' function to get its value (the other direction of assign). But I would still suggest trying to use lists, then you can just use mylist[[ i ]] or mylist[[ names[i] ]] to grab the value or mylist[[ i ]] - something to assign. Or even better, newlist - lapply( oldlist, function ) and avoid the explicit loop altogether (then if you want to use the individual variables by name, just use with or within). Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r_lo...@web.de [mailto:r_lo...@web.de] Sent: Thursday, January 22, 2009 1:27 PM To: Greg Snow; r-help@R-project.org Subject: Re: [R] looping over a string Greg Snow schrieb: I don't see right off why the one works and the other doesn't, but this looks like one of those cases that would be better done using a list rather than global variables. Instead of assigning the variables in the global workspace, create a list and assign them there. Then you can use lapply instead of a loop and you avoid the potential pitfalls associated with globals. Hope this helps, Greg, thanks for the answer. The difference is, that in the first case I assign a value to a string, but afterwards I want to read the value of the string. Trying to get it with lists. Cheers, Thomas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with statistics
n.means = with(my.data,aggregate(n_red,list(n=n),mean)) plot(n.means) On Thu, Jan 22, 2009 at 5:17 PM, o...@gmx.de wrote: Hello, I have the following csv file n, n_red 1, 0 1, 1 2, 1 2, 1 3, 0 4, 1 4, 2 4, 3 I would like to plot this data. On the x-axis there should be n and on the y-axis the mean of all n_red where n is the according value on the x-axis. The plot should look like plotting the following data: n, n_red 1, 0.5 2, 1 3, 0 4, 2 Is there any simple way to do this? Greetings odif __ 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. -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University www.thatmike.com Looking to arrange a meeting? Check my public calendar: http://www.thatmike.com/mikes-public-calendar ~ Certainty is folly... I think. ~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get a primitive function object
Yi Zhang wrote:
# now what?? %#*
now you are really motivated to use '=' instead of '-':
x = 3
x
# 3
vQ
Thanks. That certainly is an option. But I want to preserve `-`'s
functionality because I'm writing a package and I don't want to limit
the package user's freedom to use `-`...
i was sort-of joking, though it's a real option if you want it.
but seriously, there's no reason for the %#* lamenting:
x - 1
'-' = function(x,y) 0
x - 2
# 0
.Primitive('-')(x,2)
x
# 2
base::'-'(x, 3)
x
# 3
base::'-'('-', base::'-')
x - 4
x
# 4
vQ
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[R] detecting the source of memory consumption (example provided)
I have read in a file (call it myData). The actual file is about
3000x30,000 columns and object.size() says myData takes:
737910472/(1024^2)
[1] 703.7263
Unfortunately, my program ends up using 40GB as indicated by maxvmem
on Unix, which causes my department's cluster to stop working.
Perhaps, I have some copying going on that I cannot find. I have
created an example below that mimics my program. Could someone help me
find my error? I am also confused about how to use Rprofmem to study
this problem. Thanks for your time.
Regards,
Juliet
#begin example
response - rnorm(50);
x1 - sample(c(1,2),50,replace=TRUE)
age - sample(seq(20,80),50,replace=TRUE)
id - rep(1:25,each=2)
var1 - rnorm(50);
var2 - rnorm(50);
var3 - rnorm(50);
myData - data.frame(response,x1,age,id,var1,var2,var3)
numVars - ncol(myData)-4;
pvalues - rep(-1,numVars);
names(pvalues) - colnames(myData)[5:ncol(myData)];
library(yags)
for (Var_num in 1:numVars)
{
fit.yags - yags(myData$response ~
myData$age+myData$x1*myData[,(Var_num+4)], id=myData$id,
family=gaussian,corstr=exchangeable,alphainit=0.05)
z.gee - fit.y...@coefficients[5]/sqrt(fit.y...@robust.parmvar[5,5]);
pval - 2 * pnorm(abs(z.gee), lower.tail = FALSE);
pvalues[Var_num] - signif(pval,3);
}
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Re: [R] how to get a primitive function object
i was sort-of joking, though it's a real option if you want it.
but seriously, there's no reason for the %#* lamenting:
x - 1
'-' = function(x,y) 0
x - 2
# 0
.Primitive('-')(x,2)
x
# 2
base::'-'(x, 3)
x
# 3
base::'-'('-', base::'-')
x - 4
x
# 4
vQ
I'm still not sure if this can help solve my problem. If I want to
overwrite the `-` operator for a particular type of objects, but
preserve its effect for other regular objects (in other words, if I do
x-5 with my new -, x will be 5 and nothing strange happens), then
what should I put in the [ ] below?
old - `-`
old(`-`, function(x, value){
if (value is my type) do something
[ ] # to bind the object value to symbol x: no matter what you do
here, the binding/assignment is local within this function?!
})
Hope I have made myself clear. Thanks,
--
Yi
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Re: [R] Problems with statistics
And to do the input section of the task, you should first read an introductory text and then refer to the help pages: ?read.table ?read.csv # same page And don't forget: http://www.R-project.org/posting-guide.html -- David Winsemius On Jan 22, 2009, at 4:33 PM, Mike Lawrence wrote: n.means = with(my.data,aggregate(n_red,list(n=n),mean)) plot(n.means) On Thu, Jan 22, 2009 at 5:17 PM, o...@gmx.de wrote: Hello, I have the following csv file n, n_red 1, 0 1, 1 2, 1 2, 1 3, 0 4, 1 4, 2 4, 3 I would like to plot this data. On the x-axis there should be n and on the y-axis the mean of all n_red where n is the according value on the x-axis. The plot should look like plotting the following data: n, n_red 1, 0.5 2, 1 3, 0 4, 2 Is there any simple way to do this? Greetings odif __ 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. -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University www.thatmike.com Looking to arrange a meeting? Check my public calendar: http://www.thatmike.com/mikes-public-calendar ~ Certainty is folly... I think. ~ __ 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.
