Re: [R] Difficulty Compiling RSQLite on Solaris x86 Using Studio 12 Compilers
This isn't really an appropriate forum, and the problem seems to be
related to how you built R (why is dmake being used?)
I've just tried RSQLite on our x86_64 Solaris 10 box (as far as I know
SunOS 5.11 is not yet released but a preview), and it worked out of the
box.
You need help from someone familiar with your OS installation: this is
neither an R nor a generic Solaris issue.
On Tue, 30 Oct 2007, Aric Gregson wrote:
Apologies if this is not the best list on which to ask for help. I have
compiled R 2.6.0 using Sun Studio 12 compilers. I can install most CRAN
and bioconductor packages that I need, with the exception of RSQLite.
Unfortunately this is critical for other packages that I need. I have
tried to compile it using R CMD INSTALL to generate a config.log file.
I don't know how to fix the reported error. I have tried commenting
out most of the test language in the configure file, but then there are
other complaints.
I used Studio 12 to build 2.5.1 and it worked perfectly. The only issue
with the 2.6.0 build is that 'make test' fails and this did not happen
with 2.5.1. However, it appears to run fine.
What is 'make test'? We recommend 'make check', and it should work on a
properly set up Solaris system.
Any ideas of how I can get RSQLite to compile? Or is there another list
to which I should address my question.
thanks,
aric
Here is an except from the config.log:
/usr/bin/uname -p = i386
/bin/uname -X = System = SunOS
Node = solenv
Release = 5.11
KernelID = snv_69
Machine = i86pc
## --- ##
## Core tests. ##
## --- ##
configure:1313: checking for gcc
configure:1339: result: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64
configure:1583: checking for C compiler version
configure:1586: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64 --version /dev/null 5
./configure: line 1587: dmake:: command not found
configure:1589: $? = 127
configure:1591: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64 -v /dev/null 5
./configure: line 1592: dmake:: command not found
configure:1594: $? = 127
configure:1596: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64 -V /dev/null 5
./configure: line 1597: dmake:: command not found
configure:1599: $? = 127
configure:1622: checking for C compiler default output file name
configure:1625: dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
/opt/studio12/SUNWspro/bin/cc -m64 dmake: defaulting to parallel mode.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
-xO5 -xc99 -xlibmieee -xlibmil -nofstore conftest.c 5
./configure: line 1626: dmake:: command not found
configure:1628: $? = 127
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME
| #define PACKAGE_TARNAME
| #define PACKAGE_VERSION
| #define PACKAGE_STRING
| #define PACKAGE_BUGREPORT
| /* end confdefs.h. */
|
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:1667: error: C compiler cannot create executables
See `config.log' for more details.
## - ##
## Output variables. ##
## - ##
-xO5 -xc99 -xlibmieee -xlibmil -nofstore'
/opt/studio12/SUNWspro/bin/cc -m64'
/opt/studio12/SUNWspro/bin/cc -m64'
CC='dmake: defaulting to parallel mode.
CFLAGS='dmake: defaulting to parallel mode.
CPP=''
CPPFLAGS=''
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EXEEXT=''
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
OBJEXT=''
PACKAGE_BUGREPORT=''
PACKAGE_NAME=''
PACKAGE_STRING=''
PACKAGE_TARNAME=''
PACKAGE_VERSION=''
PATH_SEPARATOR=':'
PKG_CPPFLAGS=''
PKG_LIBS=''
SHELL='/bin/bash'
See the man page dmake(1) for more information on setting up
the .dmakerc file.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
See the man page dmake(1) for more information on setting up
the .dmakerc file.
ac_ct_CC='dmake: defaulting to parallel mode.
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${prefix}/share'
exec_prefix='NONE'
host_alias=''
includedir='${prefix}/include'
infodir='${prefix}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
oldincludedir='/usr/include'
prefix='NONE'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## --- ##
## confdefs.h. ##
## --- ##
Re: [R] DBI Package
On Wed, 31 Oct 2007, Germán Carrillo wrote: Hello everyone! Congratulations by this gorgeous software. My name is Germán Carrillo, I'm writting from Colombia. I don't have much experience with R, reason why I use the R-GUI (version 2.5.1) on Windows. I have some problems with DBI package, I want to connect to PostgreSQL database but I don't know the way to do it. As far as I am aware DBI does not currently have a PostgreSQL driver. To connect to PostgreSQL you can use RODBC (easy) or RdbiPgSQL (and Rdbi) from Bioconductor, which uses a precursor to DBI. Unfortunately, I don't see a Windows binary for RdbiPgSQL on the Bioconductor site so you would need to compile it from sources (not easy). I was reading the DBI manual and I tried write in my R Console the next command: pg - dbDriver(PostgreSQL) But R says: Error en do.call(as.character(drvName), list(...)) : no se pudo encontrar la función PostgreSQL I don't know what's happen, I would like to receive some help about this topic, I was looking for in the internet but there's few documentation about this package. Thanks in advance. Best regards. Pdt: Sorry by my english, I'm learning... :) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: Fwd: data format
Hi [EMAIL PROTECTED] napsal dne 30.10.2007 21:49:37: Excuse me for less detailed e-mail I've sent before, I guess there's a misunderstanding here. And still is. You even did not show us how are your data stored in R. My problem is to use the data in the order I've typed below without splitting it. Is it possible? I really don't know. Some statistics packages do it. Original Data is; Good,Bad 10,12 15,15 18,10 12 But I have the data in the following form, Label,Value Good,10 Bad,12 Good,15 Good,18 Good,12 Bad,15 Bad,10 If you have data frame test like this you can do: selection-test$Label==Good ks.test(test[selection,2], test[!selection,2]) or test.s-split(test$Value, test$Label) ks.test(test.s[[1]], test.s[[2]]) If you prefer you can use selection or split inside *.test functions, however it seems to me that separated version is more readable. I also wander why you so much resist to split data into list? It is quite natural way how to handle them and R is pretty good in work with lists with its *apply functions. Regards Petr And I want to analyze the data without splitting it. I guessed whether there's a quick/simple solution to my problem. Array functions do solve this problem in general. Now I'm reading the help files about How to deal with arrays in R environment?. Thx a lot for your concern Emre -- Forwarded message -- From: Emre Unal [EMAIL PROTECTED] Date: Oct 30, 2007 4:39 PM Subject: data format To: r-help@r-project.org Hi, How can I analyze the data collected in database formatting (with labels) rather than splitted by individual columns (almost in excel)? For example (comma separated data); Label,Value Good,10 Bad,12 Good,15 Good,18 Good,12 Bad,15 Bad,10 etc... ks.test or chisq.test can be done. Splitting the data into new columns is not applicable cos' I'll use R-integration in another software. Thanks for your concern Emre -- --- Emre ÜNAL -- --- Emre ÜNAL http://www.geocities.com/dusemre http://dusemre.blogspot.com ICQ: 5712269 [[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] strwidth of bold font
Hi Henrique Dallazuanna wrote: Perhaps: strwidth(expression(bold(text))) Or set the default font face ... plot(1:10) text(4, 6, testing, adj=c(0, 0)) segments(4, 6, 4 + strwidth(testing), 6, col=red) par(font=2) text(4, 8, testing, adj=c(0, 0)) segments(4, 8, 4 + strwidth(testing), 8, col=red) Paul On 30/10/2007, Roland Kaiser [EMAIL PROTECTED] wrote: Hi! Is there a way to get the string width of the bold typefaces? like: strwidth(text, family = serif, font = 2). Thanks Roland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 in display function of the ARM package
Hi, I get the following error message when trying to use the display function on the ARM package: display(model) Error in .Internal(round(x, digits)) : no internal function round Looks like some kind of mismatch between the ARM package and some others? Can I somehow get around it? I have learned to like the display function to print model summaries. Here is my sessionInfo(): sessionInfo() R version 2.6.0 (2007-10-03) i486-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=en_US.UTF-8;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 other attached packages: [1] foreign_0.8-23car_1.2-5 arm_1.0-34 R2WinBUGS_2.1-6 [5] coda_0.12-1 lme4_0.99875-9Matrix_0.999375-3 lattice_0.17-2 [9] MASS_7.2-37 loaded via a namespace (and not attached): [1] grid_2.6.0 Thanks, Kari __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 in display function of the ARM package
On Wed, 31 Oct 2007, Kari Ruohonen wrote: Hi, I get the following error message when trying to use the display function on the ARM package: You seem to mean 'arm' not 'ARM'. display(model) Error in .Internal(round(x, digits)) : no internal function round Looks like some kind of mismatch between the ARM package and some others? You mayneed to reinstall your packages under R 2.6.0, in particular Matrix: see https://stat.ethz.ch/pipermail/r-help/2007-October/142367.html This is a symptom of not doing so. Without reproducible code we can't tell if there is anything else amiss. Can I somehow get around it? I have learned to like the display function to print model summaries. Here is my sessionInfo(): sessionInfo() R version 2.6.0 (2007-10-03) i486-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=en_US.UTF-8;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 other attached packages: [1] foreign_0.8-23car_1.2-5 arm_1.0-34 R2WinBUGS_2.1-6 [5] coda_0.12-1 lme4_0.99875-9Matrix_0.999375-3 lattice_0.17-2 [9] MASS_7.2-37 loaded via a namespace (and not attached): [1] grid_2.6.0 Thanks, Kari -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Biostatics position
Dear All, Please respond to my personal email in case of queries -- not on the list at the moment. Best Marwan The Faculty of Health Sciences of the American University of Beirut currently seeks for its Department of Epidemiology and Population Health a candidate with a Ph.D. degree in Biostatistics, or a related discipline with strong methodological background. Experience in health research is strongly valued. This position is available at the ranks of assistant, associate or full professor depending on qualifications. Visiting positions at all levels may be considered. The Faculty of Health Sciences (FHS) offers MPH and MS degrees and contributes public health courses to the MD program at the Faculty of Medicine. It also offers undergraduate degrees in Health Sciences. The language of instruction is English. For more information please visit http:// fhs.aub.edu.lb Interested candidates should submit a complete resume, statement of teaching and research interests and three letters of reference to: Huda Zurayk, Dean, Faculty of Health Sciences, American University of Beirut, 3 Dag Hammarskjold Plaza, 8th Floor, New York, NY 10017-2303. Fax in Beirut +961-1-744470. Electronic submissions may be sent to [EMAIL PROTECTED] Deadline for receipt of applications is December 31, 2007 for a starting date of September 15, 2008 The American University of Beirut is an Affirmative Action/Equal Opportunity Employer. -- Marwan Khawaja, Ph.D. Professor Director Center for Research on Population Health American University of Beirut P.O. Box 11-0236, Riad El Solh Beirut 1107 2020 Lebanon Email: [EMAIL PROTECTED] Url: http://staff.aub.edu.lb/~webcrph Tel: +961 1 35 00 00 ext. 4668 Fax: +961 1 74 44 70 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] NAIVE BAYES with 10-fold cross validation
thx for your help, i checked the caret package out and the tuning works. but i can't find a way to make a contingency table in order to see the classification result. e.g. like: table(outcome NaiveBayes, mydata$code) Is there something like that? Julia Original-Nachricht Datum: Tue, 30 Oct 2007 17:03:49 -0400 Von: Kuhn, Max [EMAIL PROTECTED] An: Julia Kröpfl [EMAIL PROTECTED], r-help@r-project.org Betreff: RE: [R] NAIVE BAYES with 10-fold cross validation am trying to implement the code of the e1071 package for naive bayes, but it doens't really work, any ideas?? am very glad about any help!! need a naive bayes with 10-fold cross validation: The caret package will do this. Use fit - train( x, y, method = nb, trControl = trainControl(method = cv, number = 10)) (there is no formula interface yet). It will use the naïve Bayes implementation in klaR. Unless you specify otherwise, it will train naïve Bayes models with and without using kernel density estimation (but you can change that). The object fit$finalModel will contain the model fit that is cv optimal. For example: fit - train( +iris[,-5], iris$Species, nb, +trControl = trainControl(method = cv, number = 10)) Iter 1 Values: TRUE Loading required package: MASS Loading required package: class Iter 2 Values: FALSE fit Call: train.default(x = iris[, -5], y = iris$Species, method = nb, trControl = trainControl(method = cv, number = 10)) 150 samples 4 predictors summary of cross-validation (10 fold) sample sizes: 135, 135, 135, 135, 135, 135, ... cv resampled training results across tuning parameters: usekernel Accuracy Kappa Accuracy SD Kappa SD Optimal FALSE 0.953 0.93 0.0706 0.106 TRUE 0.96 0.94 0.0562 0.0843* Accuracy was used to select the optimal model Max -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Julia Kröpfl Sent: Tuesday, October 30, 2007 4:46 PM To: r-help@r-project.org Subject: [R] NAIVE BAYES with 10-fold cross validation hi there!! i am trying to implement the code of the e1071 package for naive bayes, but it doens't really work, any ideas?? i am very glad about any help!! i need a naive bayes with 10-fold cross validation: code: library(e1071) model - naiveBayes(code ~ ., mydata) tune.control - tune.control(random = FALSE, nrepeat = 1, repeat.aggregate = min, sampling = c(cross), sampling.aggregate = mean, cross = 10, best.model = TRUE, performances = TRUE) pred - predict(model, mydata[,-12], type=class) tune(naiveBayes, code~., mydata, predict.fun=pred, tune.control) thx for your help! cheers, julia -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Pt! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] drawing direction fields
Jong-Hoon Kim wrote:
Dear useRs,
I am trying to draw direction fields for some differential equations.
So for I couldn't find much information on that. Could anybody give
me a hint how to draw a direction field using R?
Hi Jong-Hoon,
Here's a start on a function.
direction.field-function(dydx,xlim=c(-1,1),ylim=c(-1,1),
nxarrows=20,nyarrows=20,length=NA) {
xinc-diff(xlim)/(nxarrows*2)
yinc-diff(ylim)/(nyarrows*2)
if(is.na(length)) length-par(pin)[1]/100
plot(0,xlim=xlim,ylim=ylim,type=n)
for(x in seq(xlim[1]+xinc,xlim[2]-xinc,length=nxarrows)) {
for(y in seq(ylim[1]+yinc,ylim[2]-yinc,length=nyarrows)) {
stan-atan(eval(parse(text=dydx)))
arrows(x-xinc*cos(stan),y-yinc*sin(stan),
x+xinc*cos(stan),y+yinc*sin(stan),
length=length)
}
}
}
direction.field(0*x+1*y)
Jim
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] strwidth of bold font
Hi Henrique Dallazuanna wrote: Perhaps: strwidth(expression(bold(text))) Or set the default font face ... Thanks! Things can often be so easy! Roland plot(1:10) text(4, 6, testing, adj=c(0, 0)) segments(4, 6, 4 + strwidth(testing), 6, col=red) par(font=2) text(4, 8, testing, adj=c(0, 0)) segments(4, 8, 4 + strwidth(testing), 8, col=red) Paul On 30/10/2007, Roland Kaiser [EMAIL PROTECTED] wrote: Hi! Is there a way to get the string width of the bold typefaces? like: strwidth(text, family = serif, font = 2). Thanks Roland __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] reversing the scale on ggplot
Dear All, I am trying to build a simple ggplot, but where the scale is reversed, i.e. the largest numbers are on the bottom. An example of the code I am using is plotdata-data.frame(x=1:10, y=runif(10)) plot-ggplot() plot-plot+layer(data=plotdata, mapping=aes_string(x='x',y='y'), geom='point', stat='identity', size=4) plot-plot+ scale_y_continuous(limits=c(1,0)) print(plot) I was hoping that by reversing the limits argument I would obtain the result I wanted, but to no avail. I have searched the ggplot help and the archives, but cannot find the answer to this issue. I would really appreciate if anyone could give me a pointer. I am using R2.6.0 (patched) on Windows Thanks, Pedro __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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() device uses fonts to represent points - data alteration?
Hi jiho wrote: Hello all, I discovered that the pdf device uses fonts to represent points symbols (as in plot(...,type=p,...) ). Namely it uses ZapfDingbats with symbol U+25cf. This can lead to problems when the font is not available, or available in another version (such as points being replaced by other symbols, or worst: slightly displaced). Furthermore, it also causes problems when opening the pdf files for editing in other programs. I know that for reproducibility one should avoid doing this but there are cases where R is simply not suited to produce the end result graphic directly using code (Ex: replace some colors by CMYK versions for color consistency in print). In addition, publishers also often like being able to retouch graphics to ensure fonts consistency or such, and this will be destructive in the case of these pdfs. For example, Inkscape interprets points as squares (more like U+2751 in ZapfDingbats) and Adobe Illustrator does not even recognize the font (substituting AdobePiStd). I tried to embed fonts with embedFonts() but his does not solves the issue with editing (Inkscape produces a kind of star and AI still chokes on the font) and worst, it modifies how the original graphic renders in pdf viewers: the circles are now filled (I believe this is because this is the default state of the ZapfDingbats character). So my questions are: - does anyone have a work around this? - why can't the pdf device use shapes instead of fonts to represent data point? It would appear as a much more robust approach and would ensure that the points are rendered the same everywhere. Font substitution in axes labels is not as bad since it does not modify the data itself (at worst the labels are offset a little bit) but font substitution on the data points can really harm the graphic. If I recall correctly, the PDF device uses a character for small circles because that looks better. There is no PDF circle primitive, so circles have to be drawn using bezier curves. The original author may be able to elaborate on that. Two suggestions for workarounds: (i) produce PostScript and then convert to PDF using something like ghostscript (e.g., ps2pdf) (ii) use an almost-but-not-quite opaque colour, e.g., rgb(0, 0, 0, .99) for the points. If the points are not fully opaque, the character is not used. Paul Examples of code: pdf(test.pdf) plot(0,0,xlab=,ylab=,bty=n,xaxt=n,yaxt=n); grid(lty=1); dev.off() embedFonts(test.pdf,pdfwrite,test_embed.pdf) visualize the fonts: pdffonts test.pdf and a package with the two pdf files and bitmaps of how they render or are interpreted in various programs: http://jo.irisson.free.fr/dropbox/test_R_pdf_fonts.zip Thank you in advance for your attention and help. JiHO --- http://jo.irisson.free.fr/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 in display function of the ARM package
Thank you very much for the answer. Re-installation (I did a full reinstall of R and packages I use) helped and cured the problem. I had somehow missed the advice to re-install packages when upgrading to 2.6.0 and had only used update.packages(). regards, Kari On Wed, 2007-10-31 at 09:30 +, Prof Brian Ripley wrote: On Wed, 31 Oct 2007, Kari Ruohonen wrote: Hi, I get the following error message when trying to use the display function on the ARM package: You seem to mean 'arm' not 'ARM'. display(model) Error in .Internal(round(x, digits)) : no internal function round Looks like some kind of mismatch between the ARM package and some others? You mayneed to reinstall your packages under R 2.6.0, in particular Matrix: see https://stat.ethz.ch/pipermail/r-help/2007-October/142367.html This is a symptom of not doing so. Without reproducible code we can't tell if there is anything else amiss. Can I somehow get around it? I have learned to like the display function to print model summaries. Here is my sessionInfo(): sessionInfo() R version 2.6.0 (2007-10-03) i486-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=en_US.UTF-8;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 other attached packages: [1] foreign_0.8-23car_1.2-5 arm_1.0-34 R2WinBUGS_2.1-6 [5] coda_0.12-1 lme4_0.99875-9Matrix_0.999375-3 lattice_0.17-2 [9] MASS_7.2-37 loaded via a namespace (and not attached): [1] grid_2.6.0 Thanks, Kari __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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() device uses fonts to represent points - data alteration?
Thank you very much for your answer, even so long after I first posted the message. On 2007-October-31 , at 12:00 , Paul Murrell wrote: Hi jiho wrote: Hello all, I discovered that the pdf device uses fonts to represent points symbols (as in plot(...,type=p,...) ). Namely it uses ZapfDingbats with symbol U+25cf. This can lead to problems when the font is not available, or available in another version (such as points being replaced by other symbols, or worst: slightly displaced). Furthermore, it also causes problems when opening the pdf files for editing in other programs. I know that for reproducibility one should avoid doing this but there are cases where R is simply not suited to produce the end result graphic directly using code (Ex: replace some colors by CMYK versions for color consistency in print). In addition, publishers also often like being able to retouch graphics to ensure fonts consistency or such, and this will be destructive in the case of these pdfs. For example, Inkscape interprets points as squares (more like U +2751 in ZapfDingbats) and Adobe Illustrator does not even recognize the font (substituting AdobePiStd). I tried to embed fonts with embedFonts() but his does not solves the issue with editing (Inkscape produces a kind of star and AI still chokes on the font) and worst, it modifies how the original graphic renders in pdf viewers: the circles are now filled (I believe this is because this is the default state of the ZapfDingbats character). So my questions are: - does anyone have a work around this? - why can't the pdf device use shapes instead of fonts to represent data point? It would appear as a much more robust approach and would ensure that the points are rendered the same everywhere. Font substitution in axes labels is not as bad since it does not modify the data itself (at worst the labels are offset a little bit) but font substitution on the data points can really harm the graphic. If I recall correctly, the PDF device uses a character for small circles because that looks better. There is no PDF circle primitive, so circles have to be drawn using bezier curves. The original author may be able to elaborate on that. OK. I was suspecting that PDF did not have circle primitives indeed. That's a good reason. Two suggestions for workarounds: (i) produce PostScript and then convert to PDF using something like ghostscript (e.g., ps2pdf) (ii) use an almost-but-not-quite opaque colour, e.g., rgb(0, 0, 0, .99) for the points. If the points are not fully opaque, the character is not used. (ii) is really good to know (and I would probably never have found it myself). (i) is not applicable since I use PDF to keep transparency. Thanks for your help. I still think that not using fonts at all should be preferred because really strange things can happen with fonts while bezier curves are robust and do not depend at all on the rest of the OS. In this precise matter, robustness is probably to be preferred over appearance, since it involves the data directly. Anyway, I'm fine now with your workaround. I should file a bug report for this to be solved in a future release maybe. JiHO --- http://jo.irisson.free.fr/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Performance of concatenating strings
Hi, I would like to ask how the paste(S1, S2, sep=) function internally works. Are the two stings copied to a new String? I have a program where successively strings are build up. First the program calls an external function and depending on the result it builds up strings to visualize the result. The external function is really fast, also for huge input data. But the building of the strings takes much to long for huge input sizes. So I'm wondering if the concatenating could be the problem, like using String in Java instead of StringBuffer. Is there something like StringBuffers in R also? Thanks, T. Steijger __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] cbind()
Hi
Perhaps:
Hi,
Try this:
do.call(rbind, lapply(a, function(x)do.call(cbind, x)))
On 31/10/2007, livia [EMAIL PROTECTED] wrote:
Hello,
I would like to use the cbind() function to construct a matrix used in the
middle of a function as following
for (i in 1:1000) {
b[i] - function(cbind(a[[1]][[i]],
a[[2]][[i]],a[[3]][[i]],...a[[67]][[i]]))
}
Is there an easy way of achieving this rather than cbind every column?
--
View this message in context:
http://www.nabble.com/cbind%28%29-tf4724534.html#a13507633
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.
--
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] cbind()
On 10/31/2007 8:06 AM, livia wrote:
Hello,
I would like to use the cbind() function to construct a matrix used in the
middle of a function as following
for (i in 1:1000) {
b[i] - function(cbind(a[[1]][[i]],
a[[2]][[i]],a[[3]][[i]],...a[[67]][[i]]))
}
Is there an easy way of achieving this rather than cbind every column?
What you're doing is a little complicated (taking the i'th element out
of elements 1:67 in a list), so the solution is bound to be a little
complicated too. But something like this will save you typing:
# construct a list of the i'th elements
ithelements - lapply(a[1:67], function(e) e[[i]])
# pass them as args to cbind
do.call(cbind, ithelements)
I haven't tested this (not having your data at hand), but if it doesn't
work, something like it should.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] drawing direction fields
Dear useRs, I am trying to draw direction fields for some differential equations. So for I couldn't find much information on that. Could anybody give me a hint how to draw a direction field using R? -- 734 274 2394 Jong-Hoon Kim [[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] ylim in barplot2 function?
Hi list,
I'm using barplot2 form the gplots package to plot a few numbers (I want to add
SD bars later).
However, I would like the y-axis not to start from 0 but 500. When I add the
parameters YLIM, something goes wrong. The graph is not 'cut off' at 500.
Instead the bars seems to sink trough the bottom of the graph.
Because its a little hard to explain, here is a self-containing example:
library(gplots)
ABrt-c(588,589,593,588)
Wrt-c(580,583,592,612)
RT-rbind(ABrt,Wrt)
barplot2(RT,beside=T,col=c('black','white'),ylim=c(500,1000))
Does anybody know of a solution?
Regards,
Dieter
--
Dieter Vanderelst
dieter _ vanderelst AT emailengine DOT org
d DOT vanderelst AT tue DOT nl
Eindhoven University of Technology
Faculty of Industrial Design
Designed Intelligence Group
Den Dolech 2
5612 AZ Eindhoven
The Netherlands
Tel +31 40 247 91 11
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] timezone conversion difficulties with the new US daylight saving time switch over
Mike Waters wrote: Tony Plate wrote: [...] You don't say if this an R-specific problem, or if it afflicts your computer system clock as well. Thanks, I should have noted that my computer system clock is fine, and as far as I can tell it (correctly) believes we are still in Daylight Saving mode. It did not incorrectly fall back last Sunday at the date that would have been the end of Daylight Saving under the old rules. In case it matters, I do have a program running on my computer that synchronizes time: Domain Time II version 3.1.b.20040724R -- Tony Plate __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] NAIVE BAYES with 10-fold cross validation
Julia, i checked the caret package out and the tuning works. but i can't find a way to make a contingency table in order to see the classification result. You should read the vignettes for the package at: http://cran.r-project.org/src/contrib/Descriptions/caret.html these have the details for caret. There are many other methods. Typing help.search(confusion) yields four different implementations on my system. Looking at your email, you need to read something about basic predict methods. Please read ?predict.NaiveBayes Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ylim in barplot2 function?
I'm not sure exactly why it won't work but it could be
that conceptually a bar plot starting at 500 does not
make a lot of sense and the package writers did not
entertain such an idea?
I'd suggest having a look at ?dotchart as an
alternative why to plot the data or perhaps have a
look at errplot() in Hmisc.
If you really need a barplot you might have a look at
gap.barplot in plotrix.
--- Dieter Vanderelst
[EMAIL PROTECTED] wrote:
Hi list,
I'm using barplot2 form the gplots package to plot a
few numbers (I want to add SD bars later).
However, I would like the y-axis not to start from 0
but 500. When I add the parameters YLIM, something
goes wrong. The graph is not 'cut off' at 500.
Instead the bars seems to sink trough the bottom of
the graph.
Because its a little hard to explain, here is a
self-containing example:
library(gplots)
ABrt-c(588,589,593,588)
Wrt-c(580,583,592,612)
RT-rbind(ABrt,Wrt)
barplot2(RT,beside=T,col=c('black','white'),ylim=c(500,1000))
Does anybody know of a solution?
Regards,
Dieter
--
Dieter Vanderelst
dieter _ vanderelst AT emailengine DOT org
d DOT vanderelst AT tue DOT nl
Eindhoven University of Technology
Faculty of Industrial Design
Designed Intelligence Group
Den Dolech 2
5612 AZ Eindhoven
The Netherlands
Tel +31 40 247 91 11
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Splitting up the micEcon package?
Dear Arne and Ott-Siim,
my personal opinion is that one single package is easiest both for the
useR who wants to keep track of the add-ins he might need and for the
maintainer(s) of the relevant Task Views. I'd prefer to have one single
micEcon as long as I know that I've to look there both for micro demand
models and for sample selection. Moreover, I feel they fit together
nicely from a broad econometric viewpoint (if this means anything).
Of course, if splitting the package up means easing the maintenance
burden in any way, we'll just keep track of one more package... :^)
Best regards and many thanks for your effort
Giovanni
Giovanni Millo
Research Dept.,
Assicurazioni Generali SpA
Via Machiavelli 4,
34131 Trieste (Italy)
tel. +39 040 671184
fax +39 040 671160
#
Original message:
Message: 34
Date: Tue, 30 Oct 2007 18:44:12 +0200
From: Arne Henningsen [EMAIL PROTECTED]
Subject: [R] Splitting up the micEcon package?
To: r-help@r-project.org
Cc: Ott-Siim Toomet [EMAIL PROTECTED]
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=us-ascii
Dear R Users:
The functions of our micEcon package [1,2] can be subdivided into
three
categories:
- microeconomic demand and firm models
- sample selection models (mainly selection())
- routines for (likelihood) maximisation (e.g. maxLik(), maxNR(),
maxBHHH())
(mainly used for ML estimation of sample selection models)
Although sample selection models are often used in microeconomic
analyses,
they are also used in several other disciplines. Therefore, we are
unsure
whether it is better to keep these different functionalities in the
micEcon
package or to move the sample selection models and the routines for
(likelihood) maximisation into one or two new package(s) (increasing the
long
list of R packages even further).
What is the recommendation of the R community?
Thank you,
Ott Arne
Note: We have asked this question already on R-devel five days ago [3],
but we did not receive an answer yet.
References:
[1] http://cran.r-project.org/src/contrib/Descriptions/micEcon.html
[2] http://www.micecon.org/
[3] http://tolstoy.newcastle.edu.au/R/e3/devel/07/10/0222.html
--
Arne Henningsen
Department of Agricultural Economics
University of Kiel
Olshausenstr. 40
D-24098 Kiel (Germany)
Tel: +49-431-880 4445
Fax: +49-431-880 1397
[EMAIL PROTECTED]
http://www.uni-kiel.de/agrarpol/ahenningsen/
Ai sensi del D.Lgs. 196/2003 si precisa che le informazi...{{dropped:13}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] forecasting multiple regression model
Hi all, Does anyone have the knowledge to help me identify a package capable of forecasting a MULTIPLE regression model? i have a model with one one dependant variable and 4 independant variables. i would like to forecast confidence intervals for a few steps ahead...(DENSITY forecasting). PS i can forecast a univariate vector, with package 'forecast', however, i want one that can do forecasting on multivariate matrices. Thanks and kind regards, to all!:-) -- View this message in context: http://www.nabble.com/forecasting-multiple-regression-model-tf4725064.html#a13509244 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] DBI Package
I have some problems with DBI package, I want to connect to PostgreSQL database but I don't know the way to do it. pg - dbDriver(PostgreSQL) ... nope. That won't work. you need the RdbiPgSQL package from Bioconductor. Along with DBI, as I recall. --elijah__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ylim in barplot2 function?
On Wed, 2007-10-31 at 11:52 +0100, Dieter Vanderelst wrote:
Hi list,
I'm using barplot2 form the gplots package to plot a few numbers (I
want to add SD bars later).
However, I would like the y-axis not to start from 0 but 500. When I
add the parameters YLIM, something goes wrong. The graph is not 'cut
off' at 500. Instead the bars seems to sink trough the bottom of the
graph.
Because its a little hard to explain, here is a self-containing
example:
library(gplots)
ABrt-c(588,589,593,588)
Wrt-c(580,583,592,612)
RT-rbind(ABrt,Wrt)
barplot2(RT,beside=T,col=c('black','white'),ylim=c(500,1000))
Does anybody know of a solution?
Regards,
Dieter
The behavior here is the same for both barplot() and barplot2(). You
need to set par(xpd) to FALSE, so that the bars are clipped to the
plot region:
barplot2(RT,beside=T,col=c('black','white'),ylim=c(500,1000),
xpd = FALSE)
See ?par
That being said, this is a bad idea in general, as you impact the
ability to visually discern the relative difference (or lack of it) in
the bars. You would be better off using a dotplot.
HTH,
Marc Schwartz
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reading a file with read.csv: two character rows not interpreted as I hope
OK, I fixed it myself! Here's the code. Of course, it mostly seems simple
once one gets it working... Thanks Jim. Bryan
sample.info = read.table(input.file.name, sep=,, as.is=TRUE, nrows=3) #
get the first three lines with sample info in character format
sample.names = sample.info[1,]
sample.colors = sample.info[2,]; sample.colors =
as.character(sample.colors[-1])
sample.class = sample.info[3,]; sample.class =
as.character(sample.class[-1])
data = read.table(input.file.name, sep=,, skip=3)
colnames(data) = sample.names
On 10/30/07 10:53 PM, Bryan Hanson [EMAIL PROTECTED] wrote:
Jim, thanks for the suggestion. There is still something subtle
non-intuitive going on here. I adapted your code with minor changes
as
follows (I had to add the sep argument) but get different
behavior:
c.names - scan(file.csv, what='', nlines=1, sep=,) # read
column names
c.options - read.table(file.csv, as.is=TRUE, nrows=2, sep=,)
# get
lines 2-3
c.data - read.table(file.csv, sep=,) # rest of the
data
colnames(file.csv) - c.names
Your code works perfectly (you knew
that!). My adaptation runs, but
c.options contains the first two lines, not
lines 2 3, and c.data contains
the contents of the entire file as *factors*
(data type of c.names
c.options is correct - character). How strange!
Also,
and this is an observation rather than a question: in your code, you
call scan
and get the first line as characters, then you do read.table which
gets lines
2 3 presumably because the first line, from read.table's
perspective is a
hidden label (?), then the second time you use read.table
the hidden first
line is ignored, as are the two lines with character data.
I really don't
understand these behaviors, which is probably why I'm having
trouble parsing
the file!
Thanks, Bryan
On 10/30/07 8:40 PM, jim holtman
[EMAIL PROTECTED] wrote:
Here is one way. You will probably use 'file'
instead of textConnection
x.in - textConnection('wavelength SampleA
SampleB SampleC SampleD
+ color green black black green
+ class
Class 1 Class 2 Class 2 Class 1
+ 403 1.94E-01 2.14E-01 2.11E-01
1.83E-01
+ 409 1.92E-01 1.89E-01 2.00E-01 1.82E-01
+ 415 1.70E-01
1.99E-01 1.94E-01 1.86E-01
+ 420 1.59E-01 1.91E-01 2.16E-01 1.74E-01
+
426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
+ 432 1.42E-01 1.50E-01 1.62E-01
1.48E-01')
c.names - scan(x.in, what='', nlines=1) # read column
names
Read 5 items
c.options - read.table(x.in, as.is=TRUE, nrows=2) #
get lines 2-3
c.data - read.table(x.in) # rest of the data
colnames(c.data) - c.names
close(x.in)
c.options # here are lines
2-3
V1 V2 V3 V4 V5
1 color green black
black green
2 class Class 1 Class 2 Class 2 Class 1
c.data # your
data
wavelength SampleA SampleB SampleC SampleD
1403 0.194
0.214 0.211 0.183
2409 0.192 0.189 0.200 0.182
3
415 0.170 0.199 0.194 0.186
4420 0.159 0.191 0.216
0.174
5426 0.150 0.166 0.172 0.158
6432 0.142
0.150 0.162 0.148
On 10/30/07, Bryan Hanson [EMAIL PROTECTED]
wrote:
Hi Folks... Œbeen playing with this for a while, with no luck, so
I¹m hoping
someone knows it off the top of their head... Difficult to find
this nuance
in the archives, as so many msgs deal with read.csv!
I¹m
trying to read a data file with the following structure (a little piece
of
the actual data, they are actually csv just didn¹t paste with the
commas):
wavelength SampleA SampleB SampleC SampleD
color green
black black green
class Class 1 Class 2 Class 2 Class 1
403 1.94E-01 2.14E-01 2.11E-01 1.83E-01
409 1.92E-01 1.89E-01 2.00E-01
1.82E-01
415 1.70E-01 1.99E-01 1.94E-01 1.86E-01
420 1.59E-01 1.91E-01
2.16E-01 1.74E-01
426 1.50E-01 1.66E-01 1.72E-01 1.58E-01
432 1.42E-01
1.50E-01 1.62E-01 1.48E-01
Columns after the first one are sample
names. 2nd row is the list of colors
to use in later plotting. 3rd row is
the class for later manova. The rest
of it is x data in the first column
with y1, y2...following for plotting.
I can read the file w/o the color
or class rows with read.csv just fine,
makes a nice data frame with proper
data types. The problem comes when
parsing the 2nd and 3rd rows. Here¹s
the code:
data = read.csv(filename, header=TRUE) # read in data
color = data[1,]; color = data[-1] # capture color info throw out 1st
value
class = data[2,]; class = class[-1] # capture category info throw
out 1st
value
cleaned.data = data[-1,] # remove color category
info for matrix
operations
cleaned.data = data[-1,]
freq = data[,1] #
capture frequency info
What happens is that freq is parsed as factors,
and the color and class are
parsed as a data frames of factors.
I need
color and class to be characters which I can pass to functions in the
typical way one uses colors and levels.
I need the freq the cleaned.data
info as numeric for
Re: [R] Performance of concatenating strings
On 10/31/07, Tamara Steijger [EMAIL PROTECTED] wrote: Hi, I would like to ask how the paste(S1, S2, sep=) function internally works. Are the two stings copied to a new String? I'm not 100% sure, but I'd suspect so, as this is the default behaviour in pretty much every programming language. I have a program where successively strings are build up. First the program calls an external function and depending on the result it builds up strings to visualize the result. The external function is really fast, also for huge input data. But the building of the strings takes much to long for huge input sizes. So I'm wondering if the concatenating could be the problem, like using String in Java instead of StringBuffer. Is there something like StringBuffers in R also? If you know how many components there will be in the string, it's probably best to create a character vector (str - vector(character, 100)) filling it up as you go, and then pasting it together at the very end. If you don't know how many components there will be, you will need to do something a bit more sophisticated. You might also trying profiling your function to make sure the slowness really is being caused by what you think it is. 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] R WinEdt on Windows vista
Hi! I was trying to install the RWinEdt library on a Windows Vista machine which had R 2.6.0, WinEdt 5.4 and the RWinEdt1.7.8.zip file in the library folder under the ...\R\2.6.0 directory. I am able to install fine form the local zip but I can't launch winedt from within R for some reason. utils:::menuInstallLocal() package 'RWinEdt' successfully unpacked and MD5 sums checked updating HTML package descriptions library(RWinEdt) Error in file(file, r) : unable to open connection In addition: Warning message: In file(file, r) : cannot open file 'C:\Program Files\WinEdt Team\WinEdt\R.ver', reason 'No such file or directory' Error : .onAttach failed in 'attachNamespace' Error: package/namespace load failed for 'RWinEdt' I was hoping some one could help me interpret this error message, many thanks. Alex _ [[replacing trailing spam]] ilnews [[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] thicker axis in levelplot
Dear R-help community, I need to find out how to make the black axis line around my plot thicker in levelplot, I cannot find the correct command in ?levelplot or ?par - or if it is there I cannot get it to work - any help would be more that appreciated! Here's an example script - I would want the code for making the axis bordering the plot thicker: x- seq(pi/4, 5*pi,length=100) y- seq(pi/4, 5*pi,length=100) r- as.vector(sqrt(outer(x^2,y^2,+))) grid- expand.grid(x=x,y=y) grid$z - cos(r^2) * exp(-r/(pi^3)) levelplot(z~x*y, grid, cuts=50, scales=list(log=e), xlab=, ylab=, main=Weird Function, sub=with log scales, colorkey=FALSE, region=TRUE) Also, If anybody knows how to make the lines around the colorkey (legend) thicker too I'd like to do that as well! (I realise that the above script does not include a colorkey component but my actual work does). Many thanks, Jenny Barnes __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] quantreg log and polinomial functions
I have two variables which show a typical quantile relation I would like to fit quantile regression models based on both logarithm and polynomial of second order functions within quantreg. Any help appreciated... Cheers Duccio Herewith the values: -- var1var2 0.964290.00138 10.02316 1.031450.09323 1.240880.77128 1.398690.86732 1.337280.63674 1.482990.96194 0.760.1 0.770190.3 0.960.00028 0.934910.00057 0.824320.00171 0.730770.00275 0.746480.00313 0.96970.00361 0.792450.00439 0.929940.00586 0.821430.00858 0.73770.00862 0.807950.01053 0.870750.01407 0.829930.01936 0.845070.01968 0.851850.03322 1.050630.03341 0.901230.03621 0.994150.0386 0.857140.03873 0.762590.04932 0.751880.05513 1.131220.06014 0.853330.06636 0.904110.0732 1.297780.07327 0.842110.08094 1.060240.08509 0.922080.08662 0.843540.09211 0.93590.09642 1.062860.10479 0.90.10786 0.750.11703 0.796990.1214 0.885910.12347 0.808510.12404 0.809520.12424 0.838240.13017 0.953850.14673 1.020130.1513 0.80.1555 1.066670.15733 0.887320.16003 0.961540.18156 1.022470.18261 1.098770.18561 1.165640.18985 1.10.19068 1.182390.20152 1.156630.21013 1.029410.22034 1.323810.22261 1.094590.23226 1.00680.23951 1.036140.26169 0.972220.26258 0.938780.28128 1.01370.28627 1.460870.28714 1.144510.28726 0.929130.28782 1.075950.30899 0.96350.34355 1.16770.36839 0.945950.38738 1.141180.39093 1.154290.40374 1.16250.41852 1.082350.42404 1.129410.43112 1.081760.44307 1.3250.45221 1.383080.47239 1.00730.47427 1.171050.47728 1.139070.48632 1.343280.49487 1.209880.50787 1.363640.52367 1.217950.53399 1.238640.5 1.232880.55839 1.282610.56652 1.357890.56932 1.228070.57798 1.20530.57992 1.186670.58031 1.12230.58048 1.109380.58197 1.296970.58868 1.220930.61025 1.214810.63087 1.580950.63506 1.348840.65639 1.23810.70642 1.517240.71612 1.341610.75399 1.452630.76035 1.288340.78978 1.539270.80492 1.350650.80679 1.381820.83345 1.37430.87256 1.60510.87435 1.38650.90878 1.440.94695 1.464050.95543 1.529410.96108 1.496860.98102 0.974360.00053 0.949720.03044 1.08380.04558 0.783220.04753 1.087910.06048 1.068320.06949 1.152940.13114 1.100670.18832 1.141240.23016 1.288140.25488 1.253160.25809 1.10.26702 1.137720.41137 1.123460.43028 1.153850.47513 1.186210.48385 1.253010.52187 1.109590.56926 1.173910.57653 1.40.63667 1.223680.72883 1.417140.76351 1.30.86687 1.337580.89052 1.452380.92793 1.397440.94344 1.481010.9775 0.79470.00049 0.941180.00078 0.906830.01507 0.786210.03443 1.059520.09995 0.921570.10748 0.980650.11945 1.050.15 1.090910.19752 0.866140.22126 1.218390.27116 10.28663 1.03750.31568 1.095540.362 1.094890.48028 1.228760.6107 1.270270.82497 1.476740.88388 1.364860.91599 1.50.9485 1.464290.96476 0.984290.00017 0.960.00132 1.10160.00164 1.034880.00259 1.131310.00676 1.10.00857 1.177780.01879 0.848480.02734 1.044940.03203 0.994590.0334 1.060770.04496 0.993630.04525 0.97590.04738 0.844160.05265 10.06271 1.163840.06624 1.192550.10814 1.078650.11254 1.148390.11579 1.065870.11741 0.987950.15986 1.025640.16745 1.182320.24054 1.064750.26294 1.20280.33415 1.052630.33649 0.962030.35101 1.418990.36591 1.290320.38599 1.303370.39697 1.225810.40419 1.322310.41405 1.142860.41882 1.31210.48076 1.276840.49725 1.151520.50391 1.241030.52758 1.284850.53712 1.247060.55238 1.163120.589 1.248320.59592 1.194240.59958 1.230770.60055 1.153850.60596 1.177220.6227 1.321640.65736 1.288140.67897 1.359120.68161 1.216220.68561 1.20.69235 1.293230.69752 1.242420.72117 1.587790.7424 1.359380.75283 1.30380.76964 1.263890.78097 1.266190.78649 1.284670.78969 1.468210.81551 1.294960.82751 1.328860.82946 1.383460.86327 1.396230.88525 1.365850.89968 1.369860.91253 1.418440.92278 1.472970.92683 1.58940.93875 1.452050.95307 1.440.96991 1.516340.97627 1.114750.01352 0.952380.07429 0.949370.15717 1.326730.19765 1.10490.3566 1.142860.35769 1.1750.38035 1.339810.38826 1.211010.39268 1.238710.41222 1.396230.43026 1.065420.45457 1.236360.46048 1.115380.50053 1.181210.50146 1.282050.5199 1.591160.53439
Re: [R] R WinEdt on Windows vista
Alexander Nervedi wrote: Hi! I was trying to install the RWinEdt library on a Windows Vista machine which had R 2.6.0, WinEdt 5.4 and the RWinEdt1.7.8.zip file in the library folder under the ...\R\2.6.0 directory. I am able to install fine form the local zip but I can't launch winedt from within R for some reason. utils:::menuInstallLocal() package 'RWinEdt' successfully unpacked and MD5 sums checked updating HTML package descriptions library(RWinEdt) Error in file(file, r) : unable to open connection In addition: Warning message: In file(file, r) : cannot open file 'C:\Program Files\WinEdt Team\WinEdt\R.ver', reason 'No such file or directory' At first make sure that WinEdt is installed and registered. Then, please start R with a right click (and choose start with Administrator privileges - don't know the exact english translation) and reinstall RWinEdt. Everything should work after that. I just found out that there might be a minor problem with unregistered versions of WinEdt - and a fix will be committed shortly (but not that important, because people who do not own a copy can make use of other editors such as Tinn-R, which is better supported than my RWinEdt extension, I hope... Uwe Ligges Error : .onAttach failed in 'attachNamespace' Error: package/namespace load failed for 'RWinEdt' I was hoping some one could help me interpret this error message, many thanks. Alex _ [[replacing trailing spam]] ilnews [[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] SAS ODBC DRIVER
Has anyone been able to successfully query SAS libraries from R using RODBC?
While I believe I have configured the SAS ODBC Driver properly (I can query
SAS libraries from MS Access) when I try to query SAS libraries from R, I
only seem to get back the column names of the table I am querying.
Sample Code:
# open connection to SAS library 'Common'
conn = odbcConnect('Common')
# query test table I made in SAS
mytable = sqlQuery(conn, 'select * from Common.Mydata')
# mytable only has the names of the the Common.Mydata Dataset, it did not
# retrieve the values
mytable
[1] var1 var2 var3
0 rows (or 0-length row.names)
Thanks for your help.
-Mike King
[[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] accessing SAS libraries using RODBC
Has anyone been able to successfully query SAS libraries from R using RODBC?
While I believe I have configured the SAS ODBC Driver properly (I can query
SAS libraries from MS Access) when I try to query SAS libraries from R, I
only seem to get back the column names of the table I am querying.
Sample Code:
# open connection to SAS library 'Common'
conn = odbcConnect('Common')
# query test table I made in SAS
mytable = sqlQuery(conn, 'select * from Common.Mydata')
# mytable only has the names of the the Common.Mydata Dataset, it did not
# retrieve the values
mytable
[1] var1 var2 var3
0 rows (or 0-length row.names)
Thanks for your help.
-Mike King
[[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] find overlap between intervals - Correction
I'm not sure if i got the idea of what you want. At fist i thought that
you wanted this output:
Output:
290 380
380 440
440 443
443 468
to get it, you can use the following function:
intervals - function(Input)
{
all - c(Input$Start, Input$End)
numbers - sort(all[-which(duplicated(all))])
Output - NULL
for(i in 1:(length(numbers) - 1))
{
Output - rbind(Output, c(numbers[i], numbers[i+1]))
}
Output
}
## then write:
intervals(Input)
but your output it's a little diferent:
CORRECTED Desired output:
Start End
290 380
380 440
443 468
and i noticed too late... ¿maybe you missed one interval (440 to 443) in
the desired Output?
JM
On Wed, 2007-10-31 at 15:01 +0100, João Fadista wrote:
Dear all,
Sorry for the previous email. I had a wrong example output:
Input:
Start End
440 443
380 443
290 468
CORRECTED Desired output:
Start End
290 380
380 440
443 468
Best regards,
Joo Fadista
[[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] set initial parameter values for GLMM estimation
Dear list members, I look for a way (or alternative) to specify initial values when estimating linear mixed models in R, and to avoid iterative estimation. This is a way to control specific parameter values (eg. variance parameter values) such that the result (F-value) is based on them. This result can then be used for power analyses that uses the non-central F-distribution, as is done with SAS using the -PARMS- and -noiter- statements, indicated in the following SAS example: after using/constructing a data set, with actual scores changed into predicted scores (no error) proc mixed data = dataSet; class treat group; model y = treat*time ; random intercept / subject=group(treat); PARMS (2.1) (1.2) / NOITER; contrast 'slopes' treat*time 1 -1 0,treat*time 1 0 -1; ods output contrasts=c; run; data dataSet; set c; alpha=0.05; ncparm=numdf*fvalue; fc=finv(1-alpha,numdf,dendf,0); power=1-probf(fc,numdf,dendf,ncparm); run; proc print;run; cheers, Wilfried Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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() device uses fonts to represent points - dataalteration?
Another approach is to use the my.symbols function in the TeachingDemos package (in place of the points function) and define how you want your circles represented (a polygon with enough sides is a good approximation to a circle for most cases). Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of jiho Sent: Wednesday, October 31, 2007 5:40 AM To: Paul Murrell Cc: R-help Subject: Re: [R] pdf() device uses fonts to represent points - dataalteration? Thank you very much for your answer, even so long after I first posted the message. On 2007-October-31 , at 12:00 , Paul Murrell wrote: Hi jiho wrote: Hello all, I discovered that the pdf device uses fonts to represent points symbols (as in plot(...,type=p,...) ). Namely it uses ZapfDingbats with symbol U+25cf. This can lead to problems when the font is not available, or available in another version (such as points being replaced by other symbols, or worst: slightly displaced). Furthermore, it also causes problems when opening the pdf files for editing in other programs. I know that for reproducibility one should avoid doing this but there are cases where R is simply not suited to produce the end result graphic directly using code (Ex: replace some colors by CMYK versions for color consistency in print). In addition, publishers also often like being able to retouch graphics to ensure fonts consistency or such, and this will be destructive in the case of these pdfs. For example, Inkscape interprets points as squares (more like U +2751 in ZapfDingbats) and Adobe Illustrator does not even recognize the font (substituting AdobePiStd). I tried to embed fonts with embedFonts() but his does not solves the issue with editing (Inkscape produces a kind of star and AI still chokes on the font) and worst, it modifies how the original graphic renders in pdf viewers: the circles are now filled (I believe this is because this is the default state of the ZapfDingbats character). So my questions are: - does anyone have a work around this? - why can't the pdf device use shapes instead of fonts to represent data point? It would appear as a much more robust approach and would ensure that the points are rendered the same everywhere. Font substitution in axes labels is not as bad since it does not modify the data itself (at worst the labels are offset a little bit) but font substitution on the data points can really harm the graphic. If I recall correctly, the PDF device uses a character for small circles because that looks better. There is no PDF circle primitive, so circles have to be drawn using bezier curves. The original author may be able to elaborate on that. OK. I was suspecting that PDF did not have circle primitives indeed. That's a good reason. Two suggestions for workarounds: (i) produce PostScript and then convert to PDF using something like ghostscript (e.g., ps2pdf) (ii) use an almost-but-not-quite opaque colour, e.g., rgb(0, 0, 0, .99) for the points. If the points are not fully opaque, the character is not used. (ii) is really good to know (and I would probably never have found it myself). (i) is not applicable since I use PDF to keep transparency. Thanks for your help. I still think that not using fonts at all should be preferred because really strange things can happen with fonts while bezier curves are robust and do not depend at all on the rest of the OS. In this precise matter, robustness is probably to be preferred over appearance, since it involves the data directly. Anyway, I'm fine now with your workaround. I should file a bug report for this to be solved in a future release maybe. JiHO --- http://jo.irisson.free.fr/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] reversing perspective plot axis
A simple approach is to swap x and y and rotate the theta parameter -90 degrees (play around with this until it is what you want). Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of James Sent: Tuesday, October 30, 2007 8:17 PM To: r-help@r-project.org Subject: [R] reversing perspective plot axis Hi, I am trying to create a perspective plot with Time on the x-axis, Underlying Price on the y-axis, and Option Price on the z-axis. But I don't like the way my x-axis is setup. Right now, Time is this sequence. Time = seq(from = 1/52, to = 1, by=1/52) That results in the x-axis going from 0 at the back, to 1 near the foreground corner.(If that makes any sense) I want to do the exact opposite. When I try this sequence: Time = seq(from = 1, to = 1/52, by=-1/52) I get this error message: Error in persp.default(x = Time, y = S, z = Price, xlab = Time, ylab = S, : increasing 'x' and 'y' values expected So it seems that I can't use a descending sequence for my perspective plot. Is that true? Is there a way to work around this? persp(x=Time, y=S, z=Price, xlab=Time, ylab=S, zlab=TypeFlag, ...) Essentially, what I'm trying to create is something that looks like this. http://www.insightful.com/products/finmetrics/opSensitivity1_lg.gif You can see how Time on the x-axis diminishes as it moves to the foreground corner. Thanks in advance. 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 optimizing Poisson log-likelihood with L-BFGS-B
Dear R users,
I have following code, estimating Poisson log-likelihood a number of times:
poisson.loglik - function(mu, y){
n - NROW(y)
logl - sum(y)*log(mu)-n*mu
return(-logl)
}
estimates - numeric(1e5)
for(i in seq_along(estimates)){
estimates[i] - optim(par=1, poisson.loglik, method=L-BFGS-B,
lower=0, y=rpois(10,lambda=2))$par
}
I cannot run this because I always get an error message:
Error in optim(par = 1, poisson.loglik, lower = 0, method = L-BFGS-B, :
non-finite finite-difference value [1]
Could someone enlighten me what that means and why this happens?
THanks in advance,
Sergey
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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 generating F-distr from lme()
Dear all, Using the data set and code below, I am interested in modelling how egg temperature (egg.temp) is related to energy expenditure (kjday) and clutch size (treat) in incubating birds using the lme-function. I wish to generate the F-distribution for my model, and have tried to do so using the anova()-function. However, in the resulting anova-table, the parameter kjday has gone from being highly non-signiicant in the lme-expression, to all of a sudden being significant at the 0.05 level. At the same time, treat retains its original p-value. I've tried to understand why, but can't really figure it out. So, what has happened and why? How to best interpret it? Further, any advice on how to best generate F-distributions from the lme-function is most appreciated. Many thanks in advance, Andreas Nord Sweden ind treat egg.temp kjday 79 2 27.33241 42.048 42 2 30.73269 41.760 10 2 29.54986 38.304 206 2 31.78947 45.216 23 2 29.69114 40.896 24 2 36.48199 46.944 45 2 29.76454 44.064 29 2 30.56510 42.912 78 2 27.71468 43.200 79 3 25.88227 45.216 42 3 30.95983 44.640 10 3 28.13296 45.216 206 3 31.77147 45.216 23 3 27.5 42.336 5 3 28.16205 51.264 24 3 34.69391 48.960 45 3 28.79778 46.368 368 3 26.18006 45.792 29 3 29.75208 45.216 78 3 25.28393 43.200 44 3 23.32825 44.640 # lme-model with individual as random factor incub.lme2-lme(egg.temp~kjday+treat,random=~1|ind,data=incub.df) Fixed effects: egg.temp ~ kjday + treat Value Std.Error DF t-value p-value (Intercept) 24.937897 6.662475 11 3.743038 0.0032 kjday0.108143 0.152540 7 0.708945 0.5013 treat3 -1.506605 0.485336 7 -3.104254 0.0172 #generating an anova table to get the F-distribution anova(incub.lme2) numDF denDF F-value p-value (Intercept) 111 1176.6686 .0001 kjday 1 75.7060 0.0483 treat 1 79.6364 0.0172 -- View this message in context: http://www.nabble.com/Problems-with-generating-F-distr-from-lme%28%29-tf4726064.html#a13512770 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem with package fSeries
Helo, please look at the log below: after loading the fSeries library, I can not use the log function. Is this a bug or what am I doing wrong? Because of this, I'm unable to use the garch library. thanks a lot for any help, Balazs Torma log(1) [1] 0 require(fSeries) Loading required package: fSeries Loading required package: robustbase Loading required package: fCalendar Loading required package: fEcofin Rmetrics, (C) 1999-2006, Diethelm Wuertz, GPL fCalendar: Time, Date and Calendar Tools Package fSeries (260.72) loaded. Rmetrics - Financial Time Series Objects Rmetrics, (C) 1999-2007, Diethelm Wuertz, GPL log(1) Error in .Internal(log(x)) : no internal function log __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] datadist options error, DESIGN library
Giulia Barbati wrote: Hello, using the Design library, and the following command (from the Harrell's book, example at Ch.20): dd - datadist(rx, age, wt, pf, pf.coded, heart, map, hg, sz, sg, ap, bm) options(datadist=='dd') That command doesn't appear in the book. The == should be a single = Frank I get the following error: Error in datadist == dd : comparison (1) possible only for atomic data or list What does it means? thank you, giulia __ [[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. -- 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] drawing direction fields
For drawing the arrows look at the my.symbols and ms.arrows functions in the TeachingDemos package. If you need help with determining the directions of the arrows, then perhaps the Ryacas package or other link to a mathematics package will help. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jong-Hoon Kim Sent: Wednesday, October 31, 2007 1:50 AM To: r-help@r-project.org Subject: [R] drawing direction fields Dear useRs, I am trying to draw direction fields for some differential equations. So for I couldn't find much information on that. Could anybody give me a hint how to draw a direction field using R? Jong-Hoon __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Umacs example help..
Hello all...
I am just starting to teach myself Bayesian methods, and am
interested in learning how to use UMacs. I've read the
documentation, but the single example is a bit over my head at the
level I am at right now. I was wondering if anyone has any simple
examples they'd like to share. I've successfully done a couple of
simple gibbs examples, but have had a hard time modifying some of the
home written metropolis hastings samplers I've made to work with
Umacs. Does anyone have any pointers or simple 2 parameter
examples? Thanks.
Here is one of my simple MH samplers using a simple linear regression
with a Cauchy error term.
x - c(1.808,1.799,1.179,0.574,3.727,0.946,3.719,1.566,3.596,3.253)
y - c(1.816,1.281,-1.382,0.573,3.793,0.935,1.775,1.474,3.679,3.889)
fn = function(x,a=0,b=1){
a+b*x
}
sample.ab -function(x,y,a,b,s,da,db){
bstar = runif(1,b-db,b+db)
astar = runif(1,a-da,a+da)
logalpha = sum(dcauchy(y,location=fn(x,astar,bstar),scale=s,log=T) -
dcauchy(y,location=fn(x,a,b),scale=s,log=T))
logu = log(runif(1,0,1))
acc = (logu logalpha)
b = acc*bstar + (1-acc)*b
a = acc*astar + (1-acc)*a
list(b=b,a=a,acc=acc)
}
samples = function(x,y,a,b,s,ds){
sstar = runif(1,s-ds,s+ds)
while(sstar = 0){
sstar = runif(1,s-ds,s+ds)
}
logalpha = sum( dcauchy(y,location=fn(x,a,b),scale=sstar,log=T) -
dcauchy(y,location=fn(x,a,b),scale=s,log=T)) - log(sstar/s)
logu = log(runif(1,0,1))
acc = (logu logalpha)
s = acc*sstar + (1-acc)*s
list(s=s,accs=acc)
}
sample.abs-function(n=1,x,y,a=0,b=1,s=2,da=.2,db =.2,ds=1)
{
accab - 0
accs - 0
A = B = S = rep(NaN,n)
for(i in 1:n){
z = sampleab(x,y,a,b,s,da,db)
q - samples(x,y,a,b,s,ds)
A[i] = a = z$a
B[i] = b = z$b
S[i]=s=q$s
accab = accab + z$acc
accs - accs +q$accs
}
invisible(list(a=A, b=B, s=S, accab=accab/n,accs=accs/n))
}
Cheers,
Ted
Dept. of Biology,
University of Vermont
[[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] clim.pact: change group of stations object into a field
Hello, I have a question about one of the functions from package clim.pact. I am planning to perform canonical correlation analysis (CCA) with temperature stations data, I want to use clim.pact package for that. As I understood I should be able to use the function stations2field in order to group my stations objects into a field, so that I can include the result in CCA analysis. If I have stations objects bute.obj,braemar.obj,lerwick.obj (I have more, but this is just an example) and I write the code: field.obj-stations2field(data.set=list(bute=bute.obj,braemar=braemar.obj,lerwick=lerwick.obj)) I receive the following message: [1] stations2field [1] Presumes that 'data.set' is a list of station objects [1] bute [1] braemar [1] lerwick Error in stations2field(data.set = list(bute = bute.obj, braemar = braemar.obj, : object i.data not found I went through the code of the function stations2field and it was not clear what i.data is. I was wondering what can be done in such situation. Thank you, Irina. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 package fSeries
Are you using the latest version of R - with the patch? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Balazs Torma Sent: Wednesday, October 31, 2007 11:44 AM To: r-help@r-project.org Cc: [EMAIL PROTECTED] Subject: [R] problem with package fSeries Helo, please look at the log below: after loading the fSeries library, I can not use the log function. Is this a bug or what am I doing wrong? Because of this, I'm unable to use the garch library. thanks a lot for any help, Balazs Torma log(1) [1] 0 require(fSeries) Loading required package: fSeries Loading required package: robustbase Loading required package: fCalendar Loading required package: fEcofin Rmetrics, (C) 1999-2006, Diethelm Wuertz, GPL fCalendar: Time, Date and Calendar Tools Package fSeries (260.72) loaded. Rmetrics - Financial Time Series Objects Rmetrics, (C) 1999-2007, Diethelm Wuertz, GPL log(1) Error in .Internal(log(x)) : no internal function log __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] survey weights in sample with replacement
Thanks Thomas ! I am trying to draw random sample from a household survey which has 80,000 observations. rural is name of the dataset, while iwt is survey weights assigned to each observation. the resulting error are : z=sample(rural,5000,replace=TRUE, Prob=rural$iwt) Error in sample(rural, 5000, replace = TRUE, Prob = rural$iwt) : unused argument(s) (Prob = c(133, 133, 166, 166, 166, 166, 1047, 1047, 1047, 1047, 288, 623, 623, 240, 240, 432, 144, 144, 719, 719, 316, 342, 342, 816, 816, 105, 158, 158, 1105, 1105, 101, 557, 557, 405, 405, 101, 304, 304, 1165, 1165, 193, 771, 771, 1060, 1060, 482, 530, 530, 2024, 2024, 254, 254, 241, 241, 241, 241, 674, 674, 674, 674, 137, 137, 623, 623, 623, 623, 603, 603, 603, 603, 285, 556, 556, 970, 970, 285, 728, 728, 499, 499, 272, 1349, 1349, 218, 218, 272, 1240, 1240, 95, 95, 307, 307, 307, 307, 307, iwt=rural[,iwt] z=sample(rural,5000,replace=TRUE, Prob=iwt) Error in sample(rural, 5000, replace = TRUE, Prob = iwt) : unused argument(s) (Prob = c(133, 133, 166, 166, 166, 166, 1047, 1047, 1047, 1047, 288, 623, 623, 240, 240, 432, 144, 144, 719, 719, 316, 342, 342, 816, 816, 105, 158, 158, 1105, 1105, 101, 557, 557, 405, 405, 101, 304, 304, 1165, 1165, 193, 771, 771, 1060, 1060, 482, 530, 530, 2024, 2024, 254, 254, 241, 241, 241, 241, 674, 674, 674, 674, 137, 137, 623, 623, 623, 623, 603, 603, 603, 603, 285, 556, 556, 970, 970, 285, 728, 728, 499, 499, 272, 1349, 1349, 218, 218, 272, 1240, 1240, 95, 95, 307, 307, 307, 307, 307, iwt=as.vector(rural[,iwt]) z=sample(rural,5000,replace=TRUE, Prob=iwt) Error in sample(rural, 5000, replace = TRUE, Prob = iwt) : unused argument(s) (Prob = c(133, 133, 166, 166, 166, 166, 1047, 1047, 1047, 1047, 288, 623, 623, 240, 240, 432, 144, 144, 719, 719, 316, 342, 342, 816, 816, 105, 158, 158, 1105, 1105, 101, 557, 557, 405, 405, 101, 304, 304, 1165, 1165, 193, 771, 771, 1060, 1060, 482, 530, 530, 2024, 2024, 254, 254, 241, 241, 241, 241, 674, 674, 674, 674, 137, 137, 623, 623, 623, 623, 603, 603, 603, 603, 285, 556, 556, 970, 970, 285, 728, 728, 499, 499, 272, 1349, 1349, 218, 218, 272, 1240, 1240, 95, 95, 307, 307, 307, 307, 307, summary(rural$iwt) Min. 1st Qu. MedianMean 3rd Qu.Max. 1 400107818942981 54320 I just want that random sample look as close as possible to population ( weighted proportions generated from sample) I thought it should automatically normalize probablity vector.I am not sure, i am reading this right // I might be totally off the track. Regards, Mehtab -Original Message- From: Thomas Lumley [mailto:[EMAIL PROTECTED] Sent: Wednesday, October 31, 2007 9:44 AM To: Azam, Mehtabul Cc: [EMAIL PROTECTED] Subject: Re: [R] survey weights in sample with replacement On Tue, 30 Oct 2007, Azam, Mehtabul wrote: Hi, I am trying to draw a random sample from an household survey with sample weight. Is there any function in R or Splus which allows this. It depends on exactly what you want. The sample() function will draw unequal probability samples with replacement. sample() will also draw samples without replacement, but (as documented) it uses sequential sampling and so does not actually generate probabilities proportional to the specified weights for sample sizes greater than 1. The error in sequential sampling is pretty small, but it has attracted a lot of creativity in the survey literature (probably more than it deserves). The 'sampling' package implements several algorithms for drawing unequal probability samples without replacement that really are proportional to the specified weights where this is achievable. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] DBI Package
Ok, thanks to Prof Brian Ripley and to Elijah, I did the connection to PostgeSQL database with RODBC, it's simple. I will try with RdbiPgSQL in the next days. Thanks a lot. 2007/10/31, [EMAIL PROTECTED] [EMAIL PROTECTED]: I have some problems with DBI package, I want to connect to PostgreSQL database but I don't know the way to do it. pg - dbDriver(PostgreSQL) ... nope. That won't work. you need the RdbiPgSQL package from Bioconductor. Along with DBI, as I recall. --elijah __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- --- |\__ (:__)( |/ Soluciones Geoinformáticas Libres http://geotux.tuxfamily.org/ [[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] reversing perspective plot axis
On Oct 31, 2007, at 9:48 AM, Greg Snow wrote: A simple approach is to swap x and y and rotate the theta parameter -90 degrees (play around with this until it is what you want). Thank you. That does exactly what I wanted. Oddly enough, I had already swapped X and Y trying to get this to work -- not realizing that I could just rotate it. I've now swapped the axes back and used theta=-25 to rotate it the other direction which fixes everything. Thank you. 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] Error optimizing Poisson log-likelihood with L-BFGS-B
Sergey Goriatchev wrote:
[snip]
I cannot run this because I always get an error message:
Error in optim(par = 1, poisson.loglik, lower = 0, method = L-BFGS-B, :
non-finite finite-difference value [1]
Could someone enlighten me what that means and why this happens?
THanks in advance,
Sergey
It happens because L-BFGS-B is willing to try points that are exactly on
the boundary.
## modify likelihood function to allow debug option
poisson.loglik - function(mu, y,debug=FALSE){
n - NROW(y)
logl - sum(y)*log(mu)-n*mu
v = -logl
if (debug) cat(mu,v,\n)
return(v)
}
estimates - numeric(1e5)
## try the loop, but save yval every time so we can replicate the problem
for (i in 1:1000) {
yval = rpois(10,lambda=2)
estimates[i] - optim(par=1, poisson.loglik, method=L-BFGS-B,
lower=0, y=yval)$par
}
## now see what crashed (stopped after rep 33 for me)
optim(par=1, poisson.loglik, method=L-BFGS-B,
lower=0, y=yval)$par
## yes, it crashed. Try debugging.
optim(par=1, poisson.loglik, method=L-BFGS-B,
lower=0, y=yval, debug=TRUE)$par
## increase lower bound value ...
optim(par=1, poisson.loglik, method=L-BFGS-B,
lower=0.002, y=yval, debug=TRUE)$par
for (i in 1:1) {
yval = rpois(10,lambda=2)
estimates[i] - optim(par=1, poisson.loglik, method=L-BFGS-B,
lower=0.002, y=yval)$par
}
## works (and minimum estimate is not on the boundary)
--
View this message in context:
http://www.nabble.com/Error-optimizing-Poisson-log-likelihood-with-L-BFGS-B-tf4726144.html#a13514904
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] high RAM on Linux or Solaris platform
Dr. Lumley and Prof. Ripley, Thank you very much for your helpful responses. Have you found any particular distribution of Linux to work well with 64-bit R? For the cluster, I am currently considering Debian (since it seems popular) and SUSE (since Matlab runs on it), but I remain open to others. Best regards, David -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Tuesday, October 30, 2007 4:51 PM To: Thomas Lumley Cc: David Bickel; [EMAIL PROTECTED] Subject: Re: [R] high RAM on Linux or Solaris platform On Tue, 30 Oct 2007, Thomas Lumley wrote: On Tue, 30 Oct 2007, David Bickel wrote: To help me make choices regarding a platform for running high-memory R processes in parallel, I would appreciate any responses to these questions: 1. Does the amount of RAM available to an R session depend on the processor (Intel vs. Sun) or on the OS (various Linux distributions vs. Solaris)? Yes. It depends on whether R uses 64-bit or 32-bit pointers. For 64-bit R you need a 64-bit processor, an operating system that will run 64-bit programs, and a compiler that will produce them. I'm not sure what the current Intel offerings are, but you can compile and run 64-bit on AMD Opteron (Linux) and Sun (Solaris) systems. That is both Sparc Solaris and x86_64 Solaris (although for the latter you seem to need to use the SunStudio compilers). As far as I know all current desktop Intel processors run x86_64, and Xeons seem to have a price-performance edge at the moment. We have several boxes with dual quad-core Xeons and lots of RAM. (Not all for use with R, some Linux, some Windows.) Core 2 Duos do, and are commonplace in quite low-end systems. 2. Does R have any built-in limitations of RAM available to a session? For example, could it make use of 16 GB in one session given the right processor/OS platform? R does have built-in limitations even in a 64-bit system, but they are large. It is certainly possible to use more than 16Gb of memory. The main limit is that the length of a vector is stored in a C int, and so is no more than 2^31-1, or about two billion. A numeric vector of that length would take up 16Gb on its own. ?Memory-limits documents them. 3. Is there anything else I should consider before choosing a processor and OS? I don't think there is anything else R-specific. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] find overlap between intervals
Got a little bit of a different answer:
x - Start End
+ 440 443
+ 380 443
+ 290 468
x.in - read.table(textConnection(x), header=TRUE)
# create matrix to determine queue size (overlap)
x.q - rbind(cbind(x.in$Start, 1), cbind(x.in$End, -1))
# sort
x.q - x.q[order(x.q[,1], x.q[,2]),]
x.q - cbind(x.q, queue=cumsum(x.q[,2]))
# remove duplicated entries
x.q - x.q[!duplicated(x.q[,1]),]
x.q
queue
[1,] 290 1 1
[2,] 380 1 2
[3,] 440 1 3
[4,] 443 -1 2
[5,] 468 -1 0
# now output ranges -- '0' indicates end of an interval
x.intervals - t(sapply(seq_len(nrow(x.q) - 1), function(.row){
+ if (x.q[.row, 'queue'] == 0) next # skip
+ c(Start=x.q[.row, 1], End=x.q[.row + 1, 1])
+ }))
x.intervals
Start End
[1,] 290 380
[2,] 380 440
[3,] 440 443
[4,] 443 468
On 10/31/07, João Fadista [EMAIL PROTECTED] wrote:
Dear all,
I would like to be able to know the intervals of my data that overlap between
them. Here it goes a small example:
Input:
Start End
440 443
380 443
290 468
Desired output:
Start End
290 380
380 440
440 468
Best regards,
João Fadista
[[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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] tree problem
This is a repeat posting from 28 Oct that generated no replies. I'm hoping someone has some advice since I'm still stuck ... I am trying to use tree to partition a data set. The data set has 3924 observations. Partitioning works for small subsets of the data, but when I use the entire data set, no partitioning occurs. The variables are: RESP respondent to a survey (0 = not a respondent, 1 = respondent) AGE_P Age (continuous) ORIGIN_I Hispanic Ethnicity (1 = Hispanic, 2 = non-Hispanic) RACRECI2Race Recode (1 = White, 2 = Black, 3 = Other) parents Parent(s) present in the family (1 = Yes, 2 = No) educ Education Recode (1 = HS, GED, or less, 5 = some college, 6 = Bachelor's or AA degree, 9 = Masters higher Here are 2 calls to tree and a snip of summary results: ### Use a sample of 100 set.seed(331) nsize = 100 sam - sample(1:nrow(nhis), nsize) t1 - tree( RESP ~ AGE_P + ORIGIN_I + RACRECI2 + parents + educ, + method = class, + control = tree.control(nobs = nsize, minsize = 10), + data = nhis[sam,]) summary(t1) Classification tree: tree(formula = RESP ~ AGE_P + ORIGIN_I + RACRECI2 + parents + educ, data = nhis[sam, ], control = tree.control(nobs = nsize, minsize = 10), method = class) Number of terminal nodes: 13 # All vars were used Use entire data set nsize = 3924 sam - sample(1:nrow(nhis), nsize) t1 - tree( RESP ~ AGE_P + ORIGIN_I + RACRECI2 + parents + educ, + method = class, + control = tree.control(nobs = nsize, minsize = 10), + data = nhis[sam,]) summary(t1) Classification tree: . . . Variables actually used in tree construction: character(0) # No vars were used Number of terminal nodes: 1 It doesn't matter whether I use the categorical vars as factors or not; I still get the same results. As I increase the subsample from 100 incrementally up to 1200 , fewer vars are used in tree construction. At 1200 the point is reached where none are used. Is there a way to force tree to do something with the larger sample sizes and the whole data set? Package tree version 1.0-26 R 2.6.0 Windows XP, v.5.1, service pack 2 Thanks Richard Valliant U of Maryland, US __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Multiple calls to a function
Hi y'all, I wrote two functions; 1) sparsely samples a point pattern and calculates the Clark Evans R value and Z score, 2) calls the first function multiple times using a for loop and generates a histogram. I would like to know if there is a more efficient way of calling the first function other than using the for loop. Any ideas? cel-data.frame(R=0,RZ=0,CV=0,PVAL=0,INT=0) for(i in 1:N) cel[i,]-cezhpts(dat,np,cv) Thanks, Keith Jones __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] textplot() in gplots causes problems (0x9)
Hello, I am using textplot function in gplots package to put some model output inside a PDF file, but it does not seem to work properly with PDF. I am doing follwing: pdf(file=C:/..., paper=a4, width=8, height=12) .model - lm(.model.formula, data=database) textplot(capture.output(summary(.model)), valign=top, halign=left) I am getting these error messages: Warning messages: 1: In FUN(c(C, a, l, l, :, l, m, (, f, o, r, : font width unknown for character 0x9 2: In strwidth(object, cex = cex) : font width unknown for character 0x9 3: In FUN(c(C, a, l, l, :, l, m, (, f, o, r, : font width unknown for character 0x9 4: In strwidth(object, cex = cex) : font width unknown for character 0x9 5: In FUN(c(C, a, l, l, :, l, m, (, f, o, r, : font width unknown for character 0x9 6: In strwidth(object, cex = cex) : font width unknown for character 0x9 7: In text.default(x = xpos, y = ypos, labels = object, adj = c(0, : font width unknown for character 0x9 8: In text.default(x = xpos, y = ypos, labels = object, adj = c(0, : font width unknown for character 0x9 This is a tab character that causes problems, I guess. Is there any way to solve this? Thank you in advance -- Jonas Malmros Stockholm University Stockholm, Sweden __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Lattice: par.ylab.text alpha ?
Hi all, I've got R for windows 2.3.1 I'm trying to modify my lattice histograms. The following does reset the y-label to blue, but I cannot turn off the label (alpha=0), nor shift label position (I'm assuming that is what lineheight is for). Is 'lineheight' the equivalent of 'line' in mtext? Am I erring somehow? Thanks! trellis.par.set(list(par.ylab.text=list(col='blue'))) #- works trellis.par.set(list(par.ylab.text=list(alpha=0))) #-no change, i.e. label still there trellis.par.set(list(par.ylab.text=list(lineheight=3))) #- label not moved I assume I'm interpreting alpha correctly as this gets rid of axes: trellis.par.set(list(axis.line=list(alpha=0))) ___ Michael Folkes Salmon Stock Assessment Canadian Dept. of Fisheries Oceans Pacific Biological Station 3190 Hammond Bay Rd. Nanaimo, B.C., Canada V9T-6N7 Ph (250) 756-7264 Fax (250) 756-7053 [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple calls to a function
Since you do not change anything in your call to the function, you could just use the replicate function instead of the for loop (I don't know that it will speed things up much, but it is a bit more readable). Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Keith Jones Sent: Wednesday, October 31, 2007 1:04 PM To: r-help@r-project.org Subject: [R] Multiple calls to a function Hi y'all, I wrote two functions; 1) sparsely samples a point pattern and calculates the Clark Evans R value and Z score, 2) calls the first function multiple times using a for loop and generates a histogram. I would like to know if there is a more efficient way of calling the first function other than using the for loop. Any ideas? cel-data.frame(R=0,RZ=0,CV=0,PVAL=0,INT=0) for(i in 1:N) cel[i,]-cezhpts(dat,np,cv) Thanks, Keith Jones __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] thicker axis in levelplot
try: trellis.par.set(axis.line=list(lwd=4)) On 10/31/07, Jenny Barnes [EMAIL PROTECTED] wrote: Dear R-help community, I need to find out how to make the black axis line around my plot thicker in levelplot, I cannot find the correct command in ?levelplot or ?par - or if it is there I cannot get it to work - any help would be more that appreciated! Here's an example script - I would want the code for making the axis bordering the plot thicker: x- seq(pi/4, 5*pi,length=100) y- seq(pi/4, 5*pi,length=100) r- as.vector(sqrt(outer(x^2,y^2,+))) grid- expand.grid(x=x,y=y) grid$z - cos(r^2) * exp(-r/(pi^3)) levelplot(z~x*y, grid, cuts=50, scales=list(log=e), xlab=, ylab=, main=Weird Function, sub=with log scales, colorkey=FALSE, region=TRUE) Also, If anybody knows how to make the lines around the colorkey (legend) thicker too I'd like to do that as well! (I realise that the above script does not include a colorkey component but my actual work does). Many thanks, Jenny Barnes __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] seg fault with randomForest ( ... , xtest )
Dear R-help, what are the limits on xtest? NOT_A.rf - randomForest (log10(Y[!A] ) ~ . , data = notA_desc , proximity=T ,xtest = A_desc) *** caught segfault *** address 0x9cdd000, cause 'memory not mapped' Segmentation fault I don't think that the matrix are large: notA_desc is 651 obs of 27 variables A_desc is 17 obs of 27 variables thanks in advance, Clayton [[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 SciViews-R
After installing the SciViews-R Console I am getting the following error message when I try to run any of the commands. Error in file.info(fn - c(...)) : invalid filename argument See also the attached file Doc1. - __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Homework help: Is this how CIs of normal distributions are computed?
I'm looking for a function in R similar to t.test() which was generously pointed out to me yesterday, but which can be used for normally distributed data. To recap yesterday: x - scan() 1: 62 52 68 23 34 45 27 42 83 56 40 12: Read 11 items alpha- .05 t.test(x) One Sample t-test data: x t = 8.8696, df = 10, p-value = 4.717e-06 alternative hypothesis: true mean is not equal to 0 95 percent confidence interval: 36.21420 60.51307 sample estimates: mean of x 48.36364 What if I now mock-up my data for 100 trials: x100-sample(x, 100, replace=TRUE) I think that I should be able to use a normal distribution, because of the n30 rule-of-thumb. I can compute the 95% CI using: mean(x100) - qnorm(alpha/2)*sd(x100)/sqrt(length(x100)) [1] 51.91222 mean(x100) + qnorm(alpha/2)*sd(x100)/sqrt(length(x100)) [1] 44.80778 t.test(x100) One Sample t-test data: x100 t = 26.683, df = 99, p-value 2.2e-16 alternative hypothesis: true mean is not equal to 0 95 percent confidence interval: 44.76383 51.95617 sample estimates: mean of x 48.36 The critical values I compute manually are close to the t.test values, which is what I expect. As the number of samples increases, the t value approaches the normal distribution value. I thought I looked at all the other .test functions in the stats package, and didn't find one that computed results like the t.test for normal distributions. Is something similar to my 'manual' computations the way it's done in R, or have I overlooked something again? Thanks. -Kevin Kevin Zembower Internet Services Group manager Center for Communication Programs Bloomberg School of Public Health Johns Hopkins University 111 Market Place, Suite 310 Baltimore, Maryland 21202 410-659-6139 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Homework help: Is this how CIs of normal distributions are computed?
On Wed, Oct 31, 2007 at 03:56:37PM -0400, Zembower, Kevin wrote: I'm looking for a function in R similar to t.test() which was generously pointed out to me yesterday, but which can be used for normally distributed data. ... x100-sample(x, 100, replace=TRUE) I think that I should be able to use a normal distribution, because of the n30 rule-of-thumb. I can compute the 95% CI using: mean(x100) - qnorm(alpha/2)*sd(x100)/sqrt(length(x100)) You can compute quantiles of the particular normal distribution itself rather than transforming from the standardized normal by hand. qnorm(c(.025,.975),mean=mean(x100),sd=sd(x100)/sqrt(length(x100))) -- Daniel Lakeland [EMAIL PROTECTED] http://www.street-artists.org/~dlakelan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Find A, given B where B=A'A
Given a matrix B, where B=A'A, how can I find A? In other words, if I have a matrix B which I know is another matrix A times its transpose, can I find matrix A? Thanks, 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] Homework help: Is this how CIs of normal distributionsare computed?
Daniel, thanks, I should have remembered this, too; I've seen it and worked with it before. Thanks. -Kevin -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Daniel Lakeland Sent: Wednesday, October 31, 2007 4:04 PM To: r-help@r-project.org Subject: Re: [R] Homework help: Is this how CIs of normal distributionsare computed? On Wed, Oct 31, 2007 at 03:56:37PM -0400, Zembower, Kevin wrote: I'm looking for a function in R similar to t.test() which was generously pointed out to me yesterday, but which can be used for normally distributed data. ... x100-sample(x, 100, replace=TRUE) I think that I should be able to use a normal distribution, because of the n30 rule-of-thumb. I can compute the 95% CI using: mean(x100) - qnorm(alpha/2)*sd(x100)/sqrt(length(x100)) You can compute quantiles of the particular normal distribution itself rather than transforming from the standardized normal by hand. qnorm(c(.025,.975),mean=mean(x100),sd=sd(x100)/sqrt(length(x100))) -- Daniel Lakeland [EMAIL PROTECTED] http://www.street-artists.org/~dlakelan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] mosaic row and column order
Dear R-helpers, I wasn't able to find out how to override the alphabetical ordering of the rows and columns in a vcd::mosaic plot. I would like to have them each ordered by numerical values in a different column of the data frame that contains the contingency data. I would be most grateful for a pointer toward the solution. Thanks, MK _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Find A, given B where B=A'A
B is symmetric by definition; if it's also real positive-definite then A is the upper triangular factor of the Choleski decomposition, and you can use chol(B) to get A. On Wed, 31 Oct 2007, Michael Gormley wrote: Given a matrix B, where B=A'A, how can I find A? In other words, if I have a matrix B which I know is another matrix A times its transpose, can I find matrix A? Thanks, 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Homework help: Is this how CIs of normal distributions arecomputed?
There is a z.test function in the TeachingDemos package, but it is mainly for learning purposes to ease students into using t.test. The rule of use the normal for n30 comes from the days when computations were done by hand using tables and people did not want to carry around t-tables with 100's of rows, so they noticed that the row for 29 df on the t-table is close to the normal values for the common confidence intervals. If you are using the computer then that does not apply and you should use the t test and t intervals for any situation that the computer can compute the t-values for you. The normal based confidence intervals should only be used for the paradoxical case where you know for certain the population standard deviation, but don't know the mean. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zembower, Kevin Sent: Wednesday, October 31, 2007 1:57 PM To: r-help@r-project.org Subject: [R] Homework help: Is this how CIs of normal distributions arecomputed? I'm looking for a function in R similar to t.test() which was generously pointed out to me yesterday, but which can be used for normally distributed data. To recap yesterday: x - scan() 1: 62 52 68 23 34 45 27 42 83 56 40 12: Read 11 items alpha- .05 t.test(x) One Sample t-test data: x t = 8.8696, df = 10, p-value = 4.717e-06 alternative hypothesis: true mean is not equal to 0 95 percent confidence interval: 36.21420 60.51307 sample estimates: mean of x 48.36364 What if I now mock-up my data for 100 trials: x100-sample(x, 100, replace=TRUE) I think that I should be able to use a normal distribution, because of the n30 rule-of-thumb. I can compute the 95% CI using: mean(x100) - qnorm(alpha/2)*sd(x100)/sqrt(length(x100)) [1] 51.91222 mean(x100) + qnorm(alpha/2)*sd(x100)/sqrt(length(x100)) [1] 44.80778 t.test(x100) One Sample t-test data: x100 t = 26.683, df = 99, p-value 2.2e-16 alternative hypothesis: true mean is not equal to 0 95 percent confidence interval: 44.76383 51.95617 sample estimates: mean of x 48.36 The critical values I compute manually are close to the t.test values, which is what I expect. As the number of samples increases, the t value approaches the normal distribution value. I thought I looked at all the other .test functions in the stats package, and didn't find one that computed results like the t.test for normal distributions. Is something similar to my 'manual' computations the way it's done in R, or have I overlooked something again? Thanks. -Kevin Kevin Zembower Internet Services Group manager Center for Communication Programs Bloomberg School of Public Health Johns Hopkins University 111 Market Place, Suite 310 Baltimore, Maryland 21202 410-659-6139 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Find A, given B where B=A'A
chol(B) doesn't give the original A, which I believe is what Mike wants. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Katharine Mullen Sent: Wednesday, October 31, 2007 4:08 PM To: Michael Gormley Cc: [EMAIL PROTECTED] Subject: Re: [R] Find A, given B where B=A'A B is symmetric by definition; if it's also real positive-definite then A is the upper triangular factor of the Choleski decomposition, and you can use chol(B) to get A. On Wed, 31 Oct 2007, Michael Gormley wrote: Given a matrix B, where B=A'A, how can I find A? In other words, if I have a matrix B which I know is another matrix A times its transpose, can I find matrix A? Thanks, 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Find A, given B where B=A'A
On 1/11/2007, at 9:13 AM, Michael Gormley wrote:
Given a matrix B, where B=A'A, how can I find A?
In other words, if I have a matrix B which I know is another matrix
A times
its transpose, can I find matrix A?
You can't, because A is not unique. You can easily find ***a***
solution.
E.g. A1 - matrix(1:4,ncol=2)
B - t(A1)%*%A1
A2 - msqrt(B)
A2 != A1 (A2 is symmetric), yet t(A2)%*%A2 == B.
The function msqrt() above is a simple-minded calculation of the
square root of a positive semi-definite real matrix, the code of
which I just cribbed from an old posting by Prof. Brian Ripley:
msqrt - function(X) {
e - eigen(X)
V - e$vectors
V%*%diag(sqrt(e$values))%*%t(V)
}
The problem of finding ***all possible*** solutions A to A'A = B
(for B symmetric positive semi-definite) is likely to be hard,
but may have been solved by the linear algebraists. I dunno.
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Find A, given B where B=A'A
On Thu, 1 Nov 2007, Rolf Turner wrote:
On 1/11/2007, at 9:13 AM, Michael Gormley wrote:
Given a matrix B, where B=A'A, how can I find A?
In other words, if I have a matrix B which I know is another matrix
A times
its transpose, can I find matrix A?
You can't, because A is not unique. You can easily find ***a***
solution.
E.g. A1 - matrix(1:4,ncol=2)
B - t(A1)%*%A1
A2 - msqrt(B)
Also, see
?chol
Chuck
A2 != A1 (A2 is symmetric), yet t(A2)%*%A2 == B.
The function msqrt() above is a simple-minded calculation of the
square root of a positive semi-definite real matrix, the code of
which I just cribbed from an old posting by Prof. Brian Ripley:
msqrt - function(X) {
e - eigen(X)
V - e$vectors
V%*%diag(sqrt(e$values))%*%t(V)
}
The problem of finding ***all possible*** solutions A to A'A = B
(for B symmetric positive semi-definite) is likely to be hard,
but may have been solved by the linear algebraists. I dunno.
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] mosaic row and column order
On Wed, 31 Oct 2007, Michael Kubovy wrote: Dear R-helpers, I wasn't able to find out how to override the alphabetical ordering of the rows and columns in a vcd::mosaic plot. I would like to have them each ordered by numerical values in a different column of the data frame that contains the contingency data. mosaic() uses the same ordering as in the levels() of your factor. You probably created the factor with an alphabetical ordering (which is the default if the input is a character vector), e.g.: ## character vector x - c(a, b, b, a, c) ## use alphabetical default f - factor(x) f ## change ordering in existing factor levels(f) - c(b, c, a) f ## create from scratch I would be most grateful for a pointer toward the solution. Thanks, MK _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Axis Location/Data view in scatterplot3d
All,
I constructed a fairly simple plot using the below and scatterplot3d.
However, the axis locations in scatterplot3d seem to 'hide' quite a bit
of the points in my graphic based on the viewing angle, hence not
adhering to Tufte's rules. I tried to determine if I could rotate the
graph and relocate all three axis (origin (0, 0, 0))so they would be at
the back left so the plotted points would slope down toward the viewer.
Using 'angle' and 'axis' did not get me any closer. Does anyone have
any suggestions?
TIA,
Bret
for(Days_Nesting in 1:55){
Breeding_Period-1:118
DSR_RGWT= exp(6.6205449-0.0589883*Days_Nesting)/(1+
exp(6.6205449-0.0589883*Days_Nesting))
DSR_BS-DSR_RGWT^Breeding_Period
DSR_Final-as.data.frame(cbind(Days_Nesting, Breeding_Period, DSR_BS))
write(c(t(DSR_Final)), location.txt, append=T, ncolumns=3)
}
dsr_data-read.delim(location.txt, header=F, sep=)
attach(dsr_data)
scatterplot3d(V1, V2, V3, grid=F, box=T, pch=20, xlim=c(1,
55),ylim=c(1,118), zlim=c(0, 1))
version
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 6.0
year 2007
month 10
day03
svn rev43063
language R
version.string R version 2.6.0 (2007-10-03)
--
Bret A. Collier, Ph.D.
Department of Wildlife and Fisheries Sciences
Texas AM University
College Station TX 77843
979-458-0500; [EMAIL PROTECTED]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Find A, given B where B=A'A
Michael Gormley wrote: Thanks for your help, all those who submitted responses. I do not need a specific matrix A, any solution will do. With this said, is it possible to specify the dimensions of the A matrix in the decompostion? For example, if A is a 2X1 matrix then A'A=B would be a 2X2 as well. B would have rank 1 then, and a pivoted Choleski decomposition has zero rows e.g. B - outer(c(2,3),c(2,3)) B [,1] [,2] [1,]46 [2,]69 chol(B, pivot=TRUE) [,1] [,2] [1,]32 [2,]00 attr(,pivot) [1] 2 1 attr(,rank) [1] 1 Warning message: In chol.default(B, pivot = TRUE) : matrix not positive definite an eigen() decomposition could also be used. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] mosaic row and column order
On 31/10/2007 5:50 PM, Achim Zeileis wrote: On Wed, 31 Oct 2007, Michael Kubovy wrote: Dear R-helpers, I wasn't able to find out how to override the alphabetical ordering of the rows and columns in a vcd::mosaic plot. I would like to have them each ordered by numerical values in a different column of the data frame that contains the contingency data. mosaic() uses the same ordering as in the levels() of your factor. You probably created the factor with an alphabetical ordering (which is the default if the input is a character vector), e.g.: ## character vector x - c(a, b, b, a, c) ## use alphabetical default f - factor(x) f This prints [1] a b b a c Levels: a b c as you'd expect. ## change ordering in existing factor levels(f) - c(b, c, a) f This prints [1] b c c b a Levels: b c a which might be a surprise if you wanted the order c(a, b, b, a, c). If you don't want to change the values, use f - factor(f, levels=c(b, c, a)) f which prints [1] a b b a c Levels: b c a Duncan Murdoch ## create from scratch I would be most grateful for a pointer toward the solution. Thanks, MK _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Don't understand write.csv default: Why is column name for column of row names blank?
Would this be good enough: # example using builtin BOD data frame write.csv(cbind(Z = row.names(BOD), BOD), row.names = FALSE) On Oct 31, 2007 7:04 PM, Earl F. Glynn [EMAIL PROTECTED] wrote: I've always been frustrated that R never puts a label on the column name for a column of row names. This is usually the key in a database table, and it sure would be nice to carry a key name along with the data instead of the field being blank. So, why is it a good idea for it to be blank? ?write.csv says this: CSV files By default there is no column name for a column of row names. If col.names = NA and row.names = TRUE a blank column name is added, which is the convention used for CSV files to be read by spreadsheets. This last sentence doesn't make any sense to me: the convention used for CSV files to be read by spreadsheets. Spreadsheets don't care whether this column is blank or has useful information. R may have a convention to leave the column name for a column of row names blank (I don't understand why), but most other applications do not. I seem to spend a lot of time trying to get this blank field fixed since it's just not right to have a database key be blank. I often must manually edit the .csv file written by R since that's easier than the kludge to put the column names in a new column one so they can have a column name too, and then suppress the row names in the write.csv. What am I missing? Is there an easy way to fill this blank field with a useful name for a database key when using write.csv defaults? Thanks for any insight on this. efg Earl F. Glynn Scientific Programmer Stowers Institute for Medical Research __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Don't understand write.csv default: Why is column name for column of row names blank?
The nice thing about R is that you can always extend it in any manner
that you want. Here is some code (that you could put in a function
wrapper) that will do what you want. It just creates the header,
writes it out, and then the dataframe itself without a column header:
out - file('/tempxx.csv', 'w') #output file
header - paste(c(DB KEY, names(BOD)), collapse=',') # column names
cat(header, '\n', file=out) #write it out
write.table(BOD, out, sep=',', col.names=FALSE) #rest of table
close(out)
On 10/31/07, Earl F. Glynn [EMAIL PROTECTED] wrote:
I've always been frustrated that R never puts a label on the column name for
a column of row names. This is usually the key in a database table, and
it sure would be nice to carry a key name along with the data instead of
the field being blank. So, why is it a good idea for it to be blank?
?write.csv says this:
CSV files
By default there is no column name for a column of row names. If
col.names = NA and row.names = TRUE
a blank column name is added, which is the convention used for CSV files
to be read by spreadsheets.
This last sentence doesn't make any sense to me: the convention used for
CSV files to be read by spreadsheets. Spreadsheets don't care whether this
column is blank or has useful information. R may have a convention to leave
the column name for a column of row names blank (I don't understand why),
but most other applications do not.
I seem to spend a lot of time trying to get this blank field fixed since
it's just not right to have a database key be blank. I often must
manually edit the .csv file written by R since that's easier than the kludge
to put the column names in a new column one so they can have a column name
too, and then suppress the row names in the write.csv.
What am I missing? Is there an easy way to fill this blank field with a
useful name for a database key when using write.csv defaults?
Thanks for any insight on this.
efg
Earl F. Glynn
Scientific Programmer
Stowers Institute for Medical Research
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Axis Location/Data view in scatterplot3d
On 31/10/2007 5:51 PM, Bret Collier wrote:
All,
I constructed a fairly simple plot using the below and scatterplot3d.
However, the axis locations in scatterplot3d seem to 'hide' quite a bit
of the points in my graphic based on the viewing angle, hence not
adhering to Tufte's rules. I tried to determine if I could rotate the
graph and relocate all three axis (origin (0, 0, 0))so they would be at
the back left so the plotted points would slope down toward the viewer.
Using 'angle' and 'axis' did not get me any closer. Does anyone have
any suggestions?
TIA,
Bret
for(Days_Nesting in 1:55){
Breeding_Period-1:118
DSR_RGWT= exp(6.6205449-0.0589883*Days_Nesting)/(1+
exp(6.6205449-0.0589883*Days_Nesting))
DSR_BS-DSR_RGWT^Breeding_Period
DSR_Final-as.data.frame(cbind(Days_Nesting, Breeding_Period, DSR_BS))
write(c(t(DSR_Final)), location.txt, append=T, ncolumns=3)
}
dsr_data-read.delim(location.txt, header=F, sep=)
attach(dsr_data)
scatterplot3d(V1, V2, V3, grid=F, box=T, pch=20, xlim=c(1,
55),ylim=c(1,118), zlim=c(0, 1))
The plot3d() function in rgl allows manipulation of the viewpoint, and
fairly flexible specification of the axes.
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] RWeka and naiveBayes
Hi I'm trying to use RWeka to use a NaiveBayes Classifier(the Weka version). However it crashes whenever there is a NA in the class Gender Here is the.code I have with d2 as the data frame. The first call to NB doesn't make R crash but the second call does. NB - make_Weka_classifier(weka/classifiers/bayes/NaiveBayesSimple) d2[,64]-d2$Gender==M NB(Gender~age,d2,na.action=na.exclude) #1st call d2$Gender[d2$Gender==]-NA valid.set-(!is.na(d2$Gender)(!is.na(d2$age))) NB(formula=Gender~age,data=d2[valid.set,],subset=valid.set,na.action=na.exclude) Anybody have an idea how to fix this. or a very detailed explanation of how to use naiveBayes function from e1071 package? I tried using this function , too. However I can't figure out what the returning error means? naiveBayes(formula=Gender~age,data=d2[valid.set,],subset=valid.set,na.action=na.exclude) I get the following error Error in tapply(var, y, mean, na.rm = TRUE) : arguments must have same length Thanks -- Sancar Adali Johns Hopkins University Graduate Student __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 me in Cochran armitage trend test Coding
Dear sir, I am Shibu John from Thrombosis Research Institute India. It is a multidisciplinary organisation concerned with the interrelated problems of thrombosis and atherosclerosis. I was searching for Cochran armitage trend test program in R. Then I had seen your R coding for C-A trend test. I tried that in the R software. But I cant run the program due the [Error: could not find function independence_test]. Where is the declaration of this function? I was trying the trend test for Genotype frequency in Cases and controls. So I would like to know how to do the Monte carlo simulation test with Cochran armitage trend test. Sir can you please help me to solve the problem. Here I copied the codes from R library(coin) Loading required package: survival Loading required package: splines Loading required package: mvtnorm Error: package 'modeltools' required by 'coin' could not be found In addition: Warning messages: 1: package 'coin' was built under R version 2.6.0 2: package 'survival' was built under R version 2.5.1 3: package 'mvtnorm' was built under R version 2.5.1 lungtumor - data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)), + tumor = c(rep(c(0, 1), c(38, 2)), + rep(c(0, 1), c(43, 7)), + rep(c(0, 1), c(33, 15 table(lungtumor$dose, lungtumor$tumor) 0 1 0 38 2 1 43 7 2 33 15 independence_test(tumor ~ dose, data = lungtumor, teststat = quad) Error: could not find function independence_test sincerely, Shibu John Research Assistant Department of Bioinformatics Thrombosis Research Institute Narayana Hrudayalaya 258/A Bommasandra Industrial Area, Anekal Taluk Bangalore 560099, India __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lattice: par.ylab.text alpha ?
On 11/1/07, Folkes, Michael [EMAIL PROTECTED] wrote: wohoo! A bug. I know I wasn't the first to find it, but I had a hunch this time that it was going to be a bug and not just my poor understanding. I wasn't really thinking as just ylab= works fine too. I think I was hoping to squeeze it (the ylab) closer to the axis w/o axis labels. There's nothing specially meant for ylab, but you can supply a factor for all layout widths and heights; e.g., compare xyplot(1 ~ 1, ylab = foo, par.settings = list(layout.widths = list(ylab = 2))) xyplot(1 ~ 1, ylab = foo, par.settings = list(layout.widths = list(ylab = 0))) Now that we're on topic. If I turn off the axes lines using alpha, is there a way to turn on just axis 1/2/3/4? Not sure exactly what you mean, but try variants of xyplot(1 ~ 1, scales = list(alternating = 0/1/2/3, tck = 0/1)) -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Updating packages
I've just updated from R-2.5.1 to R-2.6.0, under Windows XP. Is there a simple way to reload into R-2.6.0 all the packages I had loaded under R-2.5.1? Thanks, John = John Field Consulting Pty Ltd 10 High Street, Burnside SA 5066 Australia Phone +61 8 8332 5294 or +61 409 097 586 Fax +61 8 8332 1229 Email [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] loops sampling
Hi,
I'm new to R (and statistics) and my boss has thrown me in the deep-end with
the following task:
We want to evaluate the impact that sampling size has on our ability to create
a robust model, or evaluate how robust the model is to sample size for the
purpose of cross-validation i.e. in our current project we have collected a
series of independent data at 250 locations, from which we have built a
predictive model, we want to know whether we could get away with collecting
fewer samples and still build a decent model; for the obvious operational
reasons of cost, time spent in the field etc..
Our thinking was that we could apply a bootstrap type procedure:
We would remove 10 records or samples from the total n=250 and then replace
those 10 removed with replacements (or copies) from the remaining 240. With
this new data-frame we would apply our model and calculate an r², we would then
repeat through looping 1000 times before generating the mean r² from those 1000
r² values generated. After which we would start the process again by remove 20
samples from our data with replacements from the remaining 230 records and so
on...
Below is a simplified version of the real code which contains most of the basic
elements. My main problem is I'm not sure what the 'for(i in 1:nboot)' line is
doing, originally I though what this meant was that it removed 1 sample or
record from the data which was replaced by a copy of one of the records from
the remaining n, such that 'for(i in 10:nboot)' when used in the context of the
below code removed 10 samples with replacements as I have said above. I'm
almost positive that this isn't happening and if not how can I make the code
below for example do what we want it to?
library(utils)
#data
a - c(5.5, 2.3, 8.5, 9.1, 8.6, 5.1)
b - c(5.2, 2.2, 8.6, 9.1, 8.8, 5.7)
c - c(5.0,14.6, 8.9, 9.0, 9.1, 5.5)
#join
abc - data.frame(a,b,c)
#set column names
names(abc)[1]-y
names(abc)[2]-x1
names(abc)[3]-x2
abc2 - abc
#sample
abc3 - as.data.frame(t(as.matrix(data.frame(abc2
n - length(abc2)
npboot.function - function(nboot)
{
boot.cor - vector(length=nboot)
for(i in 1:nboot){
rdata - sample(abc3,n,replace=T)
abc4 - as.data.frame(t(as.matrix(data.frame(rdata
model - lm(asin(sqrt(abc4$y/100)) ~ I(abc4$x1^2) + abc4$x2)
boot.cor[i] - cor(abc4$y, model$fit)}
boot.cor
}
bt.cor - npboot.function(nboot=10)
bootmean - mean(bt.cor)
Any assistance would be greatly appreciated, also the sooner the better as we
are under pressure to reach a conclusion.
Cheers,
Garth
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help me in Cochran armitage trend test Coding
Shibu John wrote: Dear sir, I am Shibu John from Thrombosis Research Institute India. It is a multidisciplinary organisation concerned with the interrelated problems of thrombosis and atherosclerosis. I was searching for Cochran armitage trend test program in R. Then I had seen your R coding for C-A trend test. I tried that in the R software. But I can’t run the program due the [Error: could not find function independence_test]. Where is the declaration of this function? In the `coin' package. I was trying the trend test for Genotype frequency in Cases and controls. So I would like to know how to do the Monte carlo simulation test with Cochran armitage trend test. Sir can you please help me to solve the problem. Here I copied the codes from R library(coin) Loading required package: survival Loading required package: splines Loading required package: mvtnorm Error: package 'modeltools' required by 'coin' could not be found So, you need to install package `modeltools'... In addition: Warning messages: 1: package 'coin' was built under R version 2.6.0 2: package 'survival' was built under R version 2.5.1 3: package 'mvtnorm' was built under R version 2.5.1 Since you've failed to provide the result of `sessionInfo()', we don't know which version of R and the packages you've installed or your platform. In any case, packages should be built using the R version you intend to use them under. Here, judging from the above warnings, you have package built under a mix of R 2.6.0 and 2.5.1. And since it complains about both, I guess your running neither. So, (re-)install R 2.6.0, the `coin' package and all its dependencies and everything is more likely to work. (As it does for me.) HTH, Henric lungtumor - data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)), + tumor = c(rep(c(0, 1), c(38, 2)), + rep(c(0, 1), c(43, 7)), + rep(c(0, 1), c(33, 15 table(lungtumor$dose, lungtumor$tumor) 0 1 0 38 2 1 43 7 2 33 15 independence_test(tumor ~ dose, data = lungtumor, teststat = quad) Error: could not find function independence_test sincerely, Shibu John Research Assistant Department of Bioinformatics Thrombosis Research Institute Narayana Hrudayalaya 258/A Bommasandra Industrial Area, Anekal Taluk Bangalore 560099, India __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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.
