Re: [R] help comparing two median with R
nonparametric confidence interval for the median (unrelated to Wilcoxon) but none exists for the mean. Cheers, Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 message when building a package
Please update your Xcode tools. According to http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html 2.2 or later is needed, and 2.4.1 is current. On Tue, 30 Jan 2007, C. Lillian Yau wrote: I'm trying to build a package. The machine is PowerPC G4 with Mac OS 10.4.8, and I'm using R2.4.1. I get R CMD build roots working, and it created roots.tar.gz. But I get the following message when I run R CMD INSTALL -l ../myrlibrary roots.tar.gz == * Installing *source* package 'roots' ... ** libs ** arch - ppc gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include-fPIC -g -O2 -c fifrt.c -o fifrt.o gfortran-4.0 -arch ppc -fPIC -g -O2 -c fthrt.f -o fthrt.o gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o roots.so fifrt.o fthrt.o -lgfortran -lgcc_s -lSystemStubs -lmx -lSystem -L/Library/Frameworks/R.framework/Resources/lib/ppc -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Resources/lib/ppc/libRblas.dy lib /usr/bin/libtool: unknown option character `m' in: -macosx_version_min [...] -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] building R on freebsd 6.2 (amd64)
On Thu, 18 Jan 2007, Hiroyuki Kawakatsu wrote: Hi, I updated my os to freebsd 6.2 and built R-patched with no changes in configure. I pass make check and copy the R executable to /usr/local/bin/R. Then when I start R, I get /libexec/ld-elf.so.1: Shared object libRblas.so not found, required by R and have to copy/link the two shared object files (libRblas.so and libRlapack.so) to somewhere visible like /usr/local/lib/ as well. I didn't have to do this last step in freebsd 6.1. Is there some configure setting I can use to avoid having to move the two shared object files? The R front end sets LD_LIBRARY_PATH to include the place it puts libR.so. It looks like that is not effective on your machine, but you will have to investigate for us why. I am pretty sure other FreeBSD users (6.2 and 7) on AMD64 reported success on R 2.4.x. How does FreeBSD 6.2 handle 64-bit systems? Most OSes would use /usr/local/lib64, and there is a configure setting LIBnn to cover that issue. Another solution for ELF systems is to include R_HOME/lib in the list of directories known to ldconfig. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Seeking advice on lattice package in R2.4.0 concerning stripplot
The problem looks to be that you are specifying the types of symbols in two ways: pch=c(0,3,6,5), points = Rows(trellis.par.get(superpose.symbol),1:4), The simplest thing to do is to run your code directly on the pdf() device, but you could experiment with other ways of setting the key. (We don't have the data, so cannot test these ideas.) On Sat, 16 Dec 2006, Dr L. Y Hin wrote: Dear all, I am using the R 2.4.0 environment on Windows XP SP2 machine and trying to use the lattice package version 0.14-9 which you have kindly written to share with the R community. I have a question concerning the stripplot which I'd be very grateful if you can kindly advise me on: I used the dataset called trydata to plot a graph using stripplot (dataset attached), and the scripts used to procude the plot is as follows: trydata-dget(trydata) stripplot(Position~Count|y*Grouping,jitter=T,group=subtype, data=trydata,xlab=Count rate (%), pch=c(0,3,6,5), key=list(text=list(c(GS in front, GS at the back, MS in front,MS at the back)), points = Rows(trellis.par.get(superpose.symbol),1:4), columns=2)) When I plotted the graph and viewed it on R, the legend and the datapoint shapes are correct. However, when I export it into .pdf form using the pulldown menu in R, the legend for GS in front is incorrect. Instead if being a prism, it became a circle. How can I get around this? I've attached the figure thus generated in pdf form for your kind consideration. Specifically, how can I modify the specifications in the command to produce the correct pch type in the legend as in the chart itself? Thank you very much in advance for your kind advice. Best Lin -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] *** caught segfault *** error
On Fri, 1 Dec 2006, Juanjo Abellan wrote: [...] Sorry, I didn't understand the issue about the locale and the C locale that Prof Ripley mentioned. Where could I learn about that? In the R-admin manual (but Roger will understand). -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install bioconductor
You are missing both the library and headers for what would be called either zlib or libz. (On an RPM-based system it would be zlib-devel that is missing.) However, this is the wrong list for questions anout installing BioC packages: please see the R posting guide. (And probably the packages should check for the headers like zlib.h as well as for -lz, something which is best discussed on the BioC list.) On Sat, 11 Nov 2006, David Hajage wrote: Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package affy : Error: package 'affy' required by 'makecdfenv' could not be found I have tryed to install 'makecdfenv' with the command : getBioC(makecdfenv) But I have this message : Running getBioC version 0.1.8 with R version 2.4.0 Running biocinstall version 1.9.9 with R version 2.4.0 Your version of R requires version 1.9 of Bioconductor. Avis dans install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using /usr/local/lib/R/site-library also installing the dependencies 'affy', 'affyio' essai de l'URL ' http://bioconductor.org/packages/1.9/bioc/src/contrib/affy_1.12.1.tar.gz' Content type 'application/x-gzip' length 1370295 bytes URL ouverte == downloaded 1338Kb essai de l'URL ' http://bioconductor.org/packages/1.9/bioc/src/contrib/affyio_1.2.0.tar.gz' Content type 'application/x-gzip' length 57410 bytes URL ouverte == downloaded 56Kb essai de l'URL ' http://bioconductor.org/packages/1.9/bioc/src/contrib/makecdfenv_1.12.0.tar.gz ' Content type 'application/x-gzip' length 3222836 bytes URL ouverte == downloaded 3147Kb * Installing *source* package 'affyio' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... no [etc] -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding predicted values as a new variable in a data frame
?na.exclude should help you: my guess is that you asked (by using the default) na.action = na.omit) for rows with missing values to be excluded from the residuals. But since you have not mentioned missing values, we have to guess what 'for some reason' was: please note the footer of this messag. On Thu, 14 Sep 2006, Robi Ragan wrote: I am running a regression: ols.reg1 - lm(y ~ x1 + x2 + x3 + x4) on a data.frame Hmm, no data frame is mentioned: you want a data= argument. and then generating fitted values: y.hat - ols.reg1$fitted.values Please use the accessor functions and not dive into the internal details, e.g. y.hat - fitted(ols.reg1) BTW: where did you get the use of ols.reg1$fitted.values from? Then I would like to add these fitted values to the data.frame as a new variable. The problem is that when the values are predicted the resulting output has too few rows. for some reason certian observations do not get predicted values. So this shrinks the column down and I then cannot combine the output into the original data.frame. fit - lm(formula, data=data_frame, na.action=na.exclude) data_frame$fitted - fitted(fit) If someone could please help I would apreciate it. Stata automatically adds a new column to the data set when you find the fitted values. So having to fight with R just to do something I used to routimely do has made me think of turning back to the dark side. I hope I have just missed something trival in all the help files I have been looking through. The above looks trivial to me. It was not in R or S when lm was first introduced (1991 White Book), but was added last century (thanks to the ideas and persistent advocacy of Terry Therneau). -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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 setting options(error=recover) in my Rprofile.site
On Thu, 14 Sep 2006, Marcus, Jeffrey wrote: I'd like to be able to set options(error=recover) in my Rprofile.site file. When I do this I get the message Error in options(error = recover) : object recover not found I assume this is because the utils package (where recover and dump.frames are defined) has not been loaded at the time I make this call. I suppose I could explicitly do library(utils) before setting the options even though it will be loaded again when the default packages are loaded. It will not be loaded again. Any simpler suggestions of how to get options(error=recover) set automatically every time I start R? options(error=utils::recover) More generally, is there a way to have code executed on startup but *after* the default packages are loaded? Load the default packages yourself in your startup code, by calling .First.sys() (and resetting it to avoid the slight overhead of subsequent require() calls if you want). -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Parameterization puzzle
On Fri, 21 Jul 2006, Berwin A Turlach wrote:
G'day all,
BDR == Prof Brian Ripley [EMAIL PROTECTED] writes:
BDR R does not know that poly(age,2) and poly(age,1) are linearly
BDR dependent.
Indeed, I also thought that this is the reason of the problem.
BDR (And indeed they only are for some functions 'poly'.)
I am surprised about this. Should probably read the help page of
'poly' once more and more carefully.
My point was perhaps simpler: if you or I or Murray had a function poly()
in our workspace, that one would be found, I think. (I have not checked
the ramifications of namespaces here, but I believe that would be the
intention, that formulae are evaluated in their defining environment.) So
omly when the model matrix is set up could the linear dependence be known
(and there is nothing in the system poly() to tell model.matrix).
What is sometimes called extrinsic aliasing is left to the fitting
function, which seems to be to do a sensible job provided the main effect
is in the model. Indeed, including interactions without main effects (as
Murray did) often makes the results hard to interpret.
BDR I cannot reproduce your example ('l' is missing), [...]
My guess is that 'l' is 'pyears'. At least, I worked under that
assumption.
Apparently l = log(pyears), which was my uncertain guess.
Interestingly, on my machine (using R 2.3.1, 2.2.1 and 2.1.1) I cannot
fit any of the Poisson GLM that Murray tried. I always get the error
message:
Error: no valid set of coefficients has been found: please supply starting
values
Related to the offset, I believe.
But I have to investigate this further. I can fit binomial models
that give me similar answers.
BDR [...] but perhaps
BDR glm(deaths ~ poly(age,2) + poly(age,1)*Smoke + offset(l),
BDR poisson)
BDR was your intention?
In this parameterisation a 'poly(age,1)' term will appear among the
coefficients with an estimated value of NA since it is aliased with
'poly(age, 2)1'. So I don't believe that this was Murray's intention.
The only suggestion I can come up with is:
summary(glm(cbind(deaths, l-deaths) ~ age*Smoke+I(age^2), family=binomial))
[...]
Coefficients:
Estimate Std. Error z value Pr(|z|)
(Intercept) -10.798950.45149 -23.918 2e-16 ***
age2.378920.20877 11.395 2e-16 ***
SmokeYes 1.445730.37347 3.871 0.000108 ***
I(age^2) -0.197060.02749 -7.168 7.6e-13 ***
age:SmokeYes -0.308500.09756 -3.162 0.001566 **
[...]
Which doesn't use orthogonal polynomials anymore. But I don't see how
you can fit the model that Murray want to fit using orthogonal
polynomials given the way R's model language operates.
So I guess the Poisson GLM that Murray wants to fit is:
glm(deaths~ age*Smoke+I(age^2)+offset(l), family=poisson)
Cheers,
Berwin
== Full address
Berwin A Turlach Tel.: +61 (8) 6488 3338 (secr)
School of Mathematics and Statistics+61 (8) 6488 3383 (self)
The University of Western Australia FAX : +61 (8) 6488 1028
35 Stirling Highway
Crawley WA 6009e-mail: [EMAIL PROTECTED]
Australiahttp://www.maths.uwa.edu.au/~berwin
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] failed installing rgl
On FC5: roc% rpm -q --file /usr/include/GL/glu.h mesa-libGLU-devel-6.4.2-6.FC5.3 Do check what the R-admin manual says about -devel RPMs. On Thu, 20 Jul 2006, James Foadi wrote: Dear all, I have tried installing rgl with the usual command: R CMD INSTALL rgl_0.67-2.tar.gz Differently from what happened last time I have succesfully installed this package, this time there was a failure: ... ...g++ -I/usr/lib/R/include -I/usr/lib/R/include -I -DHAVE_PNG_H -I/usr/include/libpng12 -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c api.cpp -o api.o In file included from glgui.hpp:9, from gui.hpp:11, from rglview.h:10, from Device.hpp:11, from DeviceManager.hpp:9, from api.cpp:14: opengl.hpp:23:20: error: GL/glu.h: No such file or directory Disposable.hpp:13: warning: ÿÿstruct IDisposeListenerÿÿ has virtual functions but non-virtual destructor types.h:77: warning: ÿÿclass DestroyHandlerÿÿ has virtual functions but non-virtual destructor gui.hpp:56: warning: ÿÿclass gui::WindowImplÿÿ has virtual functions but non-virtual destructor gui.hpp:90: warning: ÿÿclass gui::GUIFactoryÿÿ has virtual functions but non-virtual destructor pixmap.h:39: warning: ÿÿclass PixmapFormatÿÿ has virtual functions but non-virtual destructor api.cpp: In function ÿÿvoid rgl_user2window(int*, int*, double*, double*, double*, double*, int*)ÿÿ: api.cpp:707: error: ÿÿgluProjectÿÿ was not declared in this scope api.cpp: In function ÿÿvoid rgl_window2user(int*, int*, double*, double*, double*, double*, int*)ÿÿ: api.cpp:735: error: ÿÿgluUnProjectÿÿ was not declared in this scope make: *** [api.o] Error 1 chmod: cannot access `/usr/lib/R/library/rgl/libs/*': No such file or directory ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' ... ... It is clear that glu.h cannot be found during installation and, indeed, I have checked and there is no glu.h under /usr/include/GL. Any suggestion on how I could proceed? I am using FEDORA CORE 5. By typing glxinfo it seems that glu 1.3 is installed. But where's glu.h, then? Many thanks J -- Dr James Foadi Department of Physics University of York York YO10 5DD email: [EMAIL PROTECTED] Tel: 0044 1904 434622 Mobile: 0044 7740 678548 ___ All New Yahoo! Mail ? Tired of [EMAIL PROTECTED]@! come-ons? Let our SpamGuard protect you. http://uk.docs.yahoo.com/nowyoucan.html -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] install RMySQL under Mac OS X 10.4.7
If this is R as installed from CRAN, it is by default looking for a binary
and not a source package.
Please study the `R Installation and Administration' manual.
On Wed, 5 Jul 2006, Luo Weijun wrote:
Hello All,
I tried to install RMySQL package, but the error
messages says there is no such package, even though I
did see RMySQL is there in the contributed package
list in all mirror sites of CRAN I tried. Not sure
what is the problem.
mysql.home - '/usr/local/mysql'
Sys.putenv('PKG_CPPFLAGS'=paste('-I',file.path(mysql.home,'include'),sep=''))
Sys.putenv('PKG_LIBS'=paste('-L',file.path(mysql.home,'lib'),'
-lmysqlclient',sep=''))
install.packages('RMySQL', repos =
http://www.biometrics.mtu.edu/CRAN/,dependencies =T)
dependency ''RMySQL'' is not available
install.packages('RMySQL', repos =
http://www.biometrics.mtu.edu/CRAN/;)
Warning in download.packages(pkgs, destdir = tmpd,
available = available, :
no package 'RMySQL' at the repositories
I tried download the package manually under unix, and
install it from within R, and no luck too.
cd ~/download/R
curl -O
http://www.biometrics.mtu.edu/CRAN/src/contrib/RMySQL_0.5-7.tar.gz
And where did you run R from? I think you needed to give a full path here
install.packages( 'RMySQL_0.5-7.tar.gz', repos =
NULL)
Error in gzfile(file, r) : unable to open connection
In addition: Warning message:
cannot open compressed file
'RMySQL_0.5-7.tar.gz/DESCRIPTION'
sessionInfo()
Version 2.3.0 (2006-04-24)
powerpc-apple-darwin8.6.0
attached base packages:
[1] methods stats graphics grDevices
utils datasets
[7] base
could anybody tell me what happens here, and how to
fix the problem? Thank you so much!
Weijun
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
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@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R and Java
On Tue, 9 May 2006, Erin Hodgess wrote: Dear R People: Where are the rJava and SJava packages, please? I looked for them to download but they are nowhere to be found. rJava is on CRAN: http://cran.r-project.org/bin/windows/contrib/2.3/rJava_0.4-1.zip (The capitalization can cause this to sort in unexpected ways, so you can miss it in a list.) Do they have their own list serves, please? SJava is part of Omegahat, at http://www.omegahat.org/RSJava/ I think that there is no Windows binary currently available: if there were, it would be at http://www.omegahat.org/R/bin/windows/contrib/2.3/ and accessible by choosing Omegahat as a repository from the Packages | Select Repositories menu. rJava was a page at http://stats.math.uni-augsburg.de/rJava/ R Windows 2.3. Thanks in advance! Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] ___ -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to access results of survival analysis
The solution is to use a separate function to do this (and call it from the
print method).
On Mon, 8 May 2006, Heinz Tuechler wrote:
At 12:55 07.05.2006 +0100, Prof Brian Ripley wrote:
On Sun, 7 May 2006, Heinz Tuechler wrote:
Hello Xiaochun Li!
Thank you for submitting the function. At the time I had that problem I
solved it in a somewhat different way.
I changed a few lines in the print.survfit method. I introduced a parameter
ret.res=FALSE set to false to preserve the normal behaviour of print.
The second last line invisible(x) I changed to:
if (ret.res)
invisible(list(x,x1))
else
invisible(x)
So print.survfit returned the results. Of course, Your method has the
advantage to work as long as the output structure of print.survfit does not
change. At the end I would prefer the original function to be changed and
when I find the time I will submit a worked proposal to Thomas Lumley, the
maintainer of the survival package. In that way it would be available also
in future versions of survival.
But all print() methods are required to return their first argument
unchanged, so
foo
print(foo)
do the same thing. See ?print.
--
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
I see that my proposal is against the rules.
So what would be a correct solution? Using the (expanded) example from
Xiaochun Li, you see that print(fit1) does not _simply_ print its first
argument, but calculates the median and its confidence interval.
What would be the correct way to access these values?
# example:
library(survival)
fit1 - survfit(Surv(time, status) ~ 1, data=aml)
print(fit1)
Call: survfit(formula = Surv(time, status) ~ 1, data = aml)
n events median 0.95LCL 0.95UCL
23 18 27 18 45
smed - function(x) {
ox - capture.output(print(x))
n - length(ox)
tmp - t(sapply(ox[4:n],
function(l) strsplit(l, split=' +')[[1]]))
nres - strsplit(ox[3],split=' +')[[1]][2:6]
res - matrix(as.numeric(tmp[,2:6]), ncol=5,
dimnames=list(tmp[,1], nres))
res
}
sf1 - smed(fit1)
sf1
Lacking experience in R-programming, my personal opinion is that
calculations like the median and the confidence interval should not be only
side effects of a print command but accessible result objects of a
corresponding function.
Heinz Tüchler
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
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Re: [R] error in color-labeling in plot.lm
On Mon, 8 May 2006, Ulrich Halekoh wrote: I want to label groups of points in the plot of residuals against predicted values generated by plot.lm(). Labelling the points by color x-1:15 y-rnorm(15) f-factor(rep(c(1:3),each=5)) g-glm(y~x) plot(g,which=1,col=c(1,2,3)[f]) I receive the error message Error in title(main, sub, xlab, ylab, line, outer, ...) : graphical parameter col has the wrong length How can I resolve the error? Well, the help does say ...: other parameters to be passed through to plotting functions. and it really is unclear what you intended 'col' to refer to. But as title() is not going to make use of it, it should accept it. I'll see if I can adapt it suitably. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Link to useR! 2006 from ww.r-project.org not working
Yes, this has been reported to the webmasters (not really much point in telling a list). cran.r-project.org and www.r-project.org now point at machines at wu-wien.ac.at (the DNS was changed in the last 24 hours). I have also found that rsync is not being allowed through (e.g. for tools/rsync-recommended) and ftp cannot see the R data area. Doubtless it will all be back to normal in a day or two. On Wed, 3 May 2006, Pfaff, Bernhard Dr. wrote: I noticed that: http://www.r-project.org/useR-2006/ seems to be inexistent (page not found). Try http://www.ci.tuwien.ac.at/Conferences/useR-2006/ -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Mixture normal distribution
We did get your previous message. See the posting guide about what to do if you do not get an answer. See MASS4, chapter 16 (and see the FAQ for what MASS4 is) for fitting mixtures of normals and testing their fit. I want to know how to read the data to txt file. What does that mean? (You 'read from' or 'write to'.) On Wed, 8 Feb 2006 [EMAIL PROTECTED] wrote: Dear R helper, I hope that u can help me to sort out my problem because I sent an E-mail last night to R-list but I have not receive any help and at the same time I think this problem is not so hard. I have used the following functions before K-10 prime-c(2,3,5,7,11,13,17) UN-seq(1:K)%*%t(sqrt(prime)) U1-UN-as.integer(UN) U-matrix(qnorm(U1),K,7) U [,1][,2][,3][,4] [,5] [,6] [1,] -0.2167193 0.61902728 -0.71900806 0.37387492 -0.47715805 0.2677426 [2,] 0.9479680 -0.09010569 -0.06990169 -0.54900030 0.34047235 -0.8026015 [3,] -0.6978334 -0.85544499 0.54814530 1.53212280 1.64363675 0.9026864 [4,] 0.4038929 1.46253909 1.59168198 0.20958766 -0.62343558 -0.1962555 [5,] -1.4678844 0.41315654 -0.91407055 -0.74294809 0.20989183 -1.9148412 [6,] -0.0369025 -0.27331681 -0.21109168 1.14796196 1.28012119 0.3406266 [7,] 1.2786790 -1.15348516 0.39201340 0.05080407 -0.78449952 -0.7099779 [8,] -0.4853656 1.06431267 1.21882042 -0.97005119 0.08280907 1.0127500 [9,] 0.6065405 0.22357828 -1.15223725 0.88440727 1.03481830 -0.1257587 [10,] -1.0707736 -0.46627852 -0.35664238 -0.10670096 -0.96909898 -1.5936006 [,7] [1,] -1.15960110 [2,] -0.68646092 [3,] -0.33366316 [4,] -0.01899511 [5,] 0.29375681 [6,] 0.63913903 [7,] 1.08816734 [8,] 2.16601566 [9,] -1.23750068 [10,] -0.73537275 Now I want instead of using (qnorm) the inverse of slandered normal distribution, I want to use the mixture of normal distribution, and also, I want to know how to read the data to txt file. Many thanks for your help in advance. Al-Eid -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
On Wed, 8 Feb 2006, Duncan Murdoch wrote: On 2/8/2006 4:53 AM, Bj?rn-Helge Mevik wrote: Why don't you test it yourself? E.g., set.seed(42) bob1 - rnorm(1000,0,1) set.seed(42) bob2 - rnorm(500,0,1) bob3 - rnorm(500,0,1) identical(bob1, c(bob2, bob3)) I won't tell you the answer. :-) This isn't really something that can be proved by a test. Perhaps the current implementation makes those equal only because 500 is even, or divisible by 5, or whatever... I think the intention is that those should be equal, but in a quick search I've been unable to find a documented guarantee of that. So I would take a defensive stance and assume that there may be conditions where c(rnorm(m), rnorm(n)) is not equal to rnorm(m+n). If someone can point out the document I missed, I'd appreciate it. It's various source files in R_HOME/src/main. Barring bugs, they will be the same. As you know R is free software and comes with ABSOLUTELY NO WARRANTY. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] User error (was arima.sim bug?)
On Tue, 4 Oct 2005, Rolf Turner wrote: Brian Ripley wrote (in response to S. E. Kemp): I am using the arima.sim function to generate some AR time series. However, the function does not seem to produce exactly the same time series when I specify the innov parameter. For example snip Given the fact that I have provided the innovations shouldn't the time series be exactly the same? No. Hint: where does the randomness for the burn-in come from? What then, pray tell, is the point of having the ``innov'' argument at all? To allow non-Gaussian innovations, in particular for use in bootstrapping time series. (This started life in package boot and is used in example(tsboot).) -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R CMD build produces tar error under FreeBSD 5.4
On Sun, 25 Sep 2005, Andrew Robinson wrote: On Sun, Sep 25, 2005 at 12:07:02PM +0100, Prof Brian Ripley wrote: On Sun, 25 Sep 2005, Andrew Robinson wrote: I have constructed a package using package.skeleton(), when I try $ R CMD build foo * checking for file 'foo/DESCRIPTION' ... OK * preparing 'foo': * checking DESCRIPTION meta-information ... OK * cleaning src * removing junk files tar: Option -L is not permitted in mode -x Error: cannot open file 'foo/DESCRIPTION' for reading foo/DESCRIPTION exists and the permissions are correct. The same command works under Linux Fedora 2. The man pages on each OS imply that tar differs across the two platforms. Does anyone have any thoughts on a work-around? No, because R does not use tar -L (which is to do with tape lengths on GNU tar). It does use tar chf and tar xhf. The h modifier would appear to be applicable only to dumps, so at a wild guess the error message means -h is not permitted. Try replacing xhf by xf. Yes, that works. For the record: I removed the 'h' options from all tar calls in You do in principle want them for the chf calls. /usr/local/lib/R/bin/build Thanks for your speedy and accurate response. Andrew -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Help: lda predict
On Sat, 27 Aug 2005, Shengzhe Wu wrote: Hello, I use qda (package MASS) to obtain an object. If there is any function to plot density plot of qda object with one dimension$B!)(B That makes no sense. qda objects do not have a density. Please do study the background material (as you have been repeatedly asked to do). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error in contrasts in step wise regression
On Mon, 27 Jun 2005, Young Cho wrote:
Thanks for the reply. I created a new dataframe and ran step on it. But,
still it does not work.
detach(dat)
attach(ds)
dat - ds[,sapply(ds,nlevels)=2]
dat$Y - Response
detach(ds)
attach(dat)
fmla - as.formula(paste( ~
,paste(collist1[sapply(ds,nlevels)=2],collapse=+)))
fit.s - step(fit.1, direction=forward,scope=list(upper= fmla,lower= ~1))
Start: AIC= -1651.18
Y ~ 1
Error in contrasts-(`*tmp*`, value = contr.treatment) :
contrasts can be applied only to factors with 2 or more levels
R does have debugging tools: please use them.
Also, I was wondering if you know why the followings behave differently
from the above:
Yes, as I have read the help page for step(). Have you? It is discussed
there.
fit.s - step(lm(Y~1),scope=list(upper=~.,lower=~1),)
Start: AIC= -1651.18
Y ~ 1
fit.s - step(fit.1,scope=list(upper=~.,lower=~1),)
Start: AIC= -1651.18
Y ~ 1
I thought ~. uses all other variables in the data frame according to
Introduciton to R.
In contexts where there is a data frame and there is no more specific
documentation, it means `all remaining variables separated by +'.
-Young.
Prof Brian Ripley [EMAIL PROTECTED] wrote:
On Fri, 24 Jun 2005, Young Cho wrote:
Hi,
I have a problem in getting step function work.
This is not coming from step(), but (AFAIK) from model.matrix() called by
lm(). One way to debug it is to try fitting the models directly.
I am getting the following error:
fit1 - lm(Response~1)
fmla - as.formula(paste( ~ ,paste(colnames,collapse=+)))
sfit - step(fit1,scope=list(upper= fmla,lower= ~1),k=log(nrow(dat)))
Start: AIC= -1646.66
Response ~ 1
Error in contrasts-(`*tmp*`, value = contr.treatment) :
contrasts can be applied only to factors with 2 or more levels
But if i count the unique values in each column by
A - NULL
for (ii in 1:length(colnames)){
A[ii] - length(unique( eval(parse(text=paste('dat$',colnames[ii])
}
I do not see any column with only 1 value. Is there some other possible
reason why I am getting the error? Thanks a lot!
It says `levels', not values. So try
sapply(dat, nlevels)
The values can include NA, which is not a level (usually). E.g.
x - factor(c(1, NA))
nlevels(x)
[1] 1
length(unique(x))
[1] 2
(Incidentally, you are assuming variables are found in dat, and you should
use
lm(Response ~ 1, data=dat)
to ensure that. And your calculation can be done more legibly as
sapply(dat, function(x) length(unique(x)))
.)
--
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, UK Fax: +44 1865 272595
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Re: [R] modifications to text.tree function
Is this from package tree? If so treeco is in the namespace but not exported. library(tree) ls(asNamespace(tree)) [1] cv.treedata.tree descendants [4] deviance.tree labels.treemisclass.tree [7] model.frame.tree na.tree.replacenode.match [10] partition.tree plot.tree plot.tree.sequence [13] pred1.tree predict.tree print.summary.tree [16] print.tree prune.misclass prune.tree [19] residuals.tree snip.tree summary.tree [22] text.tree tile.tree tree [25] tree.control tree.depth tree.matrix [28] tree.screens treeco treepl so try e.g. tree:::treeco. On Thu, 12 May 2005, Alexander Sirotkin wrote: Hi. I have to make some minor modifications to the text.tree function - I don't like the way it prints the split labels (they are too long in my case and overlap). I tried to make s simple modification to the text.tree function so that it will limit the number of significant digits in tree labels, but could not - the original function uses some undocumented treeco function, which I can not find. Any ideas ? Thanks. -- Alexander Sirotkin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] programming conventions
On Thu, 31 Mar 2005, Sebastian Luque wrote: I'm trying to make my R scripts more readable by others, so I searched for some R programming conventions and found the following two: - http://www.ci.tuwien.ac.at/Conferences/useR-2004/Keynotes/Maechler.pdf - http://www.maths.lth.se/help/R/RCC the latter being quite extensive. Are there some other sources that might be useful? `Writing R Extensions'. Layout is by far the most common cause of hard-to-read code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] about get stdout from other program
On Fri, 1 Apr 2005, Michael S wrote: if I want to use stdout from other language as my R program input ,which is the best way for design the API,using Pipe function or produce a temporary file,using scan function to read the file ? A file for portability, since pipes do not work well on Windows 9x. A pipe or fifo if you want to wait on output from another program. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] how i can get input from user input
On Thu, 31 Mar 2005, Martin Maechler wrote: BertG == Berton Gunter [EMAIL PROTECTED] on Wed, 30 Mar 2005 10:09:38 -0800 writes: BertG If you are on Windows and want to go GUI, see BertG ?choose.files, ?winMenuAdd, ?winDialog, ?select.list with the big drawback that it will only work on Windows. I don't think that a `big' drawback if you `want to go GUI', as GUI conventions are so different between platforms (and tcltk being different from the `native' one on each platform). But we are beginning to attempt to add platform-independent wrappers to GUI widgets. As Uwe says below, it depends on your context; for relative simple things, however please consider a portable solution, using menu(), readline(), .. BTW, menu() has been improved in R 2.1.0 (alpha -- please test!), and is now connected with select.list() which should work on all platforms (and uses tcltk on Linux when available). To be a bit more specific, menu() has a 'graphics' argument that uses a listbox on Windows, MacOS or tcltk (where available). select.list() works on all platforms, graphically as for menu(graphics=TRUE), otherwise in text mode. I intend to add a tcltk-based version of choose.files(). (One of the problems with tcltk is that its widgets are OS-specific, and getting select.list to choose a reasonable height tooks ages: there needs to a fudge factor of 3 pixels/line on Unix and 1 pixel/line on Windows.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] pictex graphics device and color
On Thu, 31 Mar 2005 [EMAIL PROTECTED] wrote: Is the pictex graphics device known not to support color? Yes, amongst other settings like lwd and metric info for character output. If you read the code you will see that the arguments fg and bg are ignored. In any case, there is no obligation for a graphics device to support transparency, and in particular pictex() predates its introduction into R. As far as I am aware, pictex is a plain TeX package (that also more-or-less works in LaTeX: it is barely mentioned in the LaTeX Companion referred to on the help page, nor covered in any detail in the LaTeX Graphics Companion), and plain TeX per se does not support colour. In R 2.0.1 Patched (2004-11-17), it produced very pretty output: ## pictex(file = modern-metatheonomy.tex, bg = transparent); ## plotData(data); ## dev.off() ... but it appears to have ignored all color information. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [R-help] install problem
On Mon, 21 Mar 2005, Tae-Young Goo wrote: Hello. I've tried to install R to IBM AIX(v.5.1) machine. I've used compile options indicated by R-admin. There are several sets there, so which exactly? Then, I met following error messages. /home/local/R_2.0.1/lib/R/bin/exec/R is unchanged /home/local/R_2.0.1/lib/R/modules/R_X11.so is unchanged /home/local/R_2.0.1/lib/R/modules/internet.so is unchanged Those are not error messages. cp: lapack.so: file was not found. So there were some earlier error messages about that. This error has broken out at the last stage of make install Please let me know what is wrong. Please let us know what you did. In particular AIX is tricky, and you need to follow the instructions in the R-admin.html manual very carefully. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] save (was cl$cluster of kmeans)
On Mon, 7 Mar 2005, XP Sun wrote: hi, all, i had a problem when i used kmeans as follow: No, when you used save()! pp - scan(m0028.data, quiet= TRUE) x - matrix(pp, nc=3, byrow=TRUE) cl-kmeans(x, 4, 20) plot(x, col=cl$cluster) save(cl$cluster, file=m0028.ks, ascii=TRUE) Error in save(cl$cluster, file = m0028.ks, ascii = TRUE) : Object cl$cluster not found when i wanted to save the vector of cluster only, a reflection was thrown out as that. could i save cl$cluster only? how? thank you in advance. You can only save() named objects, not a single element, as its help page says. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R-etiquette
On Sun, 9 Jan 2005, Gabor Grothendieck wrote: Prof Brian Ripley ripley at stats.ox.ac.uk writes: : : On Sun, 9 Jan 2005, Anne wrote: : : I'm about to present a report (for internal use of governmental agency). : I used extensively R , contibuted packages, as well as communications on : the R-list : : As well as citing R, I would like to know how to cite the contributed : packages (it is not so easy, as some have been used exensively, other : marginally, some are called from another package and some were not used : as softwares but gave me insight of how to proceed), as well as thank : the persons who generously responded to my demands on the list... : : Is there an established way of doing that? : : See the citation() function, which works for packages too and a few : authors have taken advantage of the means of customizing it. Could someone point out a few packages that have a CITATION file to use as examples. In a search I did I only found one. It seems you need to learn how to search, as there are *4* in a basic installation of R. gannet% find . -name CITATION ./lmtest/inst/CITATION ./geoR/inst/CITATION ./geoRglm/inst/CITATION ./flexmix/inst/CITATION ./strucchange/inst/CITATION ./dse/dse1/inst/CITATION ./VR/class/inst/CITATION ./VR/MASS/inst/CITATION ./VR/nnet/inst/CITATION ./VR/spatial/inst/CITATION ./limma/inst/CITATION Note too that citation() works without a CITATION file and provides a basis for customization. -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Lazy-loading db setup in the R build process
On 16 Dec 2004, Peter Dalgaard wrote: Simon Pickering [EMAIL PROTECTED] writes: Hi All, I have read the article on lazy-loading in the September R news letter, and think I have at least a vague grasp on what is happening. Am I right in thinking that, assuming I were using the same packages, I could copy the .rdb .rdx files from one installation of R (2.0.0) to another? I ask this as I'm trying to cross-compile R (for ARM), and need to use R itself to perform the lazy-loading db setup (and probably other things) as part of the build process. Therefore I build a native version of R (x86) and pass the path of the native R binary as R_EXE in the arm cross-build Makefiles (in src/library and its sub-directories). This fails with the following error: | make[3]: Entering directory `/home/simon/dev/bk/build/tmp/work/r-2.0.0-r0/R-2.0.0/src/library/base' | building package 'base' | mkdir -p -- ../../../library/base/demo mkdir -p -- | ../../../library/base/man Error in eval(expr, envir, enclos) : may | already be using lazy loading on base Execution halted | make[3]: *** [all] Error 1 | make[3]: Leaving directory `/home/simon/dev/bk/build/tmp/work/r-2.0.0-r0/R-2.0.0/src/library/base' | make[2]: *** [R] Error 1 | make[2]: Leaving directory `/home/simon/dev/bk/build/tmp/work/r-2.0.0-r0/R-2.0.0/src/library' | make[1]: *** [R] Error 1 | make[1]: Leaving directory `/home/simon/dev/bk/build/tmp/work/r-2.0.0-r0/R-2.0.0/src' | make: *** [R] Error 1 My guess is that as the native version has already been built (and enabled lazy-loading, etc.), it's not happy that I'm trying to enable it again. Might this be the case? If so I can see a couple of possible options and I wonder if someone could comment on what may or may not be possible to remedy the problem: * Run the native binary without loading its various database files (is this is possible) No. * Delete the native database files so they can't be used and will be rebuilt for the arm version without complaint No. * Simply copy the database files from the native build to the appropriate locations in the cross-build (after patching the Makefiles to remove the references to R_EXE), assuming that they should be portable across architectures? The last one might work (try it and see). A little experiment, replacing Opteron base.rdb/rdx files with i386 counterparts indicated no immediate (!) ill effects. That should certainly work: I would expect them to be identical for most packages. The (first) thing that seems to bite your cross compile is in src/library/base/makebasedb.R: baseFileBase - file.path(.Library,base,R,base) if (file.info(baseFileBase)[size] 2) # crude heuristic stop(may already be using lazy loading on base); in which .Library refers to the running R process, and you probably want the cross-build library instead. I'm not sure that is the only place that needs changing though. (It *looks* like the tools for non-base packages take an argument that would allow the build library to be distinct from the the one used by the running R). Take a look at cross-compiling (Windows under Linux). We have failed to make lazy loading of base work under cross-compilation, but do this for all other packages. I thought about endian differences (which I gather you have here), but I don't think they matter as we use XDR format for the databases. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problem with postscript graphics device driver
If you mean R 2.0.1, your installation is broken. Here's a quick check of where it should be: ls(asNamespace(grDevices), all=TRUE) [1] .PSenv .Quartzenv .X11env [4] .__NAMESPACE__. .__S3MethodsTable__. .packageName On Thu, 16 Dec 2004, Jeffrey Freedman wrote: I recently installed R version 2.01 for OS X (version 10.3.6). I now get the following error message when I try to use the postscript function: Error in get(name.opt, envir = envir) : Object .PSenv not found This did not happen in previous versions of R (i.e. 1.9). I do not get this error message when using the pdf graphics device driver. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Detecting incomplete commands
On 16 Dec 2004, Peter Dalgaard wrote: Philippe Grosjean [EMAIL PROTECTED] writes: Thank you Thomas for your answer. This is of course what I intend to do (indeed, to use a tryCatch(), instead of I try(). However, I would like to have a different behaviour depending if the synthax is incorrect ls()) for instance, or incomplete ls( for instance. Indeed, exactly like the distinction made at the command line: ls()) # This generates an error Error: syntax error ls( # This is not an error, but a multiline command + If you use parse() within a try(), you got the same error message in both cases: Error in parse(file, n, text, prompt) : parse error. So, it is not possible to discriminate between the two situation in this context. Is it a way to cope with that? Here's one idea: grep(line 2,try(parse(textConnection(ls))),silent=T)) numeric(0) grep(line 2,try(parse(textConnection(ls()),silent=T)) [1] 1 This is a lot easier at C level: see R_ext/Parse.h and `Writing R Extensions'. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R does not support UTF-8 (was german umlaut problem under MacOS)
You wrote your mail in UTF-8. R does not support UTF-8, and that is both documented and announced on startup in such a locale (at least on OSes with standard-conforming implementations): gannet% env LANG=en_GB.utf8 R R : Copyright 2004, The R Foundation for Statistical Computing Version 2.0.1 (2004-11-15), ISBN 3-900051-07-0 ... WARNING: UTF-8 locales are not currently supported Solution: do not use an unsupported locale. On Wed, 15 Dec 2004, joerg van den hoff wrote: I did not find this in the archive (hope it isn't there...): the current release of R (2.0.1) for MacOS (10.3.6) seems not to handle german special characters like 'ü' correctly: I get two characters (Atilde quarter) here. f - 'ü' can be entered at the prompt, but echoing the variable yields You mean printing the contents, I presume. [1] \303\274 (I think the unicode of the character) and inserting, for instance text(1,2,f) in some plot seems to insert two characters (√º) (probably an interpretation of the first and second group of the unicode?). I believe, this is a R problem or is there a simple configuration switch? thanks joerg __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] plot with dates
On Tue, 14 Dec 2004, [ISO-8859-1] Halldor Björnsson wrote: Hi, I am trying to understand the behaviour of the plot function. If I have novdate - as.Date(2001/11/1) + (0:29) y - 1:30 b - data.frame(novdate,y) then plot(b$novdate,b$y) will produce a plot where the x-ticmarks are given as dates (Nov 04, Nov 09 etc), but plot(b) will produce a plot where the x-tickmars are integer values (#day since Jan 1st 1970) In the first case plot is getting a an x-vector of class Date, and y-vector of class integer. In the second case plot gets an object of class data.frame (but with components of class Date and integer). I am new to R so I may be wrong about this, but it seems to me that different plotting methods are invoked. methods(plot) yields a list of plot methods, but I cannot access most of them. You would be able to had you read the help page for methods(). E.g. use getS3method(plot, data.frame) Or try ?plot.data.frame. Is there a way to guide plot(b) to using the method used by plot(b$novdate,b$y), - or is that a bad idea?... It's the natural way to do so. The plot method for data frames is really designed for a quick look at multi-column numeric data frames. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R 2.0.1 and RODBC install problem
From the DESCRIPTION file: SystemRequirements: An ODBC driver manager and drivers. See README. PLEASE do as it asks. On Mon, 13 Dec 2004, doktora v wrote: Hi all, I try to install the RODBC to no avail. Where is sql.h and sqltext.h supposed to come from? I don't have such files anywhere on my hdd! [...] PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Please do as we ask. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] bootstrap package
On Mon, 13 Dec 2004, Kjetil Brinchmann Halvorsen wrote: Fredrik Lundgren wrote: Hello R'ers In previous versions of R (I now use 2.0.1) there was a package bootstrap. I wrote some programs that depended heavily on this package but can unfortunately not find it on Cran today. Is there any way to find an older version of bootstrap and use it with the new version - 2.0.1? Bootstrap should have been in the Orphaned subdierctory on CRAN, but is'nt there? What happened? Things are not done retrospectively. Package bootstrap (and multiv) was orphaned before the Orphaned subdirectory was instituted. More a question of `what didn't happen' It can be found in the Archive subdirectory, thoug. The fact that it is no longer in the main area indicates that it probably does not pass R CMD check with 2.0.x. Note to Fredrik Lundgren: it is open to you to take over as maintainer: see Orphaned/README. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Porting optimisation setup from Excel Solver to R
On Fri, 10 Dec 2004, Puneet Singh wrote: Hi all, I am currently optimising a small portfolio I have created as a part of my research project in Excel. I am unable to find the appropriate package to port this into R. My problem set up is as follows Minimise ABS(Sum(Xi-Xi')+10*Sum(XiMi)/Mavg) Subject to: 0 = Xi = 0.05 ABS(Sum(Xi)) = 0.2 But Sum(Xi) = 0, so the ABS is unneeded. So I presume the minimization is over (Xi), but you have not said. where Mi - Market Cap of Stock i Xi - Initial weight of Stock i Xi' - New weight of Stock i Mavg = Average weighted market cap of portfolio. I suspect you have the meanings of Xi and Xi' reversed here. My portfolio has a long as well as a short side, therefore the ABS. The minimisation function is basically a penalty on the change from initial weight and the distance from the Average market cap. That's quite a long way from the formula you gave us. My problem is that I need to optimise a vector X with the weights instead of one weight at a time... i.e. I need to be able to change all the stocks in the portfolio simultaneously. I am able to do this EASILY in Excel, but have not found any straightforward application/formulation in R. R is not a spreadsheet nor a general-purpose optimizer: Excel will find it very hard to do most of the things R can do. So why not use Excel? It's actually easy to solve this problem theoretically, especially once you notice that you are minimizing ABS(0.2 + 10*Sum(XiMi)/Mavg - Sum(Xi')) and the last term is a constant. But I suspect you have made several mistakes in specifying it, and will leave it to you to sort this out. It is likely that you can set up your intended problem as a linear program, and although R is not the obvious program to solve an LP, it does have at least three packages that can do so. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Returning to normal after call to layout()
On Fri, 10 Dec 2004, michael watson (IAH-C) wrote: Hi Petr Yes thanks I did get your response and it was helpful. However, I have now resorted to using barplot() to draw a legend (as all I wanted was colored boxes and text) and it works very well for my needs. Basically, with layout() I'm not getting what I would expect, which may be a problem with my expectation rather than anything else. Like I say, I have a function which draws a plot, using layout to divide the plotting region into top and bottom. Fine. If the user calls my function, and then another plotting function, I would expect the new plotting function to overwrite the whole of the old plot - but it doesn't, it draws the new plot in the top half of the old plot, and clears the bottom plot. So what I want is something which says, after calling layout(), OK, I'm done plotting in two different regions, I want you to treat the current device as a single region again. Please look at the example in ?layout, which does exactly that. Or look at ?par, especially mfrow and mfcol. You need to reset the appropriate par()s. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] system() and file names with spaces
The normal way to do this is to quote the string, here filename. See
?shQuote.
Your comments really are not fair: a lot of work has been put into
supporting paths containing spaces on both Windows and Unix by the R
developers (or warning that they are not supported), but not by users.
That includes researching and writing functions like shQuote.
On Thu, 9 Dec 2004, Richard A. O'Keefe wrote:
Consider the question we had recently: how do I count the lines in a file
without reading it into R? The solution I suggested was
as.numeric(system(paste(wc -l , filename), TRUE))
Unfortunately, it doesn't work, or at least, not all the time.
If you already know all about that, and don't care, or already have
a solution, stop reading now. Otherwise, let me try to undo any
harm I may have done by providing a fuller solution.
We've had several reports in this list about problems caused by Windows
file names with spaces in them. File names with spaces are also common
in MacOS X, so common, in fact, that file name completion in a Terminal
actually works (if you have a file name Foo Bar, and type F, o, TAB
you get Foo\ Bar). File names with spaces are possible in other Unix
systems too, and always have been, though they are less likely.
That's been a feature of Unix shells with file completion (e.g. tcsh) for
at least a decade -- credit where credit is due, please.
So suppose there is a file Foo Bar you want to find the size of.
file.name - Foo Bar
system(paste(wc -l , File.name)
executes the command
wc -l Foo Bar
which gives you the size of Bar if there is one, or fails if there is not,
and ignores Foo (should there be one) and of course ignores Foo Bar.
What can we do about it? Well, we can try this:
for.system - function (s) gsub( , , s)
system(paste(wc -l , for.system(file.name)), TRUE)
Great. Works for files with spaces in their names. Now we try some other
file names. (File names like this are abundant in MacOS X.)
file.name - Black White Minstrels/1972
Whoops. wc -l Black\ \ White\ Minstrels/1972
forks off wc -l Black\ and then tries to run
\ White\ Minstrels/1972.
file.name - Quake(R)/scores
Whoops. Badly placed ()'s.
file.name - Drunkard's walk/log-1'
Whoops. Unmatched '
So try again.
for.system -
function (s) gsub(([][)(}{'\;! \t]), \\1, s)
line.count -
function (s) as.numeric(system(paste(wc -l , for.system(s)), TRUE))
This _still_ isn't perfect, but it is a whole lot better than the naive
version. The major remaining problem is that the set of special characters
and the quoting mechanism need to be changed for Windows. I _think_ the
Windows version should be something like
for.system - function (s) {
i - grep([^-_:.A-Za-z0-9/], s)
s[i] - sapply(s[i], function (s) paste(\, s, \, sep=))
s
}
But what if a file name contains a double quote? Until someone tells me,
I'm just going to hope it doesn't happen. Putting the pieces together,
f% cat Foo Bar
a b c
d e
f
EOF
for.system -
if (.Platform$OS.type == windows) {
function (s) {
i - grep([^-_:.A-Za-z0-9/], s)
s[i] - sapply(s[i], function (s) paste(\, s, \, sep=))
s
}
} else {
function (s) gsub(([][)(}{'\;! \t\n]), \\1, s)
}
wc - function (s) {
r - scan(pipe(paste(wc , for.system(s)), open=r), n=3, quiet=TRUE)
names(r) - c(lines, words, chars)
r
}
wc(Foo Bar)
lines words chars
3 612
system(cp $HOME/.login Drunkard\\'s\\ Walk)
wc(Drunkard's Walk)[chars]
chars
3633
If there's already something like for.system() built into R, I'd be very
happy to know about it. (It's a little odd that system() and pipe()
don't already support something like this; in a multi-element character
vector the first could be taken literally and the remaining ones could be
taken quoted with leading spaces.)
__
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] POSIX
On Thu, 9 Dec 2004, Omar Lakkis wrote: if I have a variable of type POSIXt POSIXct like 1969-12-31 19:00:01 EST how can I dynamicly get the year (or years if vector) and month? See ?months, or any other official documentation on dates in R. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] install bug with specific JPEG library by exporting CPPFLAGS variable
On 8 Dec 2004, Yves Magliulo wrote: Hi there, I think I have found a small problem in the /my/path/R-2.0.1/src/modules/X11/MakeFile generation. During the configure step, I have specified a specific JPEG library by exporting CPPFLAGS variable. That only specifies a set of headers, not the library. It is up to you to ensure that the library paths you need are also specified, e.g. in LIBS. To be definite, this is not a bug/problem in R. All compilation works well for individual files in the src/modules/X11/ directory, but when linking, the -ljpeg option doesn't work. I obtain the following message (in french sorry): -- make[4]: Entre dans le repertoire `/mnt/softs/R/R-2.0.1/src/modules/X11' gcc -shared -L/usr/local/lib -o R_X11.so dataentry.lo devX11.lo rotated.lo rbitmap.lo -lSM -lICE -L/usr/X11R6/lib -lX11 -ljpeg -lpng -lz -lreadline -ldl -lncurses -lm /usr/bin/ld: ne peut trouver -ljpeg collect2: ld a retourne 1 code d'?tat d'ex?cution [...] -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] install bug with specific JPEG library by exporting CPPFLAGS variable
On Wed, 8 Dec 2004, Brian D Ripley wrote: On 8 Dec 2004, Yves Magliulo wrote: Hi there, I think I have found a small problem in the /my/path/R-2.0.1/src/modules/X11/MakeFile generation. During the configure step, I have specified a specific JPEG library by exporting CPPFLAGS variable. That only specifies a set of headers, not the library. It is up to you to ensure that the library paths you need are also specified, e.g. in LIBS. It's best to set these in LDFLAGS: see config.site and the documentation in R-admin.html. To be definite, this is not a bug/problem in R. especially as how to do it is documented in the appropriate manual. [...] -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] RODBC on linux
If you look in the RODBC help pages for odbcConnect you will see this mentioned with respect to Oracle and Sybase. Try the fix mentioned there. On Wed, 8 Dec 2004, Omar Lakkis wrote: I am using RODBC 1.1-2 with R 2.0.0 on a Debian box with a singel Pentium processor. My database is Informix 7.32. When I run a sql query I get the table header back but no data is selected. Please note this example: Table t1 has two columns, a and b. The table is populated with three rows. Thi si the definition of the table: Column name TypeNulls a smallintyes b integer yes sqlQuery(pricedb, select * from t1) [1] a b 0 rows (or 0-length row.names) class(a$a) [1] integer class(a$b) [1] integer using my C code on the same box, utalizing teh same odbc installation I get: 12 34 56 Does anyone have an idea why I get the table header but no data? Also, sqlTables() return no rows. sqlTables(pricedb) [1] TABLE_QUALIFIER TABLE_OWNER TABLE_NAME TABLE_TYPE [5] REMARKS 0 rows (or 0-length row.names) __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Strange error from R CMD INSTALL
On Thu, 9 Dec 2004, Ray Brownrigg wrote: Date: Wed, 08 Dec 2004 09:33:22 -0400 From: Kjetil Brinchmann Halvorsen [EMAIL PROTECTED] I am trying to install a local package and get this unexpected error: -- Making package UMSA adding build stamp to DESCRIPTION installing R files installing data files installing man source files installing indices Error: couldn't find function na.omit Execution halted na.omit of course is in package stats, and that is listed in the Depends field in the DESCRIPTION file. Check what is in your data directory. Does something in there use (implicitly) na.omit? I have seen something like this (since 2.0.0) where a .R file in the data/ directory used a function within the package, but that function was not 'available' at the installing indices phase of the check/build. (INSTALL, actually.) That's a plausible explanation. From 200update.txt on developer.r-project.org 2) data/*.R files must be self-sufficient, and in particular not depend on the package or standard packages other than base. (This has always been documented, but is now enforced.) and see also `Writing R Extensions'. -- 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 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Spare some CPU cycles for testing lme?
As others have said, this needs tools not CPU cycles: gctorture or valgrind.
Valgrind found (after a few seconds and on the first pass)
==23057== Invalid read of size 4
==23057==at 0x3CF4E645: ssc_symbolic_permute (Mutils.c:373)
==23057==by 0x3CF5BF75: ssclme_create (ssclme.c:168)
==23057==by 0x80AF5E8: do_dotcall
(/users/ripley/R/svn/R-devel/src/main/dotcode.c:640)
==23057==by 0x80CFA84: Rf_eval
(/users/ripley/R/svn/R-devel/src/main/eval.c:399)
==23057== Address 0x3C7F3BD0 is 4 bytes before a block of size 524 alloc'd
==23057==at 0x3C01CB56: calloc (in
/opt/local/lib/valgrind/vgpreload_memcheck.so)
==23057==by 0x80F9EBE: R_chk_calloc
(/users/ripley/R/svn/R-devel/src/main/memory.c:2151)
==23057==by 0x3CF4E515: ssc_symbolic_permute (Mutils.c:352)
==23057==by 0x3CF5BF75: ssclme_create (ssclme.c:168)
==23057==
==23057== Use of uninitialised value of size 8
==23057==at 0x80C0137: Rf_duplicate
(/users/ripley/R/svn/R-devel/src/main/duplicate.c:160)
==23057==by 0x80BFA85: Rf_duplicate
(/users/ripley/R/svn/R-devel/src/main/duplicate.c:101)
==23057==by 0x80BFEB3: Rf_duplicate
(/users/ripley/R/svn/R-devel/src/main/duplicate.c:154)
==23057==by 0x816ED96: do_subset2_dflt
(/users/ripley/R/svn/R-devel/src/main/subset.c:816)
==23057==
==23057== Conditional jump or move depends on uninitialised value(s)
==23057==at 0x3CF62229: ssclme_fitted (ssclme.c:1587)
==23057==by 0x80AF646: do_dotcall
(/users/ripley/R/svn/R-devel/src/main/dotcode.c:646)
==23057==by 0x80CFA84: Rf_eval
(/users/ripley/R/svn/R-devel/src/main/eval.c:399)
==23057==by 0x80D1D80: do_set
(/users/ripley/R/svn/R-devel/src/main/eval.c:1280)
which is pretty definitive evidence of a problem (possibly 2) in the code.
I strongly recommend valgrind (http://valgrind.kde.org/) if you are using
x86 Linux. It has found quite a few errors in R and in certain packages
recently. The only thing to watch is that optimized BLASes will probably
crash it.
On Mon, 13 Sep 2004, Frank Samuelson wrote:
If anyone has a few extra CPU cycles to spare,
I'd appreciate it if you could verify a problem that I
have encountered. Run the code
below and tell me if it crashes your R before
completion.
library(lme4)
data(bdf)
dump-sapply( 1:5, function(i) {
fm - lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf,
random = ~ IQ.ver.cen | schoolNR);
cat( ,i,\r)
0
})
The above code simply reruns the example from the
lme help page a large number of times and returns a bunch
of 0's, so you'll need to have the lme4 and Matrix
packages installed. It might take a while to complete,
but you can always nice it and let it run.
I'm attempting to bootstrap lme() from the lme4 package,
but it causes a
segfault after a couple hundred iterations. This happens on
my Linux x86 RedHat 7.3, 8.0, 9.0, FC1 systems w/ 1.9.1
and devel 2.0.0 (not all possible combinations actually
tested.)
I've communicated w/ Douglas Bates about this and he
doesn't appear to have the problem.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] linking .lib and/or .dll files
On Thu, 1 Jul 2004, Samuel Kemp wrote: Linking C++ dynamic libraries has become the bane of my R life. I have a piece of C++ code that I would like to make into a .dll (to call into R). However, this piece of C++ code needs to be linked with a .dll or .lib - which I have been created in Visual C++. Is it possible to link this for use in R? Yes with .lib, if it is a recent VC++. You need to make a mingw import library, and you can use a tool called reimp to convert a VC++6.0 .lib (but not earlier). Alternatively, a tool called pexports can be used to create an exports file and dlltool can be used to make an import library from that. Finally, it is supposedly possible to link against a .dll, but I have found that to be really buggy. If so, how do I go about doing this is MINGW? Create an import library and link against it, and make sure the dlls are in your path. CAVEAT: if the C++ code you are calling contains name-mangled symbols you will be in trouble as VC++ name-mangles in a unique way. In that case you need to write a piece of C++ glue code that you can compile in VC++ and that has C entry points that you can call from R. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to sort the contents of a list-object?
On Wed, 12 May 2004, Martin Kerick wrote: I have a list-object RGList named RG containing two vectors (RG$R and RG$G) and a data.frame(RG$genes) with 8 variables. Each of the variables of the data.frame have the same length as the two vectors. I think the data in the RGList is structured in such a way, that the first entry in the vector RG$R belongs to the first entry in the data.frame variable e.g. RG$genes$Row. Now my question: Is it possible to sort the RGList object by the values of one variable of my data.frame e.g. RG$genes$Row without loosing the ties between the different parts of the list ? Yes. Did you also want to know how? If so, see later. But why? It looks like R and G should be additional columns of the data frame and if you had a better data organization you would *know* what matched what and operations like this would be obvious. ord - sort.list(RG$genes$Row) RG - lapply(RG, function(x) if(is.data.frame) x[ord,] else x[ord]) -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Size of R user base
On 20 Apr 2004, Peter Dalgaard wrote: [EMAIL PROTECTED] writes: On 20 Apr 2004 at 10:47, Philippe Grosjean wrote: Of course, this will only work with computers connected to the internet,... but at least, it could be one way to evaluate the number of R users. Would that be an infringment of Open Source, or any other rule of freedom? I don't know, but it does seem to be quite widespread (at least for commercial software). so, why an Open Source software would not be able to monitor the number of users? That would make R into spyware, and there exist software to monitore and warn aganst/automatically remove spyware, and some users have such installed (and it will grow). Not quite spyware. Spyware generally works in more covert ways and tries to hide itself from the user. However, quite a few people think that having programs connecting to places on the internet without being asked is annoying and a potential invasion of privacy and it may even cost people money if they're on a dialup non-flat-fee connection. It is possible to ask: I mentioned pine, which does, and so do some perl installers. I don't think people would mind if the rw1091.exe installer had an option (ticked by default) to `call home', but I don't think we would learn enough for this to be worth setting up. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] loading into a list
Try .saveRDS/.readRDS which enable you to save and load unnamed objects (in your case list(A, B, C)). On Tue, 20 Apr 2004, Tamas Papp wrote: I have the following problem. Use the same algorithm (with different parameters) to generate simulation results. I store these in variables, eg A, B, C, which I save into a file with save(A, B, C, file=solution001.Rdata) I do this many times. Then I would like to load the above, but in such a manner that A, B, C woule be part of a list, eg sol001 - loadIntoList(solution001.Rdata) so that sol001 is a list with elements A, B, C. I am looking for a way to implement the above function. The variables are very large and I need a lot of time to compute them, so saving loading the results is the only viable alternative. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] New unique name
On Mon, 19 Apr 2004, Barry Rowlingson wrote:
(Ted Harding) wrote:
A bit sledgehammer for nut, but as least it meets your needs!
You could even use uuidgen to create a universally unique ID, and then
use make.names to R-ify it:
make.names(system(uuidgen,intern=T))
[1] aa33d26c.88a5.4eab.94ba.5073c4718ffe
make.names(system(uuidgen,intern=T))
[1] d5aea7a0.81e9.4690.8d48.d74fd2b50a83
make.names(system(uuidgen,intern=T))
[1] X2570d3e0.6b07.42be.a9c6.3701ac82b4f0
Of course the requirement was to make an object with a name that
didn't already exist, and there's no guarantee that you haven't already
created an object called X2570d3e0.6b07.42be.a9c6.3701ac82b4f0 for
some reason.
So that's no good.
How about getting an alphabetically-sorted list of all the current
objects and then using the last one augmented with something:
makeUnique - function(){
allObjects=sort(ls(pos=seq(1:length(search()
paste(allObjects[length(allObjects)],-temp,sep='')
}
I'm sure someone can come up with a bigger sledgehammer, or a reason
why this wont always be unique. What's the longest name of an object in
R? That'll break it... Pah.
There is more to the environment than the search path, which is what makes
this tricky. I suspect Erich really only wanted to avoid objects in the
current frame (which is not on the search path except for interactive use
of R), but he didn't tell us too precisely.
--
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 272860 (secr)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R][S] library question
In some cases it is possible to port an R *package* to S-PLUS: people have done both that and the reverse. If you have some specific examples in mind we may be able to help you further. Since you are on Windows, it may not be easy unless you have the requisite tools (e.g. Visuall C++ and Fortran). On Wed, 24 Mar 2004, Erin Hodgess wrote: Is it possible to take one of the R libraries and put it into S+ please? R Windows XP 1.8.1 S+ Version 6.2 -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] rstandard does not produce standardized residuals
This has laready been changed in the R-devel version (1.9.0 to be). Pre-test versions of that for Windows are available on CRAN. From the NEWS file o rstandard() was wrongly scaled for cases where summary(model)$dispersion != 1. and that ought to mention glm somewhere On Tue, 24 Feb 2004, Ulrich Halekoh wrote: Dear all, the application of the function rstandard() in the base package to a glm object does not produce residuals standardized to have variance one: the reason is that the deviance residuals are divided by the dispersion estimate and not by the square root of the estimate for the dispersion. Should the function not be changed to produce residuals with a variance about 1? R 1.8.1 on windows 2000 ulrich == Ulrich Halekoh, PhD Phone: +45 8999 1825 Biometry Research Unit Fax: +45 8999 1300 Danish Institute of Agricultural SciencesE-mail: [EMAIL PROTECTED] Research Centre Foulum, DK-8830 Tjele, Denmark __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Latin 2 encoding + fonts
On Wed, 4 Feb 2004, Miha STAUT wrote: Hi, In the FAQ I read about options to specify different fonts than the default ones for the console (in the file Rprofile) and for the graphical output (Rdevga). I would however like to replace Latin 1 with Latin 2 enconding for both (console and graphical) output in Windows and just graphical output in Linux. You are confusing fonts with encodings. Windows does not use either Latin 1 or Latin 2, and R for Windows does not encode for the console or the graphical device. Just use the Windows version of a ISO-8859-2 locale and a font supported by your locale (almost all under NT, fewer under Win9x). I guess it is possible but I did not find the way. How can I use the fonts (*.afm) and the (presumably) encondings (*.enc) in R/rw1081/afm? How do I know what are the real font names. Are those only the ones listed in the man page for Hershey? This is nothing to do with Hershey. All the information you need is on the help page for postscript(). -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Winedit and R
You are using mismatched versions of R and the packages, as the warnings say. Please update your version of R. On Tue, 16 Dec 2003, Patrick Giraudoux wrote: Hi all, I am trying to install add-on in R (rw1070) to work with WinEdit. Libraries Swinregistry and Rwinedt have been installed via Install Package(s) from local zip files from R. However, when I run library(Rwinedt) I get the following messages: library(Rwinedt) Loading required package: SWinRegistry Error in loadNamespace(name) : package `methods' does not have a name space In addition: Warning messages: 1: package RWinEdt was built under R version 1.8.0 2: package SWinRegistry was built under R version 1.8.0 Error in eval(expr, envir, enclos) : Package SWinRegistry is not available. Either install it or install R-WinEdt manually, as described in ReadMe.txt Intalling manually looking quite complicated, I am not tempted to take this direction... Can anybody give me a hint? -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Calling C function in R
On Tue, 16 Dec 2003, Manoj - Hachibushu Capital wrote: Hi All, I am trying to write a c function to optimize loop processing. Having read the R extension and trying out a few samples I was pretty comfortable with the basics. However, I am wondering if there is anyway to call tseries functions like adf.test or po.test from within c function. Any pointers/ code sample would be greatly appreciated. Yes, this is described with code samples in `Writing R Extensions', in the section `Evaluating R expressions from C'. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] WinMenus - is there a way of knowing if a WinMenu or WinMenuItem already exists?
On Mon, 8 Dec 2003, Finn Sando wrote: I am developing a menusystem using the functions WinMenuAdd and WinMenuAddItem etc. I want to be able to shift between different interfaces (ie. different sets of menu-trees). Therefore I would like to be able to ask whether a specific menu already exists in order to remove or add it Without errors. That is I am looking for something like: WinMenuExist(menuname) and WinMenuExistItem(menuname,itemname) Are there any way asking such question of R? No. But you could contribute such functionality. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R]: GLIM PROBLEMS
) -0.778630.04020 -19.37 2e-16 *** --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 1837.4 on 47 degrees of freedom Residual deviance: 883.8 on 44 degrees of freedom AIC: 1228.4 Number of Fisher Scoring iterations: 4 The Genstat output is displayed below. (well only some of it!!!) * Regression Analysis * Response variate: claims_r Binomial totals: exp_n Distribution: Binomial Link function: Logit Fitted terms: Constant, age *** Summary of analysis *** mean deviance approx d.f. deviance deviance ratio chi pr Regression 31298. 432.70432.70 .001 Residual441136.25.83 Total 472434.51.80 * MESSAGE: ratios are based on dispersion parameter with value 1 Dispersion parameter is fixed at 1.00 *** Estimates of parameters *** antilog of estimate s.e. t(*) t pr. estimate Constant -1.1992 0.0211-56.90 .001 0.3014 age (23-26)-0.4302 0.0326-13.20 .001 0.6504 age (27-65)-0.7999 0.0224-35.75 .001 0.4494 age (66-80)-0.9297 0.0407-22.86 .001 0.3947 * MESSAGE: s.e.s are based on dispersion parameter with value 1 Parameters for factors are differences compared with the reference level: Factor Reference level age (17-22) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Rd Files?
On Mon, 1 Dec 2003, Wolski wrote: Hi! Seems to me that package.skeleton(...) does not like assignment functions. System: Windows 2000 And that's your problem! It's a problem with your OS, not package.skeleton. And it is known. package.skeleton(name=testpack,list=ls(),path=c:/home/wolski/devel,force=T) Creating directories ... Creating DESCRIPTION ... Creating READMEs ... Saving functions and data ... Error in file(file, ifelse(append, a, w)) : unable to open connection In addition: Warning message: cannot open file `c:/home/wolski/devel/testpack/R/[[-.caliblist.R' Eryk *** REPLY SEPARATOR *** On 12/1/2003 at 1:08 PM Prof Brian Ripley wrote: ?prompt ?package.skeleton and do read `Writing R Extensions' On Mon, 1 Dec 2003, Wolski wrote: Hi Kjetil! I have an *.R file with a lot of functions and I am looking for a script which would generate the skeleton of an Rd file for all functions found in the R file. It will be nice if the can already generate the name,usage and the arguments field from the source so that i have to edit only the description and examples Eryk *** REPLY SEPARATOR *** On 12/1/2003 at 8:44 AM [EMAIL PROTECTED] wrote: On 1 Dec 2003 at 13:21, Wolski wrote: It is not entirely clear what you want, but if you want to translate S[-Plus] help files to Rd format, there is [windows] Rcmd Sd2Rd [unix] R cmd Sd2Rd Kjetil Halvorsen Hi! Are there scripts or packages for generating Rd files out of S3 code on cran? Has any one written such scripts (e.g. in Perl?) and are willing to share them? Thanks in advance. Eryk. Dipl. bio-chem. Eryk Witold Wolski@MPI-MG Dep. Vertebrate Genomics Ihnestrasse 73 14195 Berlin 'v' tel: 0049-30-84131285 / \ mail: [EMAIL PROTECTED] ---W-W [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help Dipl. bio-chem. Eryk Witold Wolski@MPI-MG Dep. Vertebrate Genomics Ihnestrasse 73 14195 Berlin 'v' tel: 0049-30-84131285 / \ mail: [EMAIL PROTECTED]---W-W http://www.molgen.mpg.de/~wolski __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- 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 Dipl. bio-chem. Eryk Witold Wolski@MPI-MG Dep. Vertebrate Genomics Ihnestrasse 73 14195 Berlin 'v' tel: 0049-30-84131285 / \ mail: [EMAIL PROTECTED]---W-Whttp://www.molgen.mpg.de/~wolski -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] howto improve sharpeness of fonts in a jpg-image produced by R ?
On Tue, 18 Nov 2003, Niels Steen Krogh wrote: I used an expression like this: bitmap(file=barplotx.jpg,type=jpeg) So that was nothing to do with R, as reading the help page would have told you. Your subject line is false: the `jpg-image' was produced by gs and you should look into fixing your problems with that. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] confint: which method attached?
On Mon, 17 Nov 2003, Ulrich Halekoh wrote: the function confint uses the profiling method of the function of the package MASS confint.glm even after the package has been detached! Why the exclamation mark? Note profile.glm is not actually in package:MASS (sic). Try looking for it: getAnywhere(profile.glm) A single object matching 'profile.glm' was found It was found in the following places registered S3 method for profile from namespace MASS namespace:MASS with value ... 1: might this be the intenden behavior? The accurate description is the intended behaviour. 2. How does the function remember its 'MASS' functionality after detaching the package? It isn't in the package There is currently no way to remove registered S3 methods like confint.glm in an R session. Nor is there likely to be in the near future, General comment: R has changed quite a lot recently, and older preconceptions do need to be checked against current information. The article `Name Space Management for R' in R-news 2003/1 may help (although it may tell you mor ethan you want to know). -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Problem with parser and if/else
On Thu, 13 Nov 2003, Ben Bolker wrote:
In the second case, R stops when it has a syntactically complete clause:
if (...) {
...
}
is complete since an else{} clause is not required. R evaluates it, then
moves onto
else { ... }
which is a syntax error (since it doesn't have an if {} in front of it,
since that has already been evaluated)
One way to see this illustrated is to enter these commands a line at a
time in interactive mode.
I don't know exactly where this appears in the documentation, probably
someone will point to it in another message.
help(if), for example (the most obvious place to look?)
MASS4, p.58
On Thu, 13 Nov 2003, Brown, Simon wrote:
Dear r-help people,
could you confirm that this is correct behaviour for R? I am using RH9.
the code:
x1 - 1:6
t1 - 5
if (length(x1) = t1) {
cat(in the if \n)
} else {
cat(in the else\n)
}
runs fine:
source(test_if_else.R)
in the if
but the code:
x1 - 1:6
t1 - 5
if (length(x1) = t1) {
cat(in the if 2\n)
}
else {
cat(in the else\n)
}
fails with the error:
source(test_if_else2.R)
Error in parse(file, n, text, prompt) : syntax error on line 6
Could someone explain this to me please?
Thanks,
Simon.
--
620B Bartram Hall[EMAIL PROTECTED]
Zoology Department, University of Floridahttp://www.zoo.ufl.edu/bolker
Box 118525 (ph) 352-392-5697
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University of Oxford, Tel: +44 1865 272861 (self)
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Re: [R] GDB under windows
It's in the rw-FAQ! That describes this as `fraught' with good reason. On Thu, 6 Nov 2003, Marsland, John wrote: Does anybody have some simple instructions to get me going using the GNU debugger GDB under windows with R? The R Extensions manual mentions briefly debugging under unix, but I've seen seen GDB mention in the Bloodshed Dev C++ IDE so it should be possible to use it with R? Regards, John [Using R-1.8.0 under Windows NT 4.0] -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] map does not display maps, MacOSX
Notice the // in the path
/Users/glaziou/Library/R/maps/mapdata//world.N
Some Windows filesystems do not like that, and my guess is that some MacOS
X ones may not either.
On Wed, 5 Nov 2003, Philippe Glaziou wrote:
Hi,
I installed the maps and mapdata libraries on my R-1.8.0 on
MacOSX 10.2.8 (jaguar on a powerbook G4), and failed to make the
map function work properly:
R : Copyright 2003, The R Development Core Team
Version 1.8.0 (2003-10-08)
[...]
library(maps)
map()
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file `/Users/glaziou/Library/R/maps/mapdata//world.N'
map('usa')
Error in file(file, r) : unable to open connection
In addition: Warning message:
cannot open file `/Users/glaziou/Library/R/maps/mapdata//usa.N'
system('ls -l /Users/glaziou/Library/R/maps/mapdata')
total 1796
-rw-r--r-- 1 root staff 143902 Oct 14 11:30 county.G
-rw-r--r-- 1 root staff 690260 Oct 14 11:30 county.L
-rw-r--r-- 1 root staff 618 Oct 14 11:30 nz.G
-rw-r--r-- 1 root staff 13040 Oct 14 11:30 nz.L
-rw-r--r-- 1 root staff2642 Oct 14 11:30 state.G
-rw-r--r-- 1 root staff 96892 Oct 14 11:30 state.L
-rw-r--r-- 1 root staff 282 Oct 14 11:30 usa.G
-rw-r--r-- 1 root staff 58232 Oct 14 11:30 usa.L
-rw-r--r-- 1 root staff 74434 Oct 14 11:30 world.G
-rw-r--r-- 1 root staff 295152 Oct 14 11:30 world.L
-rw-r--r-- 1 root staff 74434 Oct 14 11:30 world2.G
-rw-r--r-- 1 root staff 295152 Oct 14 11:30 world2.L
-rw-r--r-- 1 root staff 54832 Oct 14 11:30 world2.N
Most of contributed libraries are installed in ~/Library/R
because I am the only user of that mac and this simplifies
backup. I checked the access rights of relevant files and
directories and they all seem correct (these are owned by root
but are world readable and directories are world cd'able).
Compilation of both libraries maps and mapdata went ok. I have
the same libraries installed on a linux server where they work
perfectly well.
A similar error message occurs whether R is started in an xterm,
within emacs/ESS on X11, or using the RAqua interface.
Any hint appreciated,
--
Philippe Glaziou
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University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272860 (secr)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] run R under linux
On Wed, 22 Oct 2003, Zhen Pang wrote:
Thank you for your help. But try() seems to only allow for an expression. My
simulation have serveral expressions which possibly have problem. Is there
any possibility to include them all in the try()? If not, I seem to use
several try().
{line1
line2
line3}
*is* a single expression.
As in the example on the help page for try, you can also wrap the
computation in a function call, and that is usually a good idea.
--
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 272860 (secr)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] png() and/or jpeg(): line missing by using box(which=outer)
It is probably a bug: does it happen when you copy from the screen in png? I would expect not, hence that may be a workaround for you. When I have both time and access to a Windows machine I may be able it take a closer look: meanwhile you do have access and have the source code so please investigate it yourself and submit a patch. On Tue, 21 Oct 2003, Pfaff, Bernhard wrote: Dear R list, I do encounter the following problem by generating either a png-file (example below) or a jpeg-file: By employing 'box(which=outer)' a box is drawn, except for the right line. If I generate the plot without the 'box(which=outer)', a line at the bottom in the graphics file still appears. However, both plots are displayed correctly in the R Graphics Device Window, i.e with a box including the right side or one without any lines at the outer margins of the plot. Now, I want either a file - including the right side of box or one that has none on all sides. test - rnorm(100) par(mar=c(6,4,6,4), oma=c(1,1,1,1)) png(test1.png) plot(test) grid() box(which=outer) box(which=plot) dev.off() png(test2.png) plot(test) grid() box(which=plot) dev.off() Incidentally, both functions are calling .Internal(devga()). I have not encountered this problem with version R 1.7.1 (for which I used the binary distribution on CRAN). Now, I have source compiled R 1.8.0. Although, everything passed 'make check', I am wondering if it could be possible that 'devga.c' or any other necessary file for running png() or jpeg() have not been compiled 'correctly', or do I have simply to adjust a par()-argument? Any pointers or help is appreciated. Bernhard platform: i386-pc-mingw32 arch: i386 os: mingw32 system: i386, mingw32 major: 1 minor: 8.0 Windows NT 5.0 The information contained herein is confidential and is intended solely for the addressee. Access by any other party is unauthorised without the express written permission of the sender. If you are not the intended recipient, please contact the sender either via the company switchboard on +44 (0)20 7623 8000, or via e-mail return. If you have received this e-mail in error or wish to read our e-mail disclaimer statement and monitoring policy, please refer to http://www.drkw.com/disc/email/ or contact the sender. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] ks.test()
On Thu, 28 Aug 2003, franck allaire wrote: With the Shifted Exponential test, H_0 is data is a sample coming from a Shifted Exponential distribution with shift=30 and lambda = 0.001566907 You got that after looking at the data. H_0 has to be specified before looking at the data. You appear to be applying the KS test after estimating parameters. I do in order to define H_0 as explained above That's invalid. The distribution theory is for an iid sample from a known continuous distribution (and does not otherwise depend on the distribution). That's what I thougth but this is not what I understand reading: Learn not to believe everything you read on the Web. Since your H_0 is not pre-specified, that distribution theory is not correct. please see above Rather, please take careful note yourself. (Some corrections have been worked out for say ML fitting of exponential and normal distributions -- by Michael Stephens as I recall.) Also, your `truncated LogNormal' does not appear to be truncated, rather to be shifted. That's the same thing for an exponential (for a positive shift), but not for any other distribution. Thanks for this clarification And what is the H_0 and H_1 used in the article? H_1 is that the sample is not coming from the specified distribution in H_0 Not so: perhaps an iid sample from some other continuous distribution? -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Marginal (type II) SS for powers of continuous variables ina linear model?
On Tue, 12 Aug 2003, [iso-8859-1] Bjørn-Helge Mevik wrote: Prof Brian Ripley [EMAIL PROTECTED] writes: drop1 is the part of R that does type II sum of squares, and it works in your example. So does Anova in the current car: I'm sorry, I should have included an example to clarify what I meant (or point out my misunderstandings :-). I'll do that below, but first a comment: And in summary.aov() those *are* marginal SS, as balance is assumed for aov models. (That is not to say the software does not work otherwise, but the interpretability depends on balance.) Maybe I've misunderstood, but in the documentation for aov, it says (under Details): This provides a wrapper to `lm' for fitting linear models to balanced or unbalanced experimental designs. Also, is this example (lm(y~x+I(x^2), Df)) really balanced? I think No, and I did not use summary,aov on it! of balance as the property that there is an equal number of observations for every combination of the factors. With x and x^2, this doesn't happen. For instance, x=1 and x^2=1 occurs once, but x=1 and x^2=4 never occurs (naturally). Or have I misunderstood something? Yes. summary.aov(split=) and model.tables and the like are designed for balanced data. They may or may not work in the unbalanced case. The comment you quote is for aov(), not those other functions. Now, the example: Df2 - expand.grid (A=factor(1:2), B=factor(1:2), x=1:5) Df2$y - codes(Df2$A) + 2*codes(Df2$B) + 0.05*codes(Df2$A)*codes(Df2$B) + + Df2$x + 0.1*Df2$x^2 + 0.1*(0:4) Df2 - Df2[-1,]# Remove one observation to make it unbalanced codes is deprecated! ABx2.lm - lm(y~A*B + x + I(x^2), data=Df2) The SSs I call marginal are R(A | B, x, x^2), R(B | A, x, x^2), R(A:B | A, B, x, x^2), R(x | A, B, A:B) and R(x^2 | A, B, A:B, x). That's not what most other people call marginal, though. (Here, for instance, R(x | A, B, A:B) means the reduction of SSE due to including x in a model when A, B and A:B (and the mean) are already in the model. I've omitted the mean from the notation.) anova(ABx2.lm) Analysis of Variance Table Response: y Df Sum Sq Mean Sq F valuePr(F) A 1 1.737 1.737 66.5700 1.801e-06 *** B 1 13.647 13.647 523.0292 6.953e-12 *** x 1 93.677 93.677 3590.1703 2.2e-16 *** I(x^2) 1 0.583 0.583 22.3302 0.0003966 *** A:B1 0.011 0.0110.4238 0.5263772 Residuals 13 0.339 0.026 --- Signif. codes: 0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 This gives SSs on the form R(A), R(B | A), R(x | A, B) etc. (If the design had been balanced (in A, B and x), this would have been the same as the marginal SSs above.) drop1(ABx2.lm) Single term deletions Model: y ~ A * B + x + I(x^2) Df Sum of Sq RSS AIC none0.339 -64.486 x 1 1.188 1.527 -37.901 I(x^2) 1 0.592 0.931 -47.294 A:B 1 0.011 0.350 -65.877 This gives the SSs R(x | A, B, A:B, x^2), R(x^2 | A, B, A:B, x) and R(A:B | A, B, x, x^2). The SS for x is not marginal as defined above. But that *is* how `marginal' is usually defined. Why should I(x^2) be regarded as subservient to x? It is just another function of x. Suppose we have x and log(x)? -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] label chemical formulas
On Mon, 4 Aug 2003, Roberto Canteri wrote: [This is a repeat of a post earlier today.] Dear r-help, the prcomp matrix (x$rotation) I have, has the columns labels as chemical formulas (i.e: C2H3, 37Cl,...,C10H24N3O3). Plotting them as plain text I do the following with success: xlabs - dimnames(y$rotation)[[1]] That extracts the *row* names. xlabs - as.character(xlabs) They are already character. You want to convert them to expressions. Here's one way to get you started. xx - C[2]*H[3] parse(text=xx) expression(C[2] * H[3]) It's probably easiest to plot the labels one at a time, but xx - c(C[2]*H[3], phantom()[37]*C[1]) parse(text=paste(xx, collapse=\n)) works. plot(y$rotation[,1],y$rotation[,2], ann=FALSE, type=p, col=red, pch=20) text(y$rotation[,1],y$rotation[,2], labels=xlabs, cex=0.7, font=1, pos=4, offset=0.2) I do not succed to plot the labels with subscripts and superscripts. I did many attempt trying the use of expression() or substitute() but without success. I can write the labels in the data matrix as needed (i.e.: C[2]*H[3]) to plot properly if I would know how. I peg your pardon if this is probably a silly problem, I am new user of R (I am using R 1.7.0 on win2k). -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] rterm
Well, there's a file README.rterm in the top-level (binary) installation directory, and the section `Invoking R under Windows' in `An Introduction to R' applies equally to RGui and Rterm. All the information is in one of those two places. On Fri, 18 Jul 2003, Manuel Lopez Coello wrote: I would like to use Rterm but i don`t know its parameters. I have searched about this issue but i haven´t found anything. thank you. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] sample function
R is not S-PLUS, and you need Modern Applied Statistics in S (4th ed) for a description including R. sample in R used a PRNG: see ?RNG in R for the details of PRNGs in R. On Fri, 27 Jun 2003, [iso-8859-1] Ramzi Feghali wrote: i have a question about the sample function used in R, does it work as a pseudo-dandom number generator programmed with C, like it is described in Modern Applied Statics with S-Plus 3d edition chapter 5 section 2? -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] using R as a script; getting the output to display on screen
On Fri, 27 Jun 2003, Nick Helseth wrote: So, you are using Windows: please say so up front. I'm trying to run R from the command line using a function as an input; it seems to run ok when I use Rterm --vanilla name_of_R_function.R (by ok, I mean that it will say that it's reading in the correct items) but the graphics won't display on screen. The default graphics device in non-interactive use is postscript(). Do I need to explicitly define an output device? Like Rterm --vanilla name_of_R_function.R standard_display_device? If that is the case, I don't suppose anyone happens to know the name of the screen display device in Windows, do they? Yes, lots of people do as it is in the README.RW1071: windows(). Just add an explicit call to see graphics on-screen. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Can't save a graph to pdf in R for MacOS
On Thu, 26 Jun 2003, p.b.pynsent wrote: I do not have an R solution but use eps2pdf (a Perl script) This can be installed by Fink http://sourceforge.net/projects/fink/. eps2pdf runs GhostScript: so does the R device driver bitmap(). Does the latter work on your system? If so it would save you some steps. On Wednesday, June 25, 2003, at 03:41 am, Sébastien Plante wrote: Hi, I am using R 1.7.1 (carbon) for MacOS and I am running it on MacOS X 10.2.6. When I send a graph to the pdf device (or any other devices), I get a zero KB file name Rplots.pdf. Before sending my graph to the output, I did: dev.off() pdf() boxplot(... my graph commands...) dev.off() Is this the correct procedure? I did the same procedure on another PC running Linux (R 1.6) and it work well. Please help! Thanks, Sébastien Plante __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] outlier
Please do read the help page. which explains this is a random algorithm. In your example you can try cov.rob(ap, cor=TRUE, nsamp=exact) On Wed, 18 Jun 2003, kan Liu wrote: I wrote a .R file (see below)to calculate robust measure of correlation using cov.rob. I got different correlation coefficients (0.70, 0.79, 0.63, ...) when I run the file different times. Can you tell me what this means or what is wrong in using cov.rob? - library(lqs) a - c(5.41,4.67,5.88,2.38,4.79,5.30,1.94,3.40,5.05,3.31,5.88,4.92,5.08,4.58,4.59,4.77,5.25,3.77,2.88,5.30,5.32,2.56,4.29,5.54,4.53,3.51,4.93,2.49,2.85,5.04,2.51,2.60,3.58,2.11,1.70,5.20,5.08,4.48,3.96,4.87,4.98,2.56,1.69,4.28,1.70,2.91,5.37,2.16,3.04,1.69,1.88,5.36,1.70,3.81,1.70,5.88,3.52) p - c(5.30,4.78,4.79,0.62,4.32,2.33,0.64,3.14,3.06,4.73,5.72,2.21,4.81,1.74,4.93,4.74,5.81,3.88,3.03,4.72,5.79,3.43,4.07,5.93,2.26,3.70,5.32,4.56,1.52,2.54,0.26,2.79,3.67,4.44,1.46,4.26,4.49,5.29,3.26,3.87,3.12,3.97,3.49,0.45,0.76,4.49,5.29,1.94,4.69,2.80,2.75,5.16,0.74,5.81,1.46,5.24,4.00) ap - cbind(a,p) cov.rob(ap, cor=TRUE) -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] dyn.load() function problem help!
On Wed, 18 Jun 2003, Mu Yunming wrote: Hi! I would like to call a Fortran subroutine within R. For doing this, I first built a shared library for loading into R under Unix and it was successful. How did you do this? Did you use R CMD SHLIB? But when I tried to load a shared library using dyn.load() function for use in .Fortran(), I got an error message. The command I input below in R is: dyn.load(aaa.so) The reslut is: error in dyn.load(x,as.logical(local),as.logical(now)): unable to load shared library /home/user/fortran/aaa.so: ld.so.1: /usr/local/lib/R/bin/R.bin: fatal: relocation error: file /home/ymu/ft/aaa.so: symbol _F90free: referenced symbol not found. Does this mean that the shared library was not built successfully or my fortran subroutine has some errors? The former. You appear to have used different Fortran compilers to build R and your shared object, since your Fortran support libraries are not being linked against. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] filtering ts with arima
I know that there is no direct equivalent to arima.filt in R. I also know that your R calls are *not* equivalent to the S-PLUS ones. I would use S-PLUS to run S-PLUS code: you are a commercial operation and should be able to afford it, Or you could employ an S programmer to convert the code for you. As `_' is strongly deprecated in both S-PLUS and R, it should to be used in postings. On Wed, 9 Apr 2003, Samak, Vele [EQRE] wrote: Anyone know how to do this? Thanks, -Original Message- From: Samak, Vele [EQRE] Sent: Monday, April 07, 2003 11:30 AM To: '[EMAIL PROTECTED]' Subject: [R] filtering ts with arima Hi, I have the following code from Splus that I'd like to migrate to R. So far, the only problem is the arima.filt function. This function allows me to filter an existing time-series through a previously estimated arima model, and obtain the residuals for further use. Here's the Splus code: # x is the estimation time series, new.infl is a timeseries that contains new information # a.mle is estimated result (list) from arima.mle, (1,0,1) x (1,0,1)12 seasonal model mdl _ list(list(order=c(1,0,1)), list(order=c(1,0,1), period=12)) a.mle _ arima.mle(x, model = mdl) # then, we get regular residuals: new.pred_ arima.filt(new.infl, a.mle$model)$pred new.res _ new.infl - new.pred The R code from library(ts) would be: # new.infl is a timeseries # a.mle is estimated result (list) from arima.mle, (1,0,1) x (1,0,1)12 seasonal model a2.mle _ arima(x, order=c(1,0,1), seasonal=list(order=c(1,0,1), period=12), include.mean=F, method=ML) new.infl new.res _ new.infl - new.pred What's the arima.filt equivalent in R: filter doesn't seem to take the coefficients for a seasonal model correctly, also predict isn't quite the answer? Help is appreciated. Thanks, Vele Samak Vice President Global Quantitative Research Group CITIGROUP / Smith Barney 388 Greenwich St. 29th Floor New York, NY 10013 (212) 816-0379 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] command line limit?
On Tue, 25 Mar 2003, dederderian wrote: Very insightful. Thanks Martin. Maybe, I need to explain my problem a little better. Yes, please do: you seem to be talking about console input lines, not the command line at all. I am creating an R comfile within a perl script. When I run this R comfile using: source(Rcomfile.txt) It works fine. When I run it from within my perl script using: R --no-save Rcomfile.txt It does not work. I receive this error message in the middle of a long command line: Error: syntax error Execution halted I only see this problem when I have really long command lines within the comfile. I don't really have a work around for getting rid of my long command lines so I would like to find a way to make this work. Why can't you call source() in Rcomfile.txt? AFAIK there is a 1022 char limit on input lines at the console, including redirected. From src/unix/system.txt * 2. CONSOLE I/O * * The first group of functions is concerned with reading and * writing to the system console. * *int R_ReadConsole(char *prompt, char *buf, int buflen, int hist) * * This function prints the given prompt at the console and then * does a gets(3)-like operation, transferring up to buflen characters * into the buffer buf. The last two characters are set to \n\0 * to preserve sanity. and buflen is 1024 in src/main/main.c -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] na.action in model.tables and TukeyHSD
ndata - na.omit(led1t7sts) and work with ndata. Why is that difficult? On Fri, 28 Feb 2003, CG Pettersson wrote: In 27/2, I got the following answer from Prof. Ripley: (The question is at the bottom) This ia already fixed in R-devel. The answer is the same: don't use na.omit implicitly: use it explicitly. I feel rather stupid for the moment, as I don´t understand an answer that looks very simple. What´s the code to do the trick using na.omit explicitly? (Preferably starting with my code in the question) I can´t get it to work, so my tries are not worth printing here... Thanks /CG On Wed, 26 Feb 2003, CG Pettersson wrote: Hello everybody! I use R 1.6.2 in Windows, and have a problem controlling the na.action. In a dataset with twelve trials, one of the trials lack any readings of the variable STS.SH (standing power at harvest) Fitting an aov() object with the call: led1t7sts.aov - aov(STS.SH ~ Trial/Block + Treatment + Treatment:Trial, data = led1t7, na.action=na.exclude) seems to work as it produces an object with 10 df for the factor Trial. But when I use model.tables or TukeyHSD on the object I get this: model.tables(led1t7sts.aov, means) Error in replications(paste(~, paste(names(tables), collapse = +)), : na.action must be a function I have tried to use na.action=na.exclude inside the model.tables call as well, without any bettering. I can naturally cope with the problem by taking the whole trial away from the dataset, but it doesn´t feel very sophisticated...;-) (Prof. Ripley answered a similar question from me two weeks ago. The answer was good but didn´t work as the reason of the error was the same as this time: a whole trial with only na:s in it). Thanks /CG CG Pettersson [EMAIL PROTECTED] CG Pettersson [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Why does 'exists' need a quoted argument?
foo - bar exists(foo) asks if the object whose name is bar exists, not that whose name is foo exists. There is a distinction between operating on objects (rm and is.na) and names of objects (get, exists, help). The one exception in your list is help. That should really be help(rm) (which works), but help has special semantics (as do library, require and a few others). On Thu, 20 Feb 2003, Wright, Kevin wrote: Some functions in R need quoted arguments. Consider this list: help(rm) rm(a) is.na(a) get(rm) exists(rm) Can someone explain why 'get' and 'exists' require quoted object names? Would it make sense (more consistency) to have these functions check to see if the first argument is a string, and if not, then 'substitute' it?Intuitively, 'exists' is checking to see if an object exists, not to see if a character string exists. Evidently my intuition is wrong. I can see that 'get' might need to have the option of using quotes, for example, get(?) or get(*). However, look at this: is.function(?) Error: syntax error is.function(?) [1] FALSE I grow used to not quoting things and then stumble over 'exists' from time to time. Looking forward to clarity or maybe a request for change. Get used to quoting things -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] multivariate sampling question again
R-devel already contains rmultinom. I don't see why rejection sampling on (m, n) should be slow unless m-n is very small or far out in the tails, in which case why do you want this? In any case, inversion will be a perfectly adequate method as you have pbeta and qbeta. On Mon, 17 Feb 2003, Peng Zhang wrote: Dr. Bolker I just wrote it yesterday. Thank you anyway. However do you have some ideas about sampling from restricted beta distribution. say from beta(a, b) but value between m and n. Now I generate lots of samples from beta(a, b) and then choose value between m and n, but it is very time-consuming. Do you have some good ideas? Thanks again! -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] multilm for simseg/acm
On Mon, 10 Feb 2003, Christian Schulz wrote: hi, for working with the simseg/acm approach i need multilm and it seems that the last version is 0.1-4.tar ? What's wrong in the description file, if i attempt install the package ? c:\DataMining\rw1062\binRcmd Install multilm Malformed DCF file (file multilm/DESCRIPTION, line 6) [R1.6.2 /W2K] P.S. ..hmm a solution might be import the functions from multilm in my .Rprofile, but i would like understand the package problem ! It appears to have an empty Depends: line, so delete it. Also, the wrapping on the Description: line is wrong, and there is no Maintainer field. -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] postgres/R access problems
On 10 Feb 2003, Brendan Murray wrote: I have a problem that has exhausted my ingenuity and would like pointers to a solution, or at least where to debug. - I am using R and postgresql. And which R package are you using, which version, from which repository? -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] floating point question
It's a difference in the `libc'. Asking for more precision than the arithmetic has is asking for fairly random results. The differences are as likely to be in the *printing* as in the computations. On Fri, 31 Jan 2003, Bob Gray wrote: Does anyone know precisely what is different about the arithmetic and/or storage of double precision floating point to produce the following differences between the Sun and Windows versions (Splus 6 on the same Windows 2000 machine gives the same results as Solaris)? R 1.6.1, Sun Solaris, gcc + an old Sun f77 options(digits=20) 1+(1/2^53+1/2^106) [1] 1 1+(1/2^53+1/2^105) [1] 1.0002 1+(1/2^53+1/2^64) [1] 1.0002 1+(1/2^53+1/2^63) [1] 1.0002 R 1.6.1, Windows 2000, binary downloaded from CRAN options(digits=20) 1+(1/2^53+1/2^106) [1] 1 1+(1/2^53+1/2^105) [1] 1 1+(1/2^53+1/2^64) [1] 1 1+(1/2^53+1/2^63) [1] 1.0002 (This may be frivolous, but I have been using the first 2 lines as an example in a course.) Thanks -- Bob Gray __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] printing reals from C with digits
On Wed, 29 Jan 2003, Ott Toomet wrote: I want to print real numbers in C code with different values for digits. How to do that? Use Rprintf or PrintValue. You'll need to work hard to convince me that Rprintf is not adequate. As I have understood, what I should do is to call StringFromReal() That's a coercion, not a printing routine. which calls FormatReal(), that one suggests the parameters (width, decimal places and exponential form). FormatReal() includes eps = pow(10.0, -(double)R_print.digits); So I guess I have to change the value of R_print.digits. R_print.digits is defined in include/Print.h in the package source, but unfortunately the installed version (in /usr/lib/R/include/R_ext) is quite a different. R_ext/Print.h and Print.h are not the same thing: one is not a version of the other. The routines you mention are not documented in R-exts, and are not part of the API. I guess that is because the structure is not meant to be accessible by user, although some system routines alter R_print.digits directly. (Only the coercion and print routines!) So are there any good way to achieve it? Temporarily change the options(digits) and call PrintValue(). You are not meant to (and it is not safe to) mess with R's printing internals, and these structures change even at patch releases. -- 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 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Logistic regression: At times correlation matrix ofcoefficients gets messed up
It's not messed up, just someone's idea of a compact display. Options are 1) Use vcov(fit) instead 2) Use print(summary(fit), symbolic.cor=FALSE) Does anyone think that the current arrangement (use this scheme for more than 4 coefficients) is sensible? Surely the abbreviations are not (( for intercept?), and why is the diagonal being shown but the top row and last column have been omitted? If the whole matrix was shown, the column labels could be omitted. I'd much prefer symbolic.cor=FALSE to be the default. On Mon, 20 Jan 2003, Pankaj Choudhary wrote: Hi, When I include a categorical variable (RACE with 3 levels - white, black and other) in my logistic regression model, the correlation matrix of the coefficients gets messed up. I get something like: - Correlation of Coefficients: ( A L RACEb AGE , 1 LWT , 1 RACEblack 1 RACEother . . attr(,legend) [1] 0 ` ' 0.3 `.' 0.6 `,' 0.8 `+' 0.9 `*' 0.95 `B' 1 - I couldn't figure out how to interpret it. Here is the sequence of commands and the complete output. (I am using R 1.6.2) -- 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 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] read.table(file=clipboard,...) for R?
On Mon, 20 Jan 2003, Prof Brian D Ripley wrote: On Mon, 20 Jan 2003, David Parkhurst wrote: I use read.table(file=clipboard,...) a lot in s-plus (under windows 2000), but it does not seem to work in R (and is not in the help screen for read.table). Am I missing something? Would this ability be hard to add? Yes, it was hard to add, but it already there in R-devel (to be 1.7.0). In 1.6.2 you can use read.table(textConnection(readClipboard), ...) Oops, the cut-and-paste failed: read.table(textConnection(readClipboard()), ...) -- 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 272860 (secr) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
