Re: [R] how to add error bar to the data in R?
Hello, Use the function xYplot from hmisc package cheers, Marta __ [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
[R] noncommutative addition: NA+NaN != NaN+NA
Hi guys. Check this out: NaN +NA [1] NaN NA + NaN [1] NA I thought + was commutative by definition. What's going on? R.version _ platform powerpc-apple-darwin6.8 arch powerpc os darwin6.8 system powerpc, darwin6.8 status major1 minor9.0 year 2004 month04 day 12 language R (Both give NA under linux, so it looks like a version-specific issue). -- Robin Hankin Uncertainty Analyst Southampton Oceanography Centre SO14 3ZH tel +44(0)23-8059-7743 [EMAIL PROTECTED] (edit in obvious way; spam precaution) __ [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] noncommutative addition: NA+NaN != NaN+NA
On Tue, 7 Sep 2004, Robin Hankin wrote: Check this out: I am unable to reproduce it on any of the 7 different systems I checked (Solaris, Linux, Windows with various compilers). NaN +NA [1] NaN NA + NaN [1] NA I thought + was commutative by definition. What's going on? It is clearly not under your compiler/OS. We could add a configure test for broken systems and fix it in arithmetic.c but it hardly seems worthwhile. R.version _ platform powerpc-apple-darwin6.8 arch powerpc os darwin6.8 system powerpc, darwin6.8 status major1 minor9.0 year 2004 month04 day 12 language R (Both give NA under linux, so it looks like a version-specific issue). Linux on that hardware? It might be a chip issue. -- 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] noncommutative addition: NA+NaN != NaN+NA
On Tue, 2004-09-07 at 12:47, Prof Brian Ripley wrote: On Tue, 7 Sep 2004, Robin Hankin wrote: Check this out: I am unable to reproduce it on any of the 7 different systems I checked (Solaris, Linux, Windows with various compilers). NaN +NA [1] NaN NA + NaN [1] NA I thought + was commutative by definition. What's going on? platform powerpc-apple-darwin6.8 arch powerpc os darwin6.8 system powerpc, darwin6.8 status (Both give NA under linux, so it looks like a version-specific issue). Linux on that hardware? It might be a chip issue. I tried this in Linux on Mac iBook G4, and the results were the same: NaN+NA was NaN, just like in MacOS X version. So it looks like a chip issue. However, the RPM built from the src.rpm packages at CRAN failed in some checks in Linux/iBook. cheers, jari oksanen -- Jari Oksanen [EMAIL PROTECTED] __ [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] noncommutative addition: NA+NaN != NaN+NA
Dear Professor Ripley thank you for your reply. NaN +NA [1] NaN NA + NaN [1] NA I thought + was commutative by definition. What's going on? It is clearly not under your compiler/OS. We could add a configure test for broken systems and fix it in arithmetic.c but it hardly seems worthwhile. [snip] (Both give NA under linux, so it looks like a version-specific issue). Linux on that hardware? It might be a chip issue. Sorry, that should read Both give NA under linux on an i686 system, RedHat Linux 2.4.18 In any event, + appears to be associative (which is what I was interested in). best wishes rksh -- Robin Hankin Uncertainty Analyst Southampton Oceanography Centre SO14 3ZH tel +44(0)23-8059-7743 [EMAIL PROTECTED] (edit in obvious way; spam precaution) __ [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] Error when running configure on xeon with r-1-9-patched
Prof Brian Ripley wrote:
Is libg2c.so in your library path? That's one common problem.
Many thanks for your reply Prof. Ripley. How can I check what my library
path is?
cat /etc/ld.so.conf gives
include ld.so.conf.d/*.conf
/usr/X11R6/lib
/usr/lib/qt-3.3/lib
/usr/local/lib
and I don't have LD_LIBRARY_PATH set. libg2c.so is in
/usr/lib/gcc-lib/i386-redhat-linux/3.3.3 and libg2c.so.0 and
libg2c.so.0.0.0 both link from /usr/lib to libg2c.so in
/usr/lib/gcc-lib/i386-redhat-linux/3.3.3. This is the same setup as the
other Fedora boxes I have compiled R on.
On Mon, 6 Sep 2004, Gavin Simpson wrote:
Dear list,
I'm having a problem configuring R-1-9-patched on a Intel Xeon machine
running Fedora Core 2. I used svn to checkout the source, altered
config.site to add some optimisation flags to match the Fedora rpm on
CRAN (the flags work fine on two other P3 or P4 machines I've compiled R
on).
(Configure does not know about P3 vs P4 vs Xeon.)
snip
The full section of the config log relating to this error is appended below.
Many thanks,
Gavin
##excerpt from config.log##
configure:25282: gcc -o conftest -D__NO_MATH_INLINES -mieee-fp -O2 -g
-pipe -march=i386 -mcpu=i686 -I/usr/local/include -L/usr/local/lib
conftest.c -lreadline -ldl -lncurses -lm -L/usr/local/lib
-L/usr/lib/gcc-lib/i386-redhat-linux/3.3.3
-L/usr/lib/gcc-lib/i386-redhat-linux/3.3.3/../../.. -lfrtbegin -lg2c -lm
-lgcc_s -lieee 5
/usr/lib/gcc-lib/i386-redhat-linux/3.3.3/../../../libieee.a(.data+0x0):
multiple definition of `_LIB_VERSION'
/usr/lib/gcc-lib/i386-redhat-linux/3.3.3/../../../libieee.a(.data+0x0):
first defined here
collect2: ld returned 1 exit status
configure:25288: $? = 1
configure: failed program was:
| /* confdefs.h. */
|
| #define PACKAGE_NAME R
| #define PACKAGE_TARNAME R
| #define PACKAGE_VERSION 1.9.1
| #define PACKAGE_STRING R 1.9.1
| #define PACKAGE_BUGREPORT [EMAIL PROTECTED]
| #define PACKAGE R
| #define VERSION 1.9.1
| #define R_PLATFORM i686-pc-linux-gnu
| #define R_CPU i686
| #define R_VENDOR pc
| #define R_OS linux-gnu
| #define Unix 1
| #ifdef __cplusplus
| extern C void std::exit (int) throw (); using std::exit;
| #endif
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_LIBM 1
| #define HAVE_LIBNCURSES 1
| #define HAVE_LIBDL 1
| #define HAVE_LIBREADLINE 1
| #define STDC_HEADERS 1
| #define TIME_WITH_SYS_TIME 1
| #define HAVE_DIRENT_H 1
| #define HAVE_SYS_WAIT_H 1
| #define HAVE_ARPA_INET_H 1
| #define HAVE_DLFCN_H 1
| #define HAVE_ELF_H 1
| #define HAVE_FCNTL_H 1
| #define HAVE_FPU_CONTROL_H 1
| #define HAVE_GRP_H 1
| #define HAVE_IEEE754_H 1
| #define HAVE_LOCALE_H 1
| #define HAVE_NETDB_H 1
| #define HAVE_NETINET_IN_H 1
| #define HAVE_PWD_H 1
| #define HAVE_READLINE_HISTORY_H 1
| #define HAVE_READLINE_READLINE_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_SYS_PARAM_H 1
| #define HAVE_SYS_SELECT_H 1
| #define HAVE_SYS_SOCKET_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_SYS_TIMES_H 1
| #define HAVE_SYS_UTSNAME_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_WCHAR_H 1
| #define HAVE_ERRNO_H 1
| #define HAVE_STDARG_H 1
| #define HAVE_STRING_H 1
| #define HAVE_POSIX_SETJMP 1
| #define HAVE_GLIBC2 1
| #define RETSIGTYPE void
| #define SOCKLEN_T socklen_t
| #define SIZEOF_INT 4
| #define INT_32_BITS 1
| #define SIZEOF_LONG 4
| #define SIZEOF_LONG_LONG 8
| #define SIZEOF_LONG_DOUBLE 12
| /* end confdefs.h. */
| #define F77_DUMMY_MAIN _main
| #ifdef F77_DUMMY_MAIN
|
| # ifdef __cplusplus
| extern C
| # endif
|int F77_DUMMY_MAIN() { return 1; }
|
| #endif
| int
| main ()
| {
|
| ;
| return 0;
| }
configure:25321: result: unknown
configure:25341: error: linking to Fortran libraries from C fails
See `config.log' for more details.
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson [T] +44 (0)20 7679 5522
ENSIS Research Fellow [F] +44 (0)20 7679 7565
ENSIS Ltd. ECRC [E] [EMAIL PROTECTED]
UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/
26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/
London. WC1H 0AP.
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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Re: [R] noncommutative addition: NA+NaN != NaN+NA
Robin Hankin [EMAIL PROTECTED] writes: Dear Professor Ripley thank you for your reply. NaN +NA [1] NaN NA + NaN [1] NA I thought + was commutative by definition. What's going on? It is clearly not under your compiler/OS. We could add a configure test for broken systems and fix it in arithmetic.c but it hardly seems worthwhile. Didn't we do this discussion before? AFAIR, the thing is that IEEE specifies that NaN + whatever == whatever + NaN == NaN, but NaN is only specified a bit pattern in the first couple of bytes. R uses a special value in the lower bytes (1954 -- BTW, when *is* Ross' birthday?) to signal the NA, but we can't really expect that chip makers do what we hope they'd do with that part of the value. I think we resolved that specific checking for this issue would be too much of a performance killer, especially since R generally treats NaN as NA anyway. [snip] (Both give NA under linux, so it looks like a version-specific issue). Linux on that hardware? It might be a chip issue. Sorry, that should read Both give NA under linux on an i686 system, RedHat Linux 2.4.18 In any event, + appears to be associative (which is what I was interested in). Eh? That is something that is almost certainly not true for FP arithmetic, e.g. (1 + 1e-16) + 1e-16 == 1 + (1e-16 + 1e-16) [1] FALSE -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [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] how to add error bar to the data in R?
Alternatively, use the plotCI() function from the gregmisc package.
-G
-Original Message-
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Sent: 9/7/04 5:08 AM
Subject: Re: [R] how to add error bar to the data in R?
Hello,
Use the function xYplot from hmisc package
cheers,
Marta
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LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
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Re: [R] noncommutative addition: NA+NaN != NaN+NA
On 7 Sep 2004, Peter Dalgaard wrote: Robin Hankin [EMAIL PROTECTED] writes: Dear Professor Ripley thank you for your reply. NaN +NA [1] NaN NA + NaN [1] NA I thought + was commutative by definition. What's going on? It is clearly not under your compiler/OS. We could add a configure test for broken systems and fix it in arithmetic.c but it hardly seems worthwhile. Didn't we do this discussion before? Certainly over NA vs 0+NA, as in this excerpt from reg-tests-1.R ## matching NAs on Solaris (MM 2002-08-02) # x - as.double(NA) # identical(x + 0, x) # stopifnot(match(x + 0, x, 0) == 1) ## match failed on Solaris with some compiler settings ## NA+0 is not guaranteed to be NA: could be NaN AFAIR, the thing is that IEEE specifies that NaN + whatever == whatever + NaN == NaN, but NaN is only specified a bit pattern in the first couple of bytes. R uses a special value in the lower bytes (1954 -- BTW, when *is* Ross' birthday?) to signal the NA, but we can't really expect that chip makers do what we hope they'd do with that part of the value. I think we resolved that specific checking for this issue would be too much of a performance killer, especially since R generally treats NaN as NA anyway. -- 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] Cox regression for prevalence estimates
Bernardo Rangel Tura wrote: At , The Michaelson Institute wrote: How can R be used to calculate the prevalence ratios using Cox regression + robust variance estimates ? Well, In Design package have a command: cph This command have a option robsut with default=FALSE, but in help is write: ... robust if TRUE a robust variance estimate is returned. ... I think that is your response... bye Bernardo Rangel Tura, MD, MSc National Institute of Cardiology Laranjeiras Rio de Janeiro Brazil No, robust is an option to coxph, not cph. cph uses 'after the fit' correction using the robcov or bootcov functions in Design. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ [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] Error when running configure on xeon with r-1-9-patched
Peter Dalgaard wrote: Gavin Simpson [EMAIL PROTECTED] writes: configure:25282: gcc -o conftest -D__NO_MATH_INLINES -mieee-fp -O2 -g -pipe -march=i386 -mcpu=i686 -I/usr/local/include -L/usr/local/lib conftest.c -lreadline -ldl -lncurses -lm -L/usr/local/lib -L/usr/lib/gcc-lib/i386-redhat-linux/3.3.3 -L/usr/lib/gcc-lib/i386-redhat-linux/3.3.3/../../.. -lfrtbegin -lg2c -lm -lgcc_s -lieee 5 /usr/lib/gcc-lib/i386-redhat-linux/3.3.3/../../../libieee.a(.data+0x0): multiple definition of `_LIB_VERSION' /usr/lib/gcc-lib/i386-redhat-linux/3.3.3/../../../libieee.a(.data+0x0): first defined here I think this means that you're linking the same library twice. Did you put the -lieee in there yourself? (via config.site, e.g.). Hi Peter, Yep, that's it. Copied far too many flags from one machine's configure output into the config.site file on the new machine - that'll teach me to do things in a hurry and late in the day! Removing the duplicated flags allows configure to work now. Thanks to Peter, Prof. Ripley and Martyn for their help solving my error. As always it is much appreciated. Gav -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [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] Cox regression for prevalence estimates
At 09:27 07/09/2004, you wrote: Bernardo Rangel Tura wrote: At , The Michaelson Institute wrote: How can R be used to calculate the prevalence ratios using Cox regression + robust variance estimates ? Well, In Design package have a command: cph This command have a option robsut with default=FALSE, but in help is write: ... robust if TRUE a robust variance estimate is returned. ... I think that is your response... bye Bernardo Rangel Tura, MD, MSc National Institute of Cardiology Laranjeiras Rio de Janeiro Brazil No, robust is an option to coxph, not cph. cph uses 'after the fit' correction using the robcov or bootcov functions in Design. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University Sorry Frank! I made a digitation mistake, but I think yours package answers the Tomas Karpati´s need. Thanks in advance Bernardo Rangel Tura, MD, MSc National Institute of Cardiology Laranjeiras Rio de Janeiro Brazil __ [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
[R] Further png() question
Ok, I have reinstalled R-1.9.0 and this appears to have fixed the problems I was having with png(). However, I have a further question regarding png() Is it possible to pass a par() argument to the png() command? I am wanting to produce 4 plots per object, which I normally acheive on an X window by par(mfrow=c(1,4)). I have tried calling a new plot and setting par in this way but this has no bearing when I call png(). Any suggestions? Thanks in advance, Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 mail: [EMAIL PROTECTED] __ [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] noncommutative addition: NA+NaN != NaN+NA
At 06:17 07/09/2004, you wrote: Hi guys. Check this out: NaN +NA [1] NaN NA + NaN [1] NA I thought + was commutative by definition. What's going on? In my version, both cases is NA: NaN +NA [1] NA NA + NaN [1] NA R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major1 minor9.1 year 2004 month06 day 21 language R Bernardo Rangel Tura, MD, MSc National Institute of Cardiology Laranjeiras Rio de Janeiro Brazil __ [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] Further png() question
Are you calling png before your par command--I think you should. png (file='filename') par(mfrow=c(1,4)) plot(1:10) plot(1:10) plot(1:10) plot(1:10) dev.off() See if that works for you. Sean On Sep 7, 2004, at 10:37 AM, Laura Quinn wrote: Ok, I have reinstalled R-1.9.0 and this appears to have fixed the problems I was having with png(). However, I have a further question regarding png() Is it possible to pass a par() argument to the png() command? I am wanting to produce 4 plots per object, which I normally acheive on an X window by par(mfrow=c(1,4)). I have tried calling a new plot and setting par in this way but this has no bearing when I call png(). Any suggestions? Thanks in advance, Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 mail: [EMAIL PROTECTED] __ [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 __ [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] debugging an S4 method
Bickel, David wrote:
Does anyone know how to use the equivalent of debug() on an S4 method? I would like
R to enter the browser not for the generic function, but for the method of the class
that I specify.
This is what the trace() function does, if you supply the signature=
argument set to the class or combination of classes for which you want
to examine the selected method.
Typically, a call would be of the form:
trace(myFun, signature=myClass, browser, exit=browser)
which would call the browser on entry to the myClass method and again
before exiting. See ?trace for details.
(There are a few bug fixes and added features in the upcoming 2.0.0
version).
Thanks,
David
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Research Scientist
Pioneer Hi-Bred International
Bioinformatics Exploratory Research
7250 NW 62nd Ave., PO Box 552
Johnston, Iowa 50131-0552
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Re: [R] Further png() question
Laura Quinn wrote: Ok, I have reinstalled R-1.9.0 and this appears to have fixed the problems I was having with png(). However, I have a further question regarding png() Is it possible to pass a par() argument to the png() command? I am wanting to produce 4 plots per object, which I normally acheive on an X window by par(mfrow=c(1,4)). I have tried calling a new plot and setting par in this way but this has no bearing when I call png(). You have to call par() after png() rather than before: png(test.png) par(mfrow=c(1,4)) replicate(4, plot(1:10)) dev.off() Uwe Ligges Any suggestions? Thanks in advance, Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 mail: [EMAIL PROTECTED] __ [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 __ [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] Further png() question
The following is not a problem in R 1.9.1: png(file = test.png) par(mfrow = c(2,2)) plot(c(1:10)) plot(c(1:10)) plot(c(1:10)) plot(c(1:10)) dev.off() null device 1 Have you tried that? HTH, Partha Laura Quinn [EMAIL PROTECTED] Sent by: [EMAIL PROTECTED] 09/07/2004 10:37 AM To: [EMAIL PROTECTED] cc: Subject:[R] Further png() question Ok, I have reinstalled R-1.9.0 and this appears to have fixed the problems I was having with png(). However, I have a further question regarding png() Is it possible to pass a par() argument to the png() command? I am wanting to produce 4 plots per object, which I normally acheive on an X window by par(mfrow=c(1,4)). I have tried calling a new plot and setting par in this way but this has no bearing when I call png(). Any suggestions? Thanks in advance, Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 mail: [EMAIL PROTECTED] __ [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 __ [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] Further png() question
Insert the par() call after png(). par() is device-specific. Andy From: Laura Quinn Ok, I have reinstalled R-1.9.0 and this appears to have fixed the problems I was having with png(). However, I have a further question regarding png() Is it possible to pass a par() argument to the png() command? I am wanting to produce 4 plots per object, which I normally acheive on an X window by par(mfrow=c(1,4)). I have tried calling a new plot and setting par in this way but this has no bearing when I call png(). Any suggestions? Thanks in advance, Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 mail: [EMAIL PROTECTED] __ [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 __ [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] Further png() question
On 7 Sep 2004 at 15:37, Laura Quinn wrote: Ok, I have reinstalled R-1.9.0 and this appears to have fixed the problems I was having with png(). However, I have a further question regarding png() Is it possible to pass a par() argument to the png() command? I am wanting to produce 4 plots per object, which I normally acheive on an X window by par(mfrow=c(1,4)). I have tried calling a new plot and setting par in this way but this has no bearing when I call png(). Hi png(myplot.png, 800,800) par(mfrow=c(1,4)) for (i in 1:4) boxplot(rnorm(10)*i) dev.off() seems to work or seems to produce 4 graphs on 1 png device. Is this what you want? Cheers Petr Any suggestions? Thanks in advance, Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 mail: [EMAIL PROTECTED] __ [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 Petr Pikal [EMAIL PROTECTED] __ [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] Further png() question
Thanks all! It appears I just had the par in the wrong place in my loop. Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 mail: [EMAIL PROTECTED] On Tue, 7 Sep 2004, Petr Pikal wrote: On 7 Sep 2004 at 15:37, Laura Quinn wrote: Ok, I have reinstalled R-1.9.0 and this appears to have fixed the problems I was having with png(). However, I have a further question regarding png() Is it possible to pass a par() argument to the png() command? I am wanting to produce 4 plots per object, which I normally acheive on an X window by par(mfrow=c(1,4)). I have tried calling a new plot and setting par in this way but this has no bearing when I call png(). Hi png(myplot.png, 800,800) par(mfrow=c(1,4)) for (i in 1:4) boxplot(rnorm(10)*i) dev.off() seems to work or seems to produce 4 graphs on 1 png device. Is this what you want? Cheers Petr Any suggestions? Thanks in advance, Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 mail: [EMAIL PROTECTED] __ [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 Petr Pikal [EMAIL PROTECTED] __ [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
[R] gridBase and heatmap
I would like to use gridBase to place four separate heatmaps (actually,
a stripped-down heatmap.2 from ght gregmisc package that contains only
the image part) into four different viewports. I can get the
placement correct, but I keep 'losing' the previous plot. Any
suggestions?
Here is some quick example code trying to put a heatmap into the left
viewport and then put a second one into the upper right.
Thanks in advance for insight
Sean
pushViewport(viewport(layout = grid.layout(1, 3, widths =
unit(rep(1,3), c(null, cm, null)
viewport[GRID.VP.177]
pushViewport(viewport(layout.pos.col=1))
viewport[GRID.VP.178]
par(omi=gridOMI(),new=T)
my.heatmap(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),],breaks=c(seq(-2.5,-0.6,0.1),
-0.1,0.10,seq(0.6,2.5,0.1)),dendrogram=none,Colv=c(9:12,5:8,1:
4),labRow=rep('',520),margin=c(10,5),colsep=c(4,8),trace=none,density.
info=none,col=greenred.colors(40),key=F)
popViewport()
viewport[GRID.VP.177]
pushViewport(viewport(layout.pos.col=3))
viewport[GRID.VP.179]
pushViewport(viewport(layout = grid.layout(3, 1, heights =
unit(rep(1,3), c(null, null, null)
viewport[GRID.VP.180]
pushViewport(viewport(layout.pos.row=1))
viewport[GRID.VP.181]
par(omi=gridOMI(),new=T)
my.heatmap(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),][tmp[505:520],],breaks=c(seq(-2.5,-0.6,0.1),
-0.1,0.10,seq(0.6,2.5,0.1)),dendrogram=none,labRow=sapply(getSYMBOL(as
.character(rownames(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),])),'BrafPkg')[tmp[505:520]],function(x)
{ifelse(is.na(x),EST,x)}),Colv=c(9:12,5:8,1:
4),margin=c(10,5),colsep=c(4,8),trace=none,density.info=none,col=gre
enred.colors(40),key=F)
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[R] contrast/test statements in polynomial mixed model
Hello I am having some trouble figuring out how to write contrast/test syntax for the following mixed model regression y ~ group*age + group*age^2 random =~1|ID (i have centered the age variable there are only 2 groups) the contrast i am trying to construct should compare the overall shape of the 2 groups -- in SAS, this does the trick -- test 'group difference in shape' age_squared*group1 -1; age_cent*group 1 -1 Suggestions would be greatly appreciated Thanks in advance Dede Greenstein __ [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] gridBase and heatmap
The problem is that most base plotting functions first wipe the graphics
device clean. To do what you want, you need to use par(new = T) liberally
between plots. Does that work for you?
Kevin
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sean Davis
Sent: Tuesday, September 07, 2004 10:01 AM
To: r-help
Subject: [R] gridBase and heatmap
I would like to use gridBase to place four separate heatmaps (actually,
a stripped-down heatmap.2 from ght gregmisc package that contains only
the image part) into four different viewports. I can get the
placement correct, but I keep 'losing' the previous plot. Any
suggestions?
Here is some quick example code trying to put a heatmap into the left
viewport and then put a second one into the upper right.
Thanks in advance for insight
Sean
pushViewport(viewport(layout = grid.layout(1, 3, widths =
unit(rep(1,3), c(null, cm, null)
viewport[GRID.VP.177]
pushViewport(viewport(layout.pos.col=1))
viewport[GRID.VP.178]
par(omi=gridOMI(),new=T)
my.heatmap(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),],breaks=c(seq(-2.5,-0.6,0.1),
-0.1,0.10,seq(0.6,2.5,0.1)),dendrogram=none,Colv=c(9:12,5:8,1:
4),labRow=rep('',520),margin=c(10,5),colsep=c(4,8),trace=none,density.
info=none,col=greenred.colors(40),key=F)
popViewport()
viewport[GRID.VP.177]
pushViewport(viewport(layout.pos.col=3))
viewport[GRID.VP.179]
pushViewport(viewport(layout = grid.layout(3, 1, heights =
unit(rep(1,3), c(null, null, null)
viewport[GRID.VP.180]
pushViewport(viewport(layout.pos.row=1))
viewport[GRID.VP.181]
par(omi=gridOMI(),new=T)
my.heatmap(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),][tmp[505:520],],breaks=c(seq(-2.5,-0.6,0.1),
-0.1,0.10,seq(0.6,2.5,0.1)),dendrogram=none,labRow=sapply(getSYMBOL(as
.character(rownames(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),])),'BrafPkg')[tmp[505:520]],function(x)
{ifelse(is.na(x),EST,x)}),Colv=c(9:12,5:8,1:
4),margin=c(10,5),colsep=c(4,8),trace=none,density.info=none,col=gre
enred.colors(40),key=F)
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Re: [R] gridBase and heatmap
Kevin,
Thanks for the advice. However, I was pretty careful to include a
par(new=T) [see below].
Sean
On Sep 7, 2004, at 1:14 PM, Kevin Bartz wrote:
The problem is that most base plotting functions first wipe the
graphics
device clean. To do what you want, you need to use par(new = T)
liberally
between plots. Does that work for you?
Kevin
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Sean Davis
Sent: Tuesday, September 07, 2004 10:01 AM
To: r-help
Subject: [R] gridBase and heatmap
I would like to use gridBase to place four separate heatmaps (actually,
a stripped-down heatmap.2 from ght gregmisc package that contains only
the image part) into four different viewports. I can get the
placement correct, but I keep 'losing' the previous plot. Any
suggestions?
Here is some quick example code trying to put a heatmap into the left
viewport and then put a second one into the upper right.
Thanks in advance for insight
Sean
pushViewport(viewport(layout = grid.layout(1, 3, widths =
unit(rep(1,3), c(null, cm, null)
viewport[GRID.VP.177]
pushViewport(viewport(layout.pos.col=1))
viewport[GRID.VP.178]
par(omi=gridOMI(),new=T)
my.heatmap(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),],breaks=c(seq(-2.5,-0.6,0.1),
-0.1,0.10,seq(0.6,2.5,0.1)),dendrogram=none,Colv=c(9:12,5:8,1:
4),labRow=rep('',520),margin=c(10,5),colsep=c(4,8),trace=none,density
.
info=none,col=greenred.colors(40),key=F)
popViewport()
viewport[GRID.VP.177]
pushViewport(viewport(layout.pos.col=3))
viewport[GRID.VP.179]
pushViewport(viewport(layout = grid.layout(3, 1, heights =
unit(rep(1,3), c(null, null, null)
viewport[GRID.VP.180]
pushViewport(viewport(layout.pos.row=1))
viewport[GRID.VP.181]
par(omi=gridOMI(),new=T)
my.heatmap(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),][tmp[505:520],],breaks=c(seq(-2.5,-0.6,0.1),
-0.1,0.10,seq(0.6,2.5,0.1)),dendrogram=none,labRow=sapply(getSYMBOL(a
s
.character(rownames(eb$coefficients[(clsum[,1]1) (clsum[,2]1)
(clsum[,3]==0),])),'BrafPkg')[tmp[505:520]],function(x)
{ifelse(is.na(x),EST,x)}),Colv=c(9:12,5:8,1:
4),margin=c(10,5),colsep=c(4,8),trace=none,density.info=none,col=gr
e
enred.colors(40),key=F)
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[R] using text on the x axis ticks rather than numbers
Hello, is there a way in which I can use text labels rather than numbers on the x axis ticks? I basically have a vector of (say) 8 points and I want to plot these sequentially. Thus the x axis would have ticks at 1 .. 8. Rather than having the labels 1 .. 8 I would like to have some arbitrary text labels. Ideally I would like the labels to be rotated (say at 45 degrees) so that they don't overlap with each other. Is this possible? Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Breadth-first search is the bulldozer of science. -- Randy Goebel __ [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] Cox regression for prevalence estimates
robust standard errors are available from coxph with the option robust=TRUE. -thomas On 6 xxx -1, The Michaelson Institute wrote: Hello, I'm an MD working in an eye clinic. I'm learning by myself to use R for use in my research works and for implementation in a software project. There are some authors who recomends the use of Cox regression as a substitute for Logistic regression (a href=http://www.biomedcentral.com/1471-2288/3/21.pdf; Barros AJD, Hirakata VN. BMCMedical Research Methodology, 2003; 3:21 /a. The use of Cox regression permit the estimation of the prevalence rates rather than Odds ratios obtained by logistic regression analysis. Cox regression is used for time-to-event data. To obtain prevalence rates the time has to be constant. One of the problems of Cox regression is that the confidence intervals are overestimated. To correct this Barros Hirakata recommend the use of robust variance estimates. How can R be used to calculate the prevalence ratios using Cox regression + robust variance estimates ? Thanks for your collaboration, Tomas Karpati MD The Michaelson Institute for Rehabilitation of Vision Hadassah Medical Organization __ [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 Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ [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] using text on the x axis ticks rather than numbers
Hi! first supress axis drawing with param axes=FALSE in your plot function. The use axis function to add your axes. ?axis /E On Tue, 7 Sep 2004, Rajarshi Guha wrote: Hello, is there a way in which I can use text labels rather than numbers on the x axis ticks? I basically have a vector of (say) 8 points and I want to plot these sequentially. Thus the x axis would have ticks at 1 .. 8. Rather than having the labels 1 .. 8 I would like to have some arbitrary text labels. Ideally I would like the labels to be rotated (say at 45 degrees) so that they don't overlap with each other. Is this possible? Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Breadth-first search is the bulldozer of science. -- Randy Goebel __ [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 __ [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] using text on the x axis ticks rather than numbers
On Tue, 2004-09-07 at 12:52, Rajarshi Guha wrote: Hello, is there a way in which I can use text labels rather than numbers on the x axis ticks? I basically have a vector of (say) 8 points and I want to plot these sequentially. Thus the x axis would have ticks at 1 .. 8. Rather than having the labels 1 .. 8 I would like to have some arbitrary text labels. Ideally I would like the labels to be rotated (say at 45 degrees) so that they don't overlap with each other. Is this possible? Thanks, Here is an example. For the axis labels, you need to use text() and not mtext() as the latter does not allow for text rotation: # Set margins to make room for x axis labels par(mar = c(7, 4, 4, 2) + 0.1) # Create plot with no x axis and no x axis label plot(1:8, xaxt = n, xlab = ) # Set up x axis with tick marks alone axis(1, labels = FALSE) # Create arbitrary text labels - paste(arbitrary text, 1:8, sep = ) # plot x axis labels using: # par(usr)[3] - 0.25 as the vertical placement # srt = 45 as text rotation angle # adj = 1 to place right end of text at tick mark # xpd = TRUE to allow for text outside the plot region text(1:8, par(usr)[1] - 0.25, srt = 45, adj = 1, labels = labels, xpd = TRUE) # plot x axis label at line 6 (of 7) mtext(1, text = X Axis Label, line = 6) You can adjust the value of the '0.25' offset as required to move the x axis labels up or down relative to the x axis. HTH, Marc Schwartz __ [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
[R] C function name garbled
I wrote an R wrapper function (phylpro) around a C function (Rphylpro). The first time I'm running my function, it runs with no errors. The second time I'm trying to run it, I get an error message with the first argument to .Call garbled. Set up: dyn.load(Phylpro.so) source(phylpro.R) WinHalfWidth-30 permReps-10 breaks-c(548, 735, 832) First call to phylpro succeeds: b-phylpro(simulinfile, breaks, WinHalfWidth, permReps) Second call to phylpro fails: b-phylpro(simulinfile, breaks, WinHalfWidth, permReps) Error in .Call(PSg\bBh\b, input_file = as.character(input_file), breaks = as.integer(breaks), : .Call function name not in load table Check if my C function name is in load table: is.loaded(Rphylpro) [1] TRUE Any ideas? Thanks for your help, S. Blay Department of Statistics and Actuarial Science Simon Fraser University, Vancouver, British Columbia __ [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
[R] Multiple comparisons in a non parametric case
Dear all, I am conducting a full factorial analysis. I have one factor consisting in algorithms, which I consider my treatments, and another factor made of the problems I want to solve. For each problem I obtain a response variable which is stochastic. I replicate the measure of this response value 10 times. When I apply ANOVA the assumptions do not hold, hence I must rely on non parametric tests. By transforming the response data in ranks, the Friedman test tells me that there is statistical significance in the difference of the sum of ranks of at least one of the treatments. I would like now to produce a plot for the multiple comparisons similar to the Least Significant Difference or the Tukey's Honest Significant Difference used in ANOVA. Since I am in the non parametric case I can not use these methods. Instead, I compare graphically individual treatments by plotting the sum of ranks of each treatment togehter with the 95% confidence interval. To compute the interval I use the Friedman test as suggested by Conover in Practical Nonparametric statistics. I obtain something like this: Treat. A|-+-| Treat. B |-+-| Treat. C |-+-| Treat. D |-+-| The intervals have all the same spread because the number of replications was the same for all experimental units. I would like to know if someone in the list had a similar experience and if what I am doing is correct. In alternative also a reference to another list which could better fit my request is welcome. Thank you for the help, Marco -- Marco Chiarandini, Fachgebiet Intellektik, Fachbereich Informatik, Technische Universität Darmstadt, Hochschulstraße 10, D-64289 Darmstadt - Germany, Office: S2/02 Raum E317 Tel: +49 (0)6151 16-6802 Fax: +49 (0)6151 16-5326 email: [EMAIL PROTECTED] web page: http://www.intellektik.informatik.tu-darmstadt.de/~machud __ [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] C function name garbled
On Tue, 7 Sep 2004 12:46:55 -0700, S Blay [EMAIL PROTECTED] wrote : I wrote an R wrapper function (phylpro) around a C function (Rphylpro). The first time I'm running my function, it runs with no errors. The second time I'm trying to run it, I get an error message with the first argument to .Call garbled. Set up: dyn.load(Phylpro.so) source(phylpro.R) WinHalfWidth-30 permReps-10 breaks-c(548, 735, 832) First call to phylpro succeeds: b-phylpro(simulinfile, breaks, WinHalfWidth, permReps) Second call to phylpro fails: b-phylpro(simulinfile, breaks, WinHalfWidth, permReps) Error in .Call(PSg\bBh\b, input_file = as.character(input_file), breaks = as.integer(breaks), : .Call function name not in load table Check if my C function name is in load table: is.loaded(Rphylpro) [1] TRUE Any ideas? It looks to me as though your function is doing something to mess up R's internal data. I'd try commenting out the whole body of the function, then adding it back gradually to find which part causes the trouble. Duncan Murdoch __ [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] using text on the x axis ticks rather than numbers
Out of curiosity, why is srt not respected in mtext ? See examples below plot(1:10, xaxt=n); par(srt=45) mtext( paste(Point, LETTERS[1:10]), side=1, at=1:10 ) plot(1:10, xaxt=n); mtext( paste(Point, LETTERS[1:10]), side=1, at=1:10, srt=45 ) It would be nice to have 'srt' as an argument in mtext in future. Regards, Adai On Tue, 2004-09-07 at 20:01, Marc Schwartz wrote: On Tue, 2004-09-07 at 12:52, Rajarshi Guha wrote: Hello, is there a way in which I can use text labels rather than numbers on the x axis ticks? I basically have a vector of (say) 8 points and I want to plot these sequentially. Thus the x axis would have ticks at 1 .. 8. Rather than having the labels 1 .. 8 I would like to have some arbitrary text labels. Ideally I would like the labels to be rotated (say at 45 degrees) so that they don't overlap with each other. Is this possible? Thanks, Here is an example. For the axis labels, you need to use text() and not mtext() as the latter does not allow for text rotation: # Set margins to make room for x axis labels par(mar = c(7, 4, 4, 2) + 0.1) # Create plot with no x axis and no x axis label plot(1:8, xaxt = n, xlab = ) # Set up x axis with tick marks alone axis(1, labels = FALSE) # Create arbitrary text labels - paste(arbitrary text, 1:8, sep = ) # plot x axis labels using: # par(usr)[3] - 0.25 as the vertical placement # srt = 45 as text rotation angle # adj = 1 to place right end of text at tick mark # xpd = TRUE to allow for text outside the plot region text(1:8, par(usr)[1] - 0.25, srt = 45, adj = 1, labels = labels, xpd = TRUE) # plot x axis label at line 6 (of 7) mtext(1, text = X Axis Label, line = 6) You can adjust the value of the '0.25' offset as required to move the x axis labels up or down relative to the x axis. HTH, Marc Schwartz __ [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 __ [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] using text on the x axis ticks rather than numbers
On Tue, 7 Sep 2004, Adaikalavan Ramasamy wrote: Out of curiosity, why is srt not respected in mtext ? See examples below It doesn't make a lot of sense. mtext is about putting text on margin lines, and even the ability to have text perpendicular to the axis (via las) is rather awkward to interpret (and the interpretation will be changed in 2.0.0). If you are going to rotate text you need to able to specify a point of rotation and that's much easier via text. It would be nice to have 'srt' as an argument in mtext in future. You haven't been listening to the discussions pre-2.0.0 on the semantics of `adj' (and now padj as well) in mtext. Experts seem to find it hard to keep even the two current cases (parallel and perpendicular) clear in their minds. BTW, if you want to use srt with mtext(at=) you can always use 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 272860 (secr) 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] Multiple comparisons in a non parametric case
It looks to me like what you are doing is trying to judge significance of differences by non-overlap of single-sample confidence intervals. While this is appealing, it's not quite right. I just looked into my copy of Applied Nonparametric Statistics (second ed.) by Wayne W. Daniel (Duxbury, 1990) but that only deals with the situation where there is a single replicate per block-treatment combination (whereas you have 10 reps) and block-treatment interaction is assumed to be non-existent. The method that Daniel prescribes in this simple setting seems to be no more than applying the Bonferroni method of multiple comparisons. (Daniel does not say; his book is very much a cook-book.) So you might simply try Bonferroni --- i.e. do all k-choose-2 pairwise comparisons between treatments (using the appropriate 2 sample method for each comparison) doing each comparison at the alpha/k-choose-2 significance level. Where k = the number of treatments = 4 in your case. This method is not going to be super-powerful but it is sometimes surprizing how well Bonferroni stacks up against more ``sophisticated'' methods. Daniel gives a reference to ``Nonparametric Statistical Methods'' by Myles Hollander and Douglas A. Wolfe, New York, Wiley, 1973, for ``an alternative multiple comparisons formula''. I don't have this book, and don't know what direction Hollander and Wolfe ride off in, but it ***might*** be worth trying to get your hands on it and see. Finally --- in what way are the assumptions of Anova violated? The conventional wisdom is that Anova is actually quite robust to non-normality. Particularly when the sample size is large --- and 10 reps per treatment combination is pretty good. Heteroskedasticity is more of a worry, but it's not so much of a worry when the design is nicely balanced. As yours is. And finally-finally --- have you tried transforming your data to make them a bit more normal and/or homoskedastic? I hope this is some help. cheers, Rolf Turner [EMAIL PROTECTED] Marco Chiarandini wrote: I am conducting a full factorial analysis. I have one factor consisting in algorithms, which I consider my treatments, and another factor made of the problems I want to solve. For each problem I obtain a response variable which is stochastic. I replicate the measure of this response value 10 times. When I apply ANOVA the assumptions do not hold, hence I must rely on non parametric tests. By transforming the response data in ranks, the Friedman test tells me that there is statistical significance in the difference of the sum of ranks of at least one of the treatments. I would like now to produce a plot for the multiple comparisons similar to the Least Significant Difference or the Tukey's Honest Significant Difference used in ANOVA. Since I am in the non parametric case I can not use these methods. Instead, I compare graphically individual treatments by plotting the sum of ranks of each treatment togehter with the 95% confidence interval. To compute the interval I use the Friedman test as suggested by Conover in Practical Nonparametric statistics. I obtain something like this: Treat. A|-+-| Treat. B |-+-| Treat. C |-+-| Treat. D |-+-| The intervals have all the same spread because the number of replications was the same for all experimental units. I would like to know if someone in the list had a similar experience and if what I am doing is correct. In alternative also a reference to another list which could better fit my request is welcome. __ [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] Multiple comparisons in a non parametric case
Great summary, Rolf. Just one minor issue that recently bit me: In a data mining application with hundred of p-values, people want to make subtle distinctions based on extremely small p-values. In such applications, even a modest amount of skewness (to say nothing of outliers) might have a surprising (and not necessarily monotonic) impact on p-values. Best Wishes, Spencer Graves Rolf Turner wrote: It looks to me like what you are doing is trying to judge significance of differences by non-overlap of single-sample confidence intervals. While this is appealing, it's not quite right. I just looked into my copy of Applied Nonparametric Statistics (second ed.) by Wayne W. Daniel (Duxbury, 1990) but that only deals with the situation where there is a single replicate per block-treatment combination (whereas you have 10 reps) and block-treatment interaction is assumed to be non-existent. The method that Daniel prescribes in this simple setting seems to be no more than applying the Bonferroni method of multiple comparisons. (Daniel does not say; his book is very much a cook-book.) So you might simply try Bonferroni --- i.e. do all k-choose-2 pairwise comparisons between treatments (using the appropriate 2 sample method for each comparison) doing each comparison at the alpha/k-choose-2 significance level. Where k = the number of treatments = 4 in your case. This method is not going to be super-powerful but it is sometimes surprizing how well Bonferroni stacks up against more ``sophisticated'' methods. Daniel gives a reference to ``Nonparametric Statistical Methods'' by Myles Hollander and Douglas A. Wolfe, New York, Wiley, 1973, for ``an alternative multiple comparisons formula''. I don't have this book, and don't know what direction Hollander and Wolfe ride off in, but it ***might*** be worth trying to get your hands on it and see. Finally --- in what way are the assumptions of Anova violated? The conventional wisdom is that Anova is actually quite robust to non-normality. Particularly when the sample size is large --- and 10 reps per treatment combination is pretty good. Heteroskedasticity is more of a worry, but it's not so much of a worry when the design is nicely balanced. As yours is. And finally-finally --- have you tried transforming your data to make them a bit more normal and/or homoskedastic? I hope this is some help. cheers, Rolf Turner [EMAIL PROTECTED] Marco Chiarandini wrote: I am conducting a full factorial analysis. I have one factor consisting in algorithms, which I consider my treatments, and another factor made of the problems I want to solve. For each problem I obtain a response variable which is stochastic. I replicate the measure of this response value 10 times. When I apply ANOVA the assumptions do not hold, hence I must rely on non parametric tests. By transforming the response data in ranks, the Friedman test tells me that there is statistical significance in the difference of the sum of ranks of at least one of the treatments. I would like now to produce a plot for the multiple comparisons similar to the Least Significant Difference or the Tukey's Honest Significant Difference used in ANOVA. Since I am in the non parametric case I can not use these methods. Instead, I compare graphically individual treatments by plotting the sum of ranks of each treatment togehter with the 95% confidence interval. To compute the interval I use the Friedman test as suggested by Conover in Practical Nonparametric statistics. I obtain something like this: Treat. A|-+-| Treat. B |-+-| Treat. C |-+-| Treat. D |-+-| The intervals have all the same spread because the number of replications was the same for all experimental units. I would like to know if someone in the list had a similar experience and if what I am doing is correct. In alternative also a reference to another list which could better fit my request is welcome. __ [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 -- Spencer Graves, PhD, Senior Development Engineer O: (408)938-4420; mobile: (408)655-4567 __ [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
[R] heatmap help
Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in advance for any help. Paul Lepp `-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=` ==/==/==/==/==/ ,=,-=`.,=,-=`.,=,-=`.,=,-=`.,=,-=`.,=, ,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' Paul Lepp, Ph.D. Stanford School of Medicine VAPAHCS, 154T Dept. of Microbiology Immunology 3801 Miranda Ave Stanford University Palo Alto, CA 94304 Stanford, CA (650) 493-5000 x66762 fax: (650) 852-3291 http://cmgm.stanford.edu/~pwlepp [EMAIL PROTECTED] __ [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] heatmap help
I believe you want to pass the (symmetric) matrix as is, rather than wrapped in as.dist(). E.g., x - as.matrix(dist(matrix(rnorm(100), 20, 5))) heatmap(x, symm=TRUE, scale=none) HTH, Andy From: Paul Lepp Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in advance for any help. Paul Lepp `-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=` ==/==/==/==/==/ ,=,-=`.,=,-=`.,=,-=`.,=,-=`.,=,-=`.,=, ,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' Paul Lepp, Ph.D. Stanford School of Medicine VAPAHCS, 154T Dept. of Microbiology Immunology 3801 Miranda Ave Stanford University Palo Alto, CA 94304 Stanford, CA (650) 493-5000 x66762fax: (650) 852-3291 http://cmgm.stanford.edu/~pwlepp [EMAIL PROTECTED] __ [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 __ [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] heatmap help
Sorry. I think you need the argument distfun=as.dist. E.g., heatmap(x, distfun=as.dist, symm=TRUE, scale=none) Andy From: Liaw, Andy I believe you want to pass the (symmetric) matrix as is, rather than wrapped in as.dist(). E.g., x - as.matrix(dist(matrix(rnorm(100), 20, 5))) heatmap(x, symm=TRUE, scale=none) HTH, Andy From: Paul Lepp Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in advance for any help. Paul Lepp `-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. ,-;`-:-. `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=` ==/==/==/==/==/ ,=,-=`.,=,-=`.,=,-=`.,=,-=`.,=,-=`.,=, ,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' `-=_,-'-' Paul Lepp, Ph.D. Stanford School of Medicine VAPAHCS, 154T Dept. of Microbiology Immunology 3801 Miranda Ave Stanford University Palo Alto, CA 94304 Stanford, CA (650) 493-5000 x66762 fax: (650) 852-3291 http://cmgm.stanford.edu/~pwlepp [EMAIL PROTECTED] __ [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 __ [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 -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- __ [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
[R] pairwise comparisons
Hello, I am a new R user. I am trying to calculate vector correlations for all pairwise comparisons in my data frame without repeats. I am familiar with the expand.grid function, but this includes repeats. Is there a way to use expand.grid and eliminate repeats? Or is there another function that can be used to do this? Thank you. Rebecca -- Rebecca Young Graduate Student Ecology Evolutionary Biology, Badyaev Lab University of Arizona 1041 E Lowell Tucson, AZ 85721-0088 Office: 425BSW [EMAIL PROTECTED] (520) 621-4005 __ [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
[R] a little question about R
Hello,sir: Here's a little question about R which needs your help.Thanks in advance. If I wanna make a sequence just like a,b,c,d (In other words,a vector consists of 4 characters :a,b,c,d ).How can I do it in a shortcut manner? Yes,I can do it as following: c(a,b,c,d) and the result is:[1] a b c d. But I remember there's a shortcut manner to do the same thing,something like c(a:d).But the system said:Error in a:d : NA/NaN argument So I wonder the correct method to do it(I remember the expression is very similar with c(a:d)). Thanks from the bottom of my heart. My best regards! __ [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] pairwise comparisons
Are you talking about repeated rows? Does unique() do what you want? -roger Rebecca Young wrote: Hello, I am a new R user. I am trying to calculate vector correlations for all pairwise comparisons in my data frame without repeats. I am familiar with the expand.grid function, but this includes repeats. Is there a way to use expand.grid and eliminate repeats? Or is there another function that can be used to do this? Thank you. Rebecca -- Rebecca Young Graduate Student Ecology Evolutionary Biology, Badyaev Lab University of Arizona 1041 E Lowell Tucson, AZ 85721-0088 Office: 425BSW [EMAIL PROTECTED] (520) 621-4005 __ [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 __ [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] a little question about R
You can use letters[1:4].
(B
(BI hope that this helps,
(B John
(B
(B -Original Message-
(B From: [EMAIL PROTECTED]
(B [mailto:[EMAIL PROTECTED] On Behalf Of ??
(B Sent: Tuesday, September 07, 2004 7:42 PM
(B To: [EMAIL PROTECTED]
(B Subject: [R] a little question about R
(B
(B Hello,sir: Here's a little question about R which needs your
(B help.Thanks in advance.
(B If I wanna make a sequence just like a,b,c,d (In other
(B words,a vector consists of 4 characters :a,b,c,d ).How can I
(B do it in a shortcut manner? Yes,I can do it as following:
(B c("a","b","c","d") and the result is:[1] "a" "b" "c" "d".
(B But I remember there's a shortcut manner to do the same
(B thing,something like c("a":"d").But the system said:"Error in
(B "a":"d" : NA/NaN argument" So I wonder the correct method to
(B do it(I remember the expression is very similar with
(B c("a":"d")). Thanks from the bottom of my heart. My best regards!
(B
(B
(B__
(B[EMAIL PROTECTED] mailing list
(Bhttps://stat.ethz.ch/mailman/listinfo/r-help
(BPLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] a little question about R
Try letters[1:4] -roger wrote: Hello,sir: Here's a little question about R which needs your help.Thanks in advance. If I wanna make a sequence just like a,b,c,d (In other words,a vector consists of 4 characters :a,b,c,d ).How can I do it in a shortcut manner? Yes,I can do it as following: c(a,b,c,d) and the result is:[1] a b c d. But I remember there's a shortcut manner to do the same thing,something like c(a:d).But the system said:Error in a:d : NA/NaN argument So I wonder the correct method to do it(I remember the expression is very similar with c(a:d)). Thanks from the bottom of my heart. My best regards! __ [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 __ [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] a little question about R
letters[1;4] LETTERS[1:4] for capitals. Hope this helps, Matt Wiener -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, September 07, 2004 8:42 PM To: [EMAIL PROTECTED] Subject: [R] a little question about R Hello,sir: Here's a little question about R which needs your help.Thanks in advance. If I wanna make a sequence just like a,b,c,d (In other words,a vector consists of 4 characters :a,b,c,d ).How can I do it in a shortcut manner? Yes,I can do it as following: c(a,b,c,d) and the result is:[1] a b c d. But I remember there's a shortcut manner to do the same thing,something like c(a:d).But the system said:Error in a:d : NA/NaN argument So I wonder the correct method to do it(I remember the expression is very similar with c(a:d)). Thanks from the bottom of my heart. My best regards! __ [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 __ [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] a little question about R
letters[1:4] Alec Stephenson Department of Statistics Macquarie University NSW 2109, Australia $(AÃÏÐÀ [EMAIL PROTECTED] 09/08/04 10:41am Hello,sir: Here's a little question about R which needs your help.Thanks in advance. If I wanna make a sequence just like a,b,c,d (In other words,a vector consists of 4 characters :a,b,c,d ).How can I do it in a shortcut manner? Yes,I can do it as following: c(a,b,c,d) and the result is:[1] a b c d. But I remember there's a shortcut manner to do the same thing,something like c(a:d).But the system said:Error in a:d : NA/NaN argument So I wonder the correct method to do it(I remember the expression is very similar with c(a:d)). Thanks from the bottom of my heart. My best regards! __ [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 __ [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] a little question about R
Hi, On Wed, 8 Sep 2004, [gb2312] ÃÏÐÀ wrote: Hello,sir: Here's a little question about R which needs your help.Thanks in advance. If I wanna make a sequence just like a,b,c,d (In other words,a vector consists of 4 characters :a,b,c,d ).How can I do it in a shortcut manner? Yes,I can do it as following: c(a,b,c,d) and the result is:[1] a b c d. But I remember there's a shortcut manner to do the same thing,something like How about letters[1:4] Ko-Kang Kevin Wang PhD Student Centre for Mathematics and its Applications Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 0200 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7407 Ph (M): +61-40-451-8301 __ [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
[R] Thanks
Thanks a lot for your timely rely. I still wonder whether I can use a:d instead of 1:4. I remember I fulfill it successfully according to the guidance of some materials on R,but fail to find it now. Thanks again! __ [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] C function name garbled
On Tue, Sep 07, 2004 at 04:57:57PM -0400, Duncan Murdoch wrote:
On Tue, 7 Sep 2004 12:46:55 -0700, S Blay [EMAIL PROTECTED] wrote :
I wrote an R wrapper function (phylpro) around a C function
(Rphylpro).
The first time I'm running my function, it runs with no errors.
The second time I'm trying to run it, I get an error message
with the first argument to .Call garbled.
Set up:
dyn.load(Phylpro.so)
source(phylpro.R)
WinHalfWidth-30
permReps-10
breaks-c(548, 735, 832)
First call to phylpro succeeds:
b-phylpro(simulinfile, breaks, WinHalfWidth, permReps)
Second call to phylpro fails:
b-phylpro(simulinfile, breaks, WinHalfWidth, permReps)
Error in .Call(PSg\bBh\b, input_file =
as.character(input_file), breaks = as.integer(breaks), :
.Call function name not in load table
Check if my C function name is in load table:
is.loaded(Rphylpro)
[1] TRUE
Any ideas?
It looks to me as though your function is doing something to mess up
R's internal data. I'd try commenting out the whole body of the
function, then adding it back gradually to find which part causes the
trouble.
Duncan Murdoch
I followed your advice - looks like I need some kind of a cast
when I assign the values of a C vector to an R vector. I think.
Below is an example of something that doesn't work -
Can someone give me a hand?
(In the real function, there are also integer and Character
string C vectors...)
Thanks.
#include R.h
#include Rdefines.h
SEXP myfunc() {
double *corrs;
corrs[0]=3.0;
SEXP Rcorrs;
double *pRcorrs;
PROTECT(Rcorrs = NEW_NUMERIC(1));
pRcorrs = NUMERIC_POINTER(Rcorrs);
pRcorrs[0] = corrs[0];
UNPROTECT(1);
return(R_NilValue);
}
/*
dyn.load(myfunc.so)
func-function().Call(myfunc)
func()
*/
Run it once, it's ok:
func()
NULL
Run it twice, not ok:
func()
Error in .Call(NULL) : function name must be a string (of length 1)
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[R] 64 bit R slower than 32 bit R on Sun Sparc Solaris?
Hello, everyone! I guess no one is still using R on Sun Sparc these days. But our department has a (pretty new) two-CPU Sun server. We recently compiled R as a 64 bit application and expected a performance boost. But it runs 25-30% slower than the 32 bit version of R. Anyone knows why this is so? Thanks! Jason = Jason Liao, http://www.geocities.com/jg_liao Dept. of Biostatistics, http://www2.umdnj.edu/bmtrxweb University of Medicine and Dentistry of New Jersey phone 732-235-5429, School of Public Health office phone 732-235-8611, Cancer Institute of New Jersey office moble phone 908-720-4205 __ [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] 64 bit R slower than 32 bit R on Sun Sparc Solaris?
Are you using an optimized BLAS for both builds? That's one possibility. Also, 64-bit builds use up more memory initially since the pointers are bigger. I've tried both 64-bit and 32-bit builds on Sparc/Solaris and haven't seen any slowdown. -roger Jason Liao wrote: Hello, everyone! I guess no one is still using R on Sun Sparc these days. But our department has a (pretty new) two-CPU Sun server. We recently compiled R as a 64 bit application and expected a performance boost. But it runs 25-30% slower than the 32 bit version of R. Anyone knows why this is so? Thanks! Jason = Jason Liao, http://www.geocities.com/jg_liao Dept. of Biostatistics, http://www2.umdnj.edu/bmtrxweb University of Medicine and Dentistry of New Jersey phone 732-235-5429, School of Public Health office phone 732-235-8611, Cancer Institute of New Jersey office moble phone 908-720-4205 __ [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 __ [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
[R] download of 1.9.1
Hi there, I downloaded version 1.9.1 WinZip file, 9.367 bytes ( so I can update my R and use the vcd package) but cannot get the download from your Web site to unzip and install. So silly! The error message is : Error reading header after processing 0 entries. I tried downloading from 3 different URLs, all yielding the same message when I try to unzip and install the file. Could you please let me know what the problem is, including operator error on my end. Thank you __ [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] download of 1.9.1
Hi, On Tue, 7 Sep 2004, Kathy DeRiemer wrote: Hi there, I downloaded version 1.9.1 WinZip file, 9.367 bytes ( so I can update my R Uit doesn't sound right, 9 bytes and use the vcd package) but cannot get the download from your Web site to unzip and install. So silly! The error message is : Error reading header after processing 0 entries. I tried downloading from 3 different URLs, all yielding the same message when I try to unzip and install the file. Well, since you mentioned WinZip I'm assuming you are using R under Windows. IN which case why don't you update the package from Rgui using the menu? See the FAQ... Cheers, Kevin Ko-Kang Kevin Wang PhD Student Centre for Mathematics and its Applications Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 0200 Australia Homepage: http://wwwmaths.anu.edu.au/~wangk/ Ph (W): +61-2-6125-2431 Ph (H): +61-2-6125-7407 Ph (M): +61-40-451-8301 __ [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] Thanks
xmeng at capitalbio.com writes: : Thanks a lot for your timely rely. : I still wonder whether I can use a:d instead of 1:4. : I remember I fulfill it successfully according to the guidance of some materials on R,but fail to find it now. You could define your own seq function and operator: R %:% - seq.character - function(x,y) letters[letters = x letters = y] R seq(a, d) [1] a b c d R a %:% d [1] a b c d __ [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] Thanks
Gabor Grothendieck ggrothendieck at myway.com writes: : : xmeng at capitalbio.com writes: : : : Thanks a lot for your timely rely. : : I still wonder whether I can use a:d instead of 1:4. : : I remember I fulfill it successfully according to the guidance of some : materials on R,but fail to find it now. : : You could define your own seq function and operator: : : R %:% - seq.character - function(x,y) letters[letters = x letters = y] : R seq(a, d) : [1] a b c d : R a %:% d : [1] a b c d And just as a follow up to my own post, if you want to make this a bit more general you might use ascii in place of letters where ascii is defined in: http://www.r-project.org/nocvs/mail/r-help/2002/0952.html __ [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] Thanks
A small drawback to Gabor's proposal:
(B
(B "aa" %:% "dd"
(B[1] "b" "c" "d"
(B "00" %:% "99"
(Bcharacter(0)
(B
(BDefining it as a seq() method for characters is probably not a terribly good
(Bidea, as one should expect it to work for any character vectors as input.
(B(One can argue that the function worked as `expected', I suppose...)
(B
(BBest,
(BAndy
(B
(B From: Gabor Grothendieck
(B
(B $BLR6U(J xmeng at capitalbio.com writes:
(B
(B : Thanks a lot for your timely rely.
(B : I still wonder whether I can use "a":"d" instead of 1:4.
(B : I remember I fulfill it successfully according to the
(B guidance of some
(B materials on R,but fail to find it now.
(B
(B You could define your own seq function and operator:
(B
(B R "%:%" - seq.character - function(x,y) letters[letters =
(B x letters = y]
(B R seq("a", "d")
(B [1] "a" "b" "c" "d"
(B R "a" %:% "d"
(B [1] "a" "b" "c" "d"
(B
(B __
(B [EMAIL PROTECTED] mailing list
(B https://stat.ethz.ch/mailman/listinfo/r-help
(B PLEASE do read the posting guide!
(B http://www.R-project.org/posting-guide.html
(B
(B
(B
(B__
(B[EMAIL PROTECTED] mailing list
(Bhttps://stat.ethz.ch/mailman/listinfo/r-help
(BPLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
