Re: [R] linux compile options (64-bit)
We find it equally strange that you posted this! The advice _is_ in the R-admin manual which the INSTALL file asks you to read if you have any questions. It covers using enhanced BLAS libraries. R builds out of the box on FC3, FC4 and Suse on AMD64. I use Goto's BLAS, but ATLAS can be used (except that building a shared version is tricky). Quite a few packages have been written in ways that stop them building on 64-bit platforms (and the maintainers have been informed but not fixed them). On Mon, 1 Aug 2005, Jacob Michaelson wrote: Sorry--sent this before I added a subject line... Begin forwarded message: From: Jacob Michaelson [EMAIL PROTECTED] Date: August 1, 2005 8:51:58 PM MDT To: r-help@stat.math.ethz.ch I've been using R for a while under Mac OS X, which thanks to the R on OS X developers, is probably the best platform for learning R. I recently built a Linux box with a Pentium D processor, and am running an AMD64 port of Ubuntu with the SMP kernel. After setting up the basics on the box, I thought I'd install R as well. I've had a very hard time finding good documentation on some configure flags/options for compiling a 64-bit version of R on Linux. I thought this was very strange, considering Linux is apparently the R developer's platform of choice. Can anyone point me to some good build instructions for 64-bit R under Linux? Should I compile it against any additional libraries for better performance? [[alternative HTML version deleted]] 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] Rgdal windows binary warning message
This is a consequence of how VC++ compiled gdal. R is protecting itself against that. Since R did not crash, there is nothing to worry about. On Tue, 2 Aug 2005, Tony Gill wrote: Hi all, I just downloaded windows binaries of RGDAL (from http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.1/) and installed. I ran the example R_HOME\library\rgdal\R-ex\getPixmapGDAL.R and everything seemed to work as expected. However I got the following warning message: DLL attempted to change FPU control word from 8001f to 9001f The R-help (?dyn.load) describes the problem as: External code must not change the floating point control word, but many DLLs do so. Common changes are to set it to use 53 bit precision instead of R's default 64 bit precision, or to unmask some exceptions. 'dyn.load' detects such changes, and restores R's control word to its default value of hex 8001F. This may cause the DLL to malfunction; if so, it should be rewritten to save and restore the control word itself. If 'warn.FPU' is set to 'TRUE' using the 'options' function, a warning will be printed. (If the warning says that the control word was changed from some other value than 8001F, please report the circumstances to the Windows maintainers: that probably indicates an internal bug.) Does anyone know if this is a major problem for reading and manipulating image files using RDAL? And if so are there windows binaries which have patched it up? Thanks in advance Tony ** Tony Gill - PhD Candidate Centre for Remote Sensing Spatial Information Science School of Geography, Planning Architecture University of Queensland Brisbane, Queensland, AUSTRALIA, 4072 Ph: 61-7-3365-7027 email: [EMAIL PROTECTED] [[alternative HTML version deleted]] __ 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] can we manage memory usage to increase speed?
On Mon, 1 Aug 2005, Haibo Huang wrote: Please refer to the following post. Which is about Windows only, not Linux. (And on Windows, the answer given is on the help page for memory.size. together with a better one.) Ed --- Mike Lawrence [EMAIL PROTECTED] wrote: Date: Mon, 1 Aug 2005 00:19:06 -0300 From: Mike Lawrence [EMAIL PROTECTED] To: Briggs, Meredith M [EMAIL PROTECTED] CC: r-help@stat.math.ethz.ch Subject: Re: [R] How do you increase memeory? memory.limit(size = x) where x is the desired memory limit in MB. Quoting Briggs, Meredith M [EMAIL PROTECTED]: Hello Function memory.size() =435109888. How do I increase it by, say 30%? Thanks Meredith --- Zhilin Liu [EMAIL PROTECTED] wrote: Hi, Thanks for reading. I am running a process in R for microarray data analysis. RedHat Enterprise Linux 4, dual AMD CPU, 6G memory. However, the R process use only a total of 200M memory. And the CPU usage is total to ~110% for two. The program takes at least 2 weeks to run at the current speed. Is there some way we can increase the usage of CPUs and memories and speed up? Any suggestion is appreciated. Thanks again. Zhilin [[alternative HTML version deleted]] __ 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 __ 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] linux compile options (64-bit)
On Tue, Aug 02, 2005 at 07:34:39AM +0100, Prof Brian Ripley wrote: We find it equally strange that you posted this! The advice _is_ in the R-admin manual which the INSTALL file asks you to read if you have any questions. It covers using enhanced BLAS libraries. R builds out of the box on FC3, FC4 and Suse on AMD64. I use Goto's BLAS, but ATLAS can be used (except that building a shared version is tricky). Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked without complaints with gcc-3.4.5, but when I tried gcc-4.0.1, 'make check' failed with a segmentation error after - R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/usr/local C compiler:/usr/bin/gcc-4.0 -g -O2 C++ compiler: /usr/bin/g++-4.0 -g -O2 Fortran compiler: /usr/bin/gfortran-4.0 -g -O2 Interfaces supported: X11, tcltk External libraries:readline, BLAS(ATLAS) Additional capabilities: PNG, JPEG, iconv, MBCS, NLS Options enabled: R profiling Recommended packages: yes --- amilo:/usr/local/src/R/R-2.1.1# make check make[1]: Entering directory `/usr/local/src/R/R-2.1.1/tests' make[2]: Entering directory `/usr/local/src/R/R-2.1.1/tests' make[3]: Enteri|ng directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[4]: Entering directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[4]: Leaving directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[4]: Entering directory `/usr/local/src/R/R-2.1.1/tests/Examples' collecting examples for package 'base' ... make[5]: Entering directory `/usr/local/src/R/R-2.1.1/src/library' Building/Updating help pages for package 'base' Formats: text html latex example make[5]: Leaving directory `/usr/local/src/R/R-2.1.1/src/library' running code in 'base-Ex.R' .../bin/sh: line 1: 9010 Segmentation fault ../../bin/R --vanilla base-Ex.R base-Ex.Rout 21 make[4]: *** [base-Ex.Rout] Error 1 make[4]: Leaving directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[3]: *** [test-Examples-Base] Error 2 make[3]: Leaving directory `/usr/local/src/R/R-2.1.1/tests/Examples' make[2]: *** [test-Examples] Error 2 make[2]: Leaving directory `/usr/local/src/R/R-2.1.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/usr/local/src/R/R-2.1.1/tests' make: *** [check] Error 2 eigen(print(cbind(c(0,1i), c(-1i,0# Hermite == real Eigen values [,1] [,2] [1,] 0+0i 0-1i [2,] 0+1i 0+0i Running it under 'R -d gdb': R hangs; after C-c: Program received signal SIGINT, Interrupt. zhetd2_ ([EMAIL PROTECTED], [EMAIL PROTECTED], a=0x10900f0, [EMAIL PROTECTED], d=0x13b06e8, e=0xb6add8, tau=0x1bb6448, [EMAIL PROTECTED], _uplo=1) at cmplx.f:8330 8330 CALL ZAXPY( N-I, ALPHA, A( I+1, I ), 1, TAU( I ), 1 ) Current language: auto; currently fortran --- [...] Göran -- Göran Broströmtel: +46 90 786 5223 Department of Statistics fax: +46 90 786 6614 Umeå University http://www.stat.umu.se/~goran.brostrom/ SE-90187 Umeå, Sweden e-mail: [EMAIL PROTECTED] __ 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
[R] Putting all elementes of the list in an enviorment of a function
Hello!
I have two functions.
The first one prepares the arguments for the second one. What is the best
way to put all resoults of the first one into the second one? I tried
attach, however the object in the main enviorment have a priority over the
ones in list. An example is at the end.
Thanks in advance for any suggestions!
Ales Ziberna
For example - I would like to use just a instead of list$a in fuction
second
first-function(a,b){
if(length(a)!=1) a - a[1]
if(length(b)!=1) b - b[1]
list(a=a,b=b)
}
second-function(list,c){
list$a + list$b + c
}
a-c(2,3)
b-4:64
c-5
res-first(a,b)
second(res,c)
__
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] linux compile options (64-bit)
On Tue, 2 Aug 2005, Göran Broström wrote: On Tue, Aug 02, 2005 at 07:34:39AM +0100, Prof Brian Ripley wrote: We find it equally strange that you posted this! The advice _is_ in the R-admin manual which the INSTALL file asks you to read if you have any questions. It covers using enhanced BLAS libraries. R builds out of the box on FC3, FC4 and Suse on AMD64. I use Goto's BLAS, but ATLAS can be used (except that building a shared version is tricky). Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked without complaints with gcc-3.4.5, There is no gcc 3.4.5! There are versions 3.3.5 and 3.4.4. but when I tried gcc-4.0.1, 'make check' failed with a segmentation error after I have seen this on FC3. Note that ZAXPY is a BLAS routine, and you are using ATLAS: was that also built with gcc-4.0.1? On FC3 I get the failure if I use its BLAS, and not if I configure R with --without-blas. (I did not see the problem using the gcc4 RPM from FC3 update, and I gather others have managed to use gcc4 from FC4.) We do not recommend gcc-4.0.x as yet: we have yet to see any performance gains (only losses) from it, and this is one of a number of known nuisances. More serious are places where it apparently generates incorrect code and so gives incorrect answers. ... eigen(print(cbind(c(0,1i), c(-1i,0# Hermite == real Eigen values [,1] [,2] [1,] 0+0i 0-1i [2,] 0+1i 0+0i Running it under 'R -d gdb': R hangs; after C-c: Program received signal SIGINT, Interrupt. zhetd2_ ([EMAIL PROTECTED], [EMAIL PROTECTED], a=0x10900f0, [EMAIL PROTECTED], d=0x13b06e8, e=0xb6add8, tau=0x1bb6448, [EMAIL PROTECTED], _uplo=1) at cmplx.f:8330 8330 CALL ZAXPY( N-I, ALPHA, A( I+1, I ), 1, TAU( I ), 1 ) Current language: auto; currently fortran -- 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] Putting all elementes of the list in an enviorment of a function
?with will help you.
I would avoid using 'list' as a function name, as it will confuse people
and might confuse R too.
On Tue, 2 Aug 2005, [iso-8859-2] Alea }iberna wrote:
Hello!
I have two functions.
The first one prepares the arguments for the second one. What is the best
way to put all resoults of the first one into the second one? I tried
attach, however the object in the main enviorment have a priority over the
ones in list. An example is at the end.
Thanks in advance for any suggestions!
Ales Ziberna
For example - I would like to use just a instead of list$a in fuction
second
first-function(a,b){
if(length(a)!=1) a - a[1]
if(length(b)!=1) b - b[1]
list(a=a,b=b)
}
second-function(list,c){
list$a + list$b + c
}
a-c(2,3)
b-4:64
c-5
res-first(a,b)
second(res,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 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] Putting all elementes of the list in an enviorment of a function
Thank you!
However, this does not do exacty what I want. I would like somehow to modify
only the function second.
BTW, I used list only to create a list, it is not one of my functions.
Thanks again,
Ales Ziberna
- Original Message -
From: Prof Brian Ripley [EMAIL PROTECTED]
To: Ales Ziberna [EMAIL PROTECTED]
Cc: R-help r-help@stat.math.ethz.ch
Sent: Tuesday, August 02, 2005 10:35 AM
Subject: Re: [R] Putting all elementes of the list in an enviorment of a
function
?with will help you.
I would avoid using 'list' as a function name, as it will confuse people
and might confuse R too.
On Tue, 2 Aug 2005, [iso-8859-2] Alea }iberna wrote:
Hello!
I have two functions.
The first one prepares the arguments for the second one. What is the best
way to put all resoults of the first one into the second one? I tried
attach, however the object in the main enviorment have a priority over
the
ones in list. An example is at the end.
Thanks in advance for any suggestions!
Ales Ziberna
For example - I would like to use just a instead of list$a in fuction
second
first-function(a,b){
if(length(a)!=1) a - a[1]
if(length(b)!=1) b - b[1]
list(a=a,b=b)
}
second-function(list,c){
list$a + list$b + c
}
a-c(2,3)
b-4:64
c-5
res-first(a,b)
second(res,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 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
__
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] linux compile options (64-bit)
On Tue, Aug 02, 2005 at 09:33:45AM +0100, Prof Brian Ripley wrote: On Tue, 2 Aug 2005, Göran Broström wrote: [...] Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked without complaints with gcc-3.4.5, There is no gcc 3.4.5! There are versions 3.3.5 and 3.4.4. I apologize for the incomplete description; gcc -v gives: gcc version 3.4.5 20050706 (prerelease) (Debian 3.4.4-5) but when I tried gcc-4.0.1, 'make check' failed with a segmentation error after I have seen this on FC3. Note that ZAXPY is a BLAS routine, and you are using ATLAS: was that also built with gcc-4.0.1? Probably not; I just 'apt-get install'ed atlas3-base etc. I'll build atlas from source and try again. On FC3 I get the failure if I use its BLAS, and not if I configure R with --without-blas. (I did not see the problem using the gcc4 RPM from FC3 update, and I gather others have managed to use gcc4 from FC4.) We do not recommend gcc-4.0.x as yet: we have yet to see any performance gains (only losses) from it, and this is one of a number of known nuisances. More serious are places where it apparently generates incorrect code and so gives incorrect answers. OK. An additional advantage with gfortran(-4.x) will be the possibility to use fortan95 code, n'est ce pas? Göran __ 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] Putting all elementes of the list in an enviorment of a function
On Tue, 2 Aug 2005, Ales Ziberna wrote:
Thank you!
However, this does not do exacty what I want. I would like somehow to modify
only the function second.
What happened when you tried my suggestion as
second - function(l, c) with(l, a + b + c)
? It does work for me.
BTW, I used list only to create a list, it is not one of my functions.
You used it as a variable within second()!
Thanks again,
Ales Ziberna
- Original Message - From: Prof Brian Ripley
[EMAIL PROTECTED]
To: Ales Ziberna [EMAIL PROTECTED]
Cc: R-help r-help@stat.math.ethz.ch
Sent: Tuesday, August 02, 2005 10:35 AM
Subject: Re: [R] Putting all elementes of the list in an enviorment of a
function
?with will help you.
I would avoid using 'list' as a function name, as it will confuse people
and might confuse R too.
On Tue, 2 Aug 2005, [iso-8859-2] Alea }iberna wrote:
Hello!
I have two functions.
The first one prepares the arguments for the second one. What is the best
way to put all resoults of the first one into the second one? I tried
attach, however the object in the main enviorment have a priority over
the
ones in list. An example is at the end.
Thanks in advance for any suggestions!
Ales Ziberna
For example - I would like to use just a instead of list$a in fuction
second
first-function(a,b){
if(length(a)!=1) a - a[1]
if(length(b)!=1) b - b[1]
list(a=a,b=b)
}
second-function(list,c){
list$a + list$b + c
}
a-c(2,3)
b-4:64
c-5
res-first(a,b)
second(res,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 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
--
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] linux compile options (64-bit)
On Tue, 2 Aug 2005, Göran Broström wrote: On Tue, Aug 02, 2005 at 09:33:45AM +0100, Prof Brian Ripley wrote: On Tue, 2 Aug 2005, Göran Broström wrote: [...] Incidentally, I have just tried building R on a Fujitsu Amilo amd64 with debian-amd64 (unstable) and ATLAS. Both 'make' and 'make check' worked without complaints with gcc-3.4.5, There is no gcc 3.4.5! There are versions 3.3.5 and 3.4.4. I apologize for the incomplete description; gcc -v gives: gcc version 3.4.5 20050706 (prerelease) (Debian 3.4.4-5) but when I tried gcc-4.0.1, 'make check' failed with a segmentation error after I have seen this on FC3. Note that ZAXPY is a BLAS routine, and you are using ATLAS: was that also built with gcc-4.0.1? Probably not; I just 'apt-get install'ed atlas3-base etc. I'll build atlas from source and try again. On FC3 I get the failure if I use its BLAS, and not if I configure R with --without-blas. (I did not see the problem using the gcc4 RPM from FC3 update, and I gather others have managed to use gcc4 from FC4.) We do not recommend gcc-4.0.x as yet: we have yet to see any performance gains (only losses) from it, and this is one of a number of known nuisances. More serious are places where it apparently generates incorrect code and so gives incorrect answers. OK. An additional advantage with gfortran(-4.x) will be the possibility to use fortan95 code, n'est ce pas? Some Fortran95 code, anyway. (It is not yet a complete implementation.) The problems we are seeing with gcc4 are mainly (but not entirely) with gfortran: it seems not quite ready for production use. -4.0.1 is already a considerable improvement over -4.0.0. There is another project (www.g95.org) that is using a slightly different version of these sources, and either g95 or gfortran can be used with gcc3 if you want to use F95 sources. However, F95 is unlikely to be suitable for use in distributed R packages for a long time to come. -- 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] Putting all elementes of the list in an enviorment of a function
I apologize, it seams did not interpret your first mail corectly!
Everything works now!
Thank you again!
Ales Ziberna
- Original Message -
From: Prof Brian Ripley [EMAIL PROTECTED]
To: Ales Ziberna [EMAIL PROTECTED]
Cc: R-help r-help@stat.math.ethz.ch
Sent: Tuesday, August 02, 2005 11:25 AM
Subject: Re: [R] Putting all elementes of the list in an enviorment of a
function
On Tue, 2 Aug 2005, Ales Ziberna wrote:
Thank you!
However, this does not do exacty what I want. I would like somehow to
modify only the function second.
What happened when you tried my suggestion as
second - function(l, c) with(l, a + b + c)
? It does work for me.
BTW, I used list only to create a list, it is not one of my
functions.
You used it as a variable within second()!
Thanks again,
Ales Ziberna
- Original Message - From: Prof Brian Ripley
[EMAIL PROTECTED]
To: Ales Ziberna [EMAIL PROTECTED]
Cc: R-help r-help@stat.math.ethz.ch
Sent: Tuesday, August 02, 2005 10:35 AM
Subject: Re: [R] Putting all elementes of the list in an enviorment of a
function
?with will help you.
I would avoid using 'list' as a function name, as it will confuse people
and might confuse R too.
On Tue, 2 Aug 2005, [iso-8859-2] Alea }iberna wrote:
Hello!
I have two functions.
The first one prepares the arguments for the second one. What is the
best
way to put all resoults of the first one into the second one? I tried
attach, however the object in the main enviorment have a priority
over the
ones in list. An example is at the end.
Thanks in advance for any suggestions!
Ales Ziberna
For example - I would like to use just a instead of list$a in
fuction
second
first-function(a,b){
if(length(a)!=1) a - a[1]
if(length(b)!=1) b - b[1]
list(a=a,b=b)
}
second-function(list,c){
list$a + list$b + c
}
a-c(2,3)
b-4:64
c-5
res-first(a,b)
second(res,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 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
--
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] converting stata's by syntax to R
Chris Wallace [EMAIL PROTECTED] writes: I am struggling with migrating some stata code to R Thanks to all who replied. It was very helpful to see a combination of more direct stata-R translations and more R-ish code. which.max() solves my problem this time, but learning about split(), unsplit() and duplicated() should make such problems fewer in the long run. C. __ 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
[R] R: regression data set
hi all i am busy teaching a regression analysis course to second year science students. the course is fairly theoretical with all of the standard theorems and proofs... i would like to give the class a practical assignment as well. could you suggest a good problem and the location of the data set/s? it would be good if the data set has been analysed by a number of other people so that students can see the different ways of tackling a regression problem. some of the issues to be covered: estimation is there really a model variable selection ... outliers and influential observations interpreting the regression model / allan__ 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] linux compile options (64-bit)
On Tue, Aug 02, 2005 at 10:58:31AM +0100, Prof Brian Ripley wrote: The problems we are seeing with gcc4 are mainly (but not entirely) with gfortran: it seems not quite ready for production use. -4.0.1 is already a considerable improvement over -4.0.0. There is another project (www.g95.org) that is using a slightly different version of these sources, and either g95 or gfortran can be used with gcc3 if you want to use F95 sources. However, F95 is unlikely to be suitable for use in distributed R packages for a long time to come. Thanks; I'll stick to 3.4.4(!) and f77 for the time being. Göran __ 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
[R] Read from data frame, and not from global environment
Dear members,
assume given a function of type
test-function(formula, data , w){
..
glm1-glm(formula, family=poisson, data=data, weights=w)
..
}
and a simple example data frame as
test.frame-data.frame(x=1:10,y=(1:10)*2,a=(1:10)^3).
Let us now execute
test(y ~ x, test.frame, a )
My question is: What do I have to insert at the first occurance of .
in the test function to ensure that
1) 'a' is read from the data frame (and is only read from the global
environment if and only if 'a' is not found in the data frame)
2) glm finds w in in the local environment of the function 'test'
The question is obviously related to Fernando's problem with
'Defining a local function' some months ago, though the discussion
there does not solve the questions above.
Cheers,
Jochen Einbeck
NUI Galway, Ireland
__
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: regression data set
Clark Allan wrote: i would like to give the class a practical assignment as well. could you suggest a good problem and the location of the data set/s? it would be good if the data set has been analysed by a number of other people so that students can see the different ways of tackling a regression problem. If you want some textbook examples I'd recommend Ripley and Venables's Modern Applied Statistics With S (VR bundle); Maindonald and Braun's Data Analysis and Graphics using R (DAAG package) Cheers, Kev -- Ko-Kang Kevin Wang PhD Student Centre for Bioinformation Science Building 27, Room 1004 Mathematical Sciences Institute (MSI) Australian National University Canberra, ACT 2601 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 __ 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] Read from data frame, and not from global environment
I don't think that is the best way to do what I guess you intended. Try
something like
test - function(formula, data , weights)
{
Call - match.call()
Call[[1]] - as.name(glm)
Call$family - quote(poisson)
glm1 - eval.parent(Call)
}
which is probably giving the scoping that you want.
You could do what you ask for at 1) by something like
wname - deparse(substitute(w))
w - if(wname %in% names(data)) data[[wname]] else get(wname, .GlobalEnv)
and for 2) by replacing .GlobalEnv by an expression constructed by calls
to environment() (I don't know exactly what you intended here).
On Tue, 2 Aug 2005, Jochen Einbeck wrote:
Dear members,
assume given a function of type
test-function(formula, data , w){
..
glm1-glm(formula, family=poisson, data=data, weights=w)
..
}
and a simple example data frame as
test.frame-data.frame(x=1:10,y=(1:10)*2,a=(1:10)^3).
Let us now execute
test(y ~ x, test.frame, a )
My question is: What do I have to insert at the first occurance of .
in the test function to ensure that
1) 'a' is read from the data frame (and is only read from the global
environment if and only if 'a' is not found in the data frame)
2) glm finds w in in the local environment of the function 'test'
That contradicts 1)!
The question is obviously related to Fernando's problem with
'Defining a local function' some months ago, though the discussion
there does not solve the questions above.
--
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] Rgdal windows binary warning message
Prof Brian Ripley wrote: This is a consequence of how VC++ compiled gdal. R is protecting itself against that. Since R did not crash, there is nothing to worry about. To add to that: the RGDAL maintainer could work around this bug in VC++. I haven't used that compiler, but with others it is sufficient to ask R to set the FPU control word. Instructions are here: http://www.stats.uwo.ca/faculty/murdoch/software/compilingDLLs/index.html#fpu Duncan Murdoch On Tue, 2 Aug 2005, Tony Gill wrote: Hi all, I just downloaded windows binaries of RGDAL (from http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.1/) and installed. I ran the example R_HOME\library\rgdal\R-ex\getPixmapGDAL.R and everything seemed to work as expected. However I got the following warning message: DLL attempted to change FPU control word from 8001f to 9001f The R-help (?dyn.load) describes the problem as: External code must not change the floating point control word, but many DLLs do so. Common changes are to set it to use 53 bit precision instead of R's default 64 bit precision, or to unmask some exceptions. 'dyn.load' detects such changes, and restores R's control word to its default value of hex 8001F. This may cause the DLL to malfunction; if so, it should be rewritten to save and restore the control word itself. If 'warn.FPU' is set to 'TRUE' using the 'options' function, a warning will be printed. (If the warning says that the control word was changed from some other value than 8001F, please report the circumstances to the Windows maintainers: that probably indicates an internal bug.) Does anyone know if this is a major problem for reading and manipulating image files using RDAL? And if so are there windows binaries which have patched it up? Thanks in advance Tony ** Tony Gill - PhD Candidate Centre for Remote Sensing Spatial Information Science School of Geography, Planning Architecture University of Queensland Brisbane, Queensland, AUSTRALIA, 4072 Ph: 61-7-3365-7027 email: [EMAIL PROTECTED] [[alternative HTML version deleted]] __ 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 __ 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
[R] question on graphs and finding area under a curve
Question on graphs: The default case for drawing a graph in R, is where a little space is left on the x and y axis before the first tick i.e. even if I say xlim=c(0,1) -- there will be some space between the edge of the x-axis and where 0 is placed. If I want 0 on the edge, how do I do it in R? Area under the curve: I have a 45 degree line and a curve above or below it. Is there a way in R to find the area between the two? Thanks, Renuka -- Renuka Sane http://www.nyx.net/~rsane [[alternative HTML version deleted]] __ 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] Conditional piece-wise dependent regression
Thank you Dimitris Reid, you were very helpful. Best wishes, Arie. __ 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] can we manage memory usage to increase speed?
If you have a code that takes 2 weeks to run, than it might be a case of inefficient algorithm design. I was able to go from overnight runs (SELDI data analysis) to 20 minute runs by identifying single inefficient function that took most of the time, and writing it in C. Jarek \=== Jarek Tuszynski, PhD. o / \ Science Applications International Corporation \__,| (703) 676-4192 \ [EMAIL PROTECTED] `\ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zhilin Liu Sent: Monday, August 01, 2005 8:28 PM To: r-help@stat.math.ethz.ch Subject: [R] can we manage memory usage to increase speed? Hi, Thanks for reading. I am running a process in R for microarray data analysis. RedHat Enterprise Linux 4, dual AMD CPU, 6G memory. However, the R process use only a total of 200M memory. And the CPU usage is total to ~110% for two. The program takes at least 2 weeks to run at the current speed. Is there some way we can increase the usage of CPUs and memories and speed up? Any suggestion is appreciated. Thanks again. Zhilin [[alternative HTML version deleted]] __ 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 __ 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] question on graphs and finding area under a curve
On Tue, 2005-08-02 at 18:20 +0530, Renuka Sane wrote: Question on graphs: The default case for drawing a graph in R, is where a little space is left on the x and y axis before the first tick i.e. even if I say xlim=c(0,1) -- there will be some space between the edge of the x-axis and where 0 is placed. If I want 0 on the edge, how do I do it in R? See ?par and take note of the 'xaxs' and 'yaxs' parameters. By default, these are set to 'r', where the axes are extended by 4% in each direction. Thus, set one or both parameters to 'i' to set the axes to exactly the ranges of xlim and/or ylim as you require. Area under the curve: I have a 45 degree line and a curve above or below it. Is there a way in R to find the area between the two? See Frank Harrell's somers2() function in the Hmisc package on CRAN. Among other things, it outputs a value C, which is the AUC. HTH, Marc Schwartz __ 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] question on graphs and finding area under a curve
Le 02.08.2005 14:50, Renuka Sane a écrit : Question on graphs: The default case for drawing a graph in R, is where a little space is left on the x and y axis before the first tick i.e. even if I say xlim=c(0,1) -- there will be some space between the edge of the x-axis and where 0 is placed. If I want 0 on the edge, how do I do it in R? Area under the curve: I have a 45 degree line and a curve above or below it. Is there a way in R to find the area between the two? Hi, integrate.xy in sfsmisc package might help you. Romain Thanks, Renuka - visit the R Graph Gallery : http://addictedtor.free.fr/graphiques ~ ~~ Romain FRANCOIS - http://addictedtor.free.fr ~~ Etudiant ISUP - CS3 - Industrie et Services ~~http://www.isup.cicrp.jussieu.fr/ ~~ Stagiaire INRIA Futurs - Equipe SELECT ~~ http://www.inria.fr/recherche/equipes/select.fr.html~~ ~ __ 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] question on graphs and finding area under a curve
How about:
trapz = function(x, y)
{ # computes the integral of y with respect to x using trapezoidal
integration.
idx = 2:length(x)
return (as.double( (x[idx] - x[idx-1]) %*% (y[idx] + y[idx-1])) / 2)
}
Jarek
\===
Jarek Tuszynski, PhD. o / \
Science Applications International Corporation \__,|
(703) 676-4192 \
[EMAIL PROTECTED] `\
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Renuka Sane
Sent: Tuesday, August 02, 2005 8:51 AM
To: r-help@stat.math.ethz.ch
Subject: [R] question on graphs and finding area under a curve
Question on graphs:
The default case for drawing a graph in R, is where a little space is left
on the x and y axis before the first tick i.e. even if I say xlim=c(0,1) --
there will be some space between the edge of the x-axis and where 0 is
placed. If I want 0 on the edge, how do I do it in R?
Area under the curve:
I have a 45 degree line and a curve above or below it. Is there a way in R
to find the area between the two?
Thanks,
Renuka
--
Renuka Sane
http://www.nyx.net/~rsane
[[alternative HTML version deleted]]
__
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
__
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] question on graphs and finding area under a curve
Hi,
To find the area lying between the curve y = y(x) and 45 degree line (which,
assuming it goes through the origin, is y = x), you can use the following
function based on trapezoidal rule:
trap.rule - function(x,f) {sum(diff(x)*(f[-1]+f[-length(f)]))/2}
trap.rule(x,f=y-x)
This area will be negative if y(x) is below the 45 degree line.
However, your question is not complete, I think. You need to specify the
interval of integration. For this you may need to determine the points of
intersection of the two curves, which involves the solution of a fixed point
problem.
Hope this helps,
Ravi.
-Original Message-
From: [EMAIL PROTECTED] [mailto:r-help-
[EMAIL PROTECTED] On Behalf Of Renuka Sane
Sent: Tuesday, August 02, 2005 8:51 AM
To: r-help@stat.math.ethz.ch
Subject: [R] question on graphs and finding area under a curve
Question on graphs:
The default case for drawing a graph in R, is where a little space is left
on the x and y axis before the first tick i.e. even if I say xlim=c(0,1) -
-
there will be some space between the edge of the x-axis and where 0 is
placed. If I want 0 on the edge, how do I do it in R?
Area under the curve:
I have a 45 degree line and a curve above or below it. Is there a way in R
to find the area between the two?
Thanks,
Renuka
--
Renuka Sane
http://www.nyx.net/~rsane
[[alternative HTML version deleted]]
__
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
__
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
[R] Contour plot crest line
Any suggestions about drawing the ridge line on a response surface represented as a contour plot? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@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
[R] how to print a data.frame without row.names
Dear All,
is there a simple way to print a data.frame without its row.names?
example:
datum - as.Date(c(2004-01-01, 2004-01-06, 2004-04-12))
content - c('Neujahr', 'Hl 3 K.', 'Ostern')
df1 - data.frame(datum, content)
print(df1)
datum content
1 2004-01-01 Neujahr
2 2004-01-06 Hl 3 K.
3 2004-04-12 Ostern
Can I get this table without 1, 2, 3 ?
Thanks in advance
Heinz Tuechler
__
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
[R] (no subject)
hi all, I wish to draw on the same graphic device 3 functions. But i don't want them to be on different graph, i want to compare them on the same I don't need mfrow or mfcol, I need something else... 1 graph on 1 device inside this graph 3 ploted function. I saw something unsing data.frame, but i think it's overkill, and something less complicated must exist, if not why? why not plot(func1,func2,func3) ?? thks. // Webmail Oreka : http://www.oreka.com __ 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
[R] plotting 3 functions on same graph
hi all, I wish to draw on the same graphic device 3 functions. But i don't want them to be on different graph, i want to compare them on the same I don't need mfrow or mfcol, I need something else... 1 graph on 1 device inside this graph 3 ploted function. I saw something unsing data.frame, but i think it's overkill, and something less complicated must exist, if not why? why not plot(func1,func2,func3) ?? thks. // Webmail Oreka : http://www.oreka.com __ 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 print a data.frame without row.names
Le 02.08.2005 15:45, Heinz Tuechler a écrit :
Dear All,
is there a simple way to print a data.frame without its row.names?
example:
datum - as.Date(c(2004-01-01, 2004-01-06, 2004-04-12))
content - c('Neujahr', 'Hl 3 K.', 'Ostern')
df1 - data.frame(datum, content)
print(df1)
datum content
1 2004-01-01 Neujahr
2 2004-01-06 Hl 3 K.
3 2004-04-12 Ostern
Can I get this table without 1, 2, 3 ?
See write.table and its row.names argument
R write.table(df1, row.names=FALSE)
Romain
--
visit the R Graph Gallery : http://addictedtor.free.fr/graphiques
~
~~ Romain FRANCOIS - http://addictedtor.free.fr ~~
Etudiant ISUP - CS3 - Industrie et Services
~~http://www.isup.cicrp.jussieu.fr/ ~~
Stagiaire INRIA Futurs - Equipe SELECT
~~ http://www.inria.fr/recherche/equipes/select.fr.html~~
~
__
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] plotting 3 functions on same graph
Hi Maybe matplot (see ?matplot) can help you. Regards, Christoph Buser -- Christoph Buser [EMAIL PROTECTED] Seminar fuer Statistik, LEO C13 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-44-632-4673 fax: 632-1228 http://stat.ethz.ch/~buser/ -- [EMAIL PROTECTED] writes: hi all, I wish to draw on the same graphic device 3 functions. But i don't want them to be on different graph, i want to compare them on the same I don't need mfrow or mfcol, I need something else... 1 graph on 1 device inside this graph 3 ploted function. I saw something unsing data.frame, but i think it's overkill, and something less complicated must exist, if not why? why not plot(func1,func2,func3) ?? thks. // Webmail Oreka : http://www.oreka.com __ 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 __ 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
[R] [R-pkgs] [ANNOUNCE] mod_R: The R/Apache Integration Project
What is it? --- mod_R is a project dedicated to embedding the R interpreter inside the Apache 2.0 (and beyond) web server for the purpose of writing web applications in R. It's composed of three parts: mod_R: the Apache 2.0 module that implements the glue to load the R interpreter. RApache: the R package that provides the API for programming web applications in R. libapreq 2.0.4: an Apache sponsored project for parsing request input. If you don't want to compile and install this version, then you can specify which libapreq2 library to use during configuration. The Latest Version -- Details of the latest version can be found at the mod_R project page: http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/ApacheRproject (mind the wrap) Prerequisites - This release has been tested under Debian Linux with Apache 2.0.54, R 2.1.1, and libapreq 2.0.4. Apache2 _MUST_ be compiled with the prefork MPM to compile mod_R. Also, R must have been compiled with the --enable-R-shlib configure flag. Installation The following is the preferred way to compile and install mod_R: $ ./configure --with-apache2-apxs=/path/to/apxs --with-R=/path/to/R $ make $ make install Both --with-apache2-apxs and --with-R _MUST_ be specified. Otherwise, trying to figure out the dependencies between the sources and headers and library paths becomes quite complex. If you don't want to compile and install the bundled libapreq2 version, then add --with-apreq2-config=/path/to/apreq2-config. The version _MUST_ be equal to or greater than 2.0.4. Configuration - In order to use mod_R and RApache, you must configure apache to find it. Type help(directives,package=RApache) once mod_R is installed for a little more detail. Add something similar to this to the apache config file: LoadModule R_Module /path/to/mod_R.so Location /URL SetHandler r-handler Rsource /path/to/R/code.R RreqHandler function-name Rlibrary library-name /Location Also, libR.so _MUST_ be found in the shared library path as it is linked to by mod_R, RApache and the rest of the packages containing shared libraries. You can either set LD_LIBRARY_PATH like this: $ export LD_LIBRARY_PATH=`/path/to/R RHOME`/lib or add that path to /etc/ld.so.conf and then run ldconfig. NOTE: the latest apache2 debian packages cause the web server to run in a very reduced environment, thus one is unable to set LD_LIBRARY_PATH before calling /etc/init.d/apache2. One option is to actually edit that file and add the LD_LIBRARY_PATH explicitly. Another is to use the apache2ctl scripts which are also bundled with the debian packages. Or you can add it to /etc/ld.so.conf. Documentation - All of the documentation is currently in the RApache package. Once you install mod_R, start R and load the RApache package. You'll get a warning that you're currently not running the R interpreter within Apache; just don't try to run any of the code. Sample session: library(RApache) Warning message: RApache is only useful within the Apache web server. It is loaded now for informational purposes only in: firstlib(which.lib.loc, package) help(package=RApache) Information on package 'RApache' Description: Package: RApache Version: 0.1-0 Date: 2005-08-02 Title: An R interface to the Apache 2.0 web server Author:Jeffrey Horner Maintainer:Jeffrey Horner [EMAIL PROTECTED] License: Apache License, Version 2.0 Description: RApache allows web applications to be written in R and executed within the Apache 2.0 web server. Built: R 2.1.0; i386-pc-linux-gnu; 2005-08-02 01:06:26; unix Index: IO IO in RApache apache.add_cookie Adding Cookies to Outgoing Headers apache.add_header Adding HTTP headers apache.allow_methodsRApache Methods apache.log_errorLogging Errors to the Apache error log apache.set_content_type Setting the Content Type header apr_table Structure of the apr_table type in RApache as.html Converting RApache objects to HTML directives RApache directives used in Apace config file intro Introduction to RApache request_rec Structure of the RApache request record return_codesRApache handler return codes Licensing - Please see the file called LICENSE. -- Jeffrey Horner Computer Systems Analyst School of Medicine 615-322-8606 Department of Biostatistics Vanderbilt University ___ R-packages
Re: [R] plotting 3 functions on same graph
Le 02.08.2005 15:56, [EMAIL PROTECTED] a écrit : hi all, I wish to draw on the same graphic device 3 functions. But i don't want them to be on different graph, i want to compare them on the same I don't need mfrow or mfcol, I need something else... 1 graph on 1 device inside this graph 3 ploted function. I saw something unsing data.frame, but i think it's overkill, and something less complicated must exist, if not why? why not plot(func1,func2,func3) ?? thks. Take a look at : ?points ?lines ?curve par(new=TRUE) -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques ~ ~~ Romain FRANCOIS - http://addictedtor.free.fr ~~ Etudiant ISUP - CS3 - Industrie et Services ~~http://www.isup.cicrp.jussieu.fr/ ~~ Stagiaire INRIA Futurs - Equipe SELECT ~~ http://www.inria.fr/recherche/equipes/select.fr.html~~ ~ __ 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] plotting 3 functions on same graph
Romain Francois [EMAIL PROTECTED] writes: Le 02.08.2005 15:56, [EMAIL PROTECTED] a écrit : hi all, I wish to draw on the same graphic device 3 functions. But i don't want them to be on different graph, i want to compare them on the same I don't need mfrow or mfcol, I need something else... 1 graph on 1 device inside this graph 3 ploted function. I saw something unsing data.frame, but i think it's overkill, and something less complicated must exist, if not why? why not plot(func1,func2,func3) ?? thks. Take a look at : ?points ?lines ?curve par(new=TRUE) ...and curve(, add=TRUE). The minor gotcha is that you need to adjust the ylim setting to make sure that all curves fit. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
[R] a question about data manipulation
Dear R-user, I have a simple question, I just can't figure out a easy way to handle it. My importing data x is like this: COL1 COL2 id 1 12 49 1 2 70 120 1 3 58 124 1 51 14 13 2 52 88 100 2 53 90 134 2 I want to change the format of the data, i want to group data into differenct part according id,so that when i use x[1], which will refer me to the information about first id.I use the command: list(list(N=2,n=c(100,150),matrix(c(x[x$id==1,][,1],x[x$id==1,][,2]),nr=2,nc=3)),list(N=2,n=c(100,150),matrix(c(x[x$id==2,][,1],x[x$id==2,][,2]),nr=2,nc=3))) so the data becomes : [[1]] [[1]]$N [1] 2 [[1]]$n [1] 100 150 [[1]][[3]] [,1] [,2] [,3] [1,] 12 58 120 [2,] 70 49 124 [[2]] [[2]]$N [1] 2 [[2]]$n [1] 100 150 [[2]][[3]] [,1] [,2] [,3] [1,] 14 90 100 [2,] 88 13 134 This is the format I want, but problem is that for my data, id is not only 1 to 2,but 1 to 100, so my code is not efficient. Could you help me find a efficient way? Thanks. Qi Zhang PhD student, University of Cincinnati [[alternative HTML version deleted]] __ 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 print a data.frame without row.names
At 16:05 02.08.2005 +0200, Romain Francois wrote:
Le 02.08.2005 15:45, Heinz Tuechler a écrit :
Dear All,
is there a simple way to print a data.frame without its row.names?
example:
datum - as.Date(c(2004-01-01, 2004-01-06, 2004-04-12))
content - c('Neujahr', 'Hl 3 K.', 'Ostern')
df1 - data.frame(datum, content)
print(df1)
datum content
1 2004-01-01 Neujahr
2 2004-01-06 Hl 3 K.
3 2004-04-12 Ostern
Can I get this table without 1, 2, 3 ?
See write.table and its row.names argument
R write.table(df1, row.names=FALSE)
Romain
write.table(df1, row.names=FALSE, quote=FALSE)
datum content
2004-01-01 Neujahr
2004-01-06 Hl 3 K.
2004-04-12 Ostern
I tried this, but then the column headers and column contents are not aligned.
If you expand the example, you see clearly the difference.
datum - as.Date(c(2004-01-01, 2004-01-06, 2004-04-12))
content - c('Neujahr', 'Hl 3 K.', 'Ostern')
number - c(1, 6, 110)
string - c('a', '', 'c')
df1 - data.frame(datum, content, number, string)
print(df1)
datum content number string
1 2004-01-01 Neujahr 1 a
2 2004-01-06 Hl 3 K. 6
3 2004-04-12 Ostern110 c
write.table(df1, row.names=FALSE, quote=FALSE)
datum content number string
2004-01-01 Neujahr 1 a
2004-01-06 Hl 3 K. 6
2004-04-12 Ostern 110 c
Maybe I missed a function like print.xtable with type=ascii. It seems
that it has to be done with cat.
Thank you
Heinz
--
visit the R Graph Gallery : http://addictedtor.free.fr/graphiques
~
~~ Romain FRANCOIS - http://addictedtor.free.fr ~~
Etudiant ISUP - CS3 - Industrie et Services
~~http://www.isup.cicrp.jussieu.fr/ ~~
Stagiaire INRIA Futurs - Equipe SELECT
~~ http://www.inria.fr/recherche/equipes/select.fr.html~~
~
__
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] can we manage memory usage to increase speed?
And you can identify inefficient code fairly easily taking snapshots from proc.time and computing elapsed time for sections of your code. spencer graves Tuszynski, Jaroslaw W. wrote: If you have a code that takes 2 weeks to run, than it might be a case of inefficient algorithm design. I was able to go from overnight runs (SELDI data analysis) to 20 minute runs by identifying single inefficient function that took most of the time, and writing it in C. Jarek \=== Jarek Tuszynski, PhD. o / \ Science Applications International Corporation \__,| (703) 676-4192 \ [EMAIL PROTECTED] `\ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zhilin Liu Sent: Monday, August 01, 2005 8:28 PM To: r-help@stat.math.ethz.ch Subject: [R] can we manage memory usage to increase speed? Hi, Thanks for reading. I am running a process in R for microarray data analysis. RedHat Enterprise Linux 4, dual AMD CPU, 6G memory. However, the R process use only a total of 200M memory. And the CPU usage is total to ~110% for two. The program takes at least 2 weeks to run at the current speed. Is there some way we can increase the usage of CPUs and memories and speed up? Any suggestion is appreciated. Thanks again. Zhilin [[alternative HTML version deleted]] __ 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 __ 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 -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ 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] a question about data manipulation
use 'split' x.1 - data.frame(COL1=1:50, COL2=50:1, id=sample(1:4,50,T)) x.2 - split(x.1, x.1$id) str(x.2) List of 4 $ 1:`data.frame': 10 obs. of 3 variables: ..$ COL1: int [1:10] 5 10 11 12 22 24 27 34 38 47 ..$ COL2: int [1:10] 46 41 40 39 29 27 24 17 13 4 ..$ id : int [1:10] 1 1 1 1 1 1 1 1 1 1 $ 2:`data.frame': 13 obs. of 3 variables: ..$ COL1: int [1:13] 1 2 14 16 19 25 26 28 30 31 ... ..$ COL2: int [1:13] 50 49 37 35 32 26 25 23 21 20 ... ..$ id : int [1:13] 2 2 2 2 2 2 2 2 2 2 ... $ 3:`data.frame': 14 obs. of 3 variables: ..$ COL1: int [1:14] 3 8 9 13 17 23 32 36 39 42 ... ..$ COL2: int [1:14] 48 43 42 38 34 28 19 15 12 9 ... ..$ id : int [1:14] 3 3 3 3 3 3 3 3 3 3 ... $ 4:`data.frame': 13 obs. of 3 variables: ..$ COL1: int [1:13] 4 6 7 15 18 20 21 29 35 37 ... ..$ COL2: int [1:13] 47 45 44 36 33 31 30 22 16 14 ... ..$ id : int [1:13] 4 4 4 4 4 4 4 4 4 4 ... names(x.2) [1] 1 2 3 4 x.2[['1']] COL1 COL2 id 5 5 46 1 10 10 41 1 11 11 40 1 12 12 39 1 22 22 29 1 24 24 27 1 27 27 24 1 34 34 17 1 38 38 13 1 47 474 1 x.2[['3']] COL1 COL2 id 3 3 48 3 8 8 43 3 9 9 42 3 13 13 38 3 17 17 34 3 23 23 28 3 32 32 19 3 36 36 15 3 39 39 12 3 42 429 3 44 447 3 45 456 3 49 492 3 50 501 3 On 8/2/05, qi zhang [EMAIL PROTECTED] wrote: Dear R-user, I have a simple question, I just can't figure out a easy way to handle it. My importing data x is like this: COL1 COL2 id 1 12 49 1 2 70 120 1 3 58 124 1 51 14 13 2 52 88 100 2 53 90 134 2 I want to change the format of the data, i want to group data into differenct part according id,so that when i use x[1], which will refer me to the information about first id.I use the command: list(list(N=2,n=c(100,150),matrix(c(x[x$id==1,][,1],x[x$id==1,][,2]),nr=2,nc=3)),list(N=2,n=c(100,150),matrix(c(x[x$id==2,][,1],x[x$id==2,][,2]),nr=2,nc=3))) so the data becomes : [[1]] [[1]]$N [1] 2 [[1]]$n [1] 100 150 [[1]][[3]] [,1] [,2] [,3] [1,] 12 58 120 [2,] 70 49 124 [[2]] [[2]]$N [1] 2 [[2]]$n [1] 100 150 [[2]][[3]] [,1] [,2] [,3] [1,] 14 90 100 [2,] 88 13 134 This is the format I want, but problem is that for my data, id is not only 1 to 2,but 1 to 100, so my code is not efficient. Could you help me find a efficient way? Thanks. Qi Zhang PhD student, University of Cincinnati [[alternative HTML version deleted]] __ 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 -- Jim Holtman Convergys +1 513 723 2929 What the problem you are trying to solve? __ 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 hiding code for a package
The problem with this is that if someone thinks it's useful, they will likely slog through the obfuscation, then offer something much simpler to do the same thing -- and then be shocked and confused if the originator doesn't thank them for their efort! I've heard that S-Plus allows you to encrypt your code. Talk with Insightful if you want to protect your intellectual property. spencer graves bogdan romocea wrote: There's something else you could try - since you can't hide the code, obfuscate it. Hide the real thing in a large pile of useless, complicated, awfully formatted code that would stop anyone except the most desperate (including yourself, after a couple of weeks/months) from trying to understand it. The best solution would be to compile the code, but R is not there yet. -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Saturday, July 30, 2005 5:35 AM To: Gary Wong Cc: r-help@stat.math.ethz.ch Subject: Re: [R] How to hiding code for a package What you ask is impossible. For a function to be callable it has to be locatable and hence can be printed. One possibility is to have a namespace, and something like foo - function(...) foo_internal(...) where foo is exported but foo_internal is not. Then foo_internal is hidden from casual inspection, but it can be listed by cognescenti. Why do you want to do this? Anyhone can read the source code of your package, and any function which can be called can be deparsed, possibly after jumping through a few hoops. On Sat, 30 Jul 2005, Gary Wong wrote: Hey everyone, I have made a package and wish to release it but before then I have a problem. I have a few functions in this package written in R that I wish to hide such that after installation, someone can use say the function foo(parameters = ) but cannot do foo. Typing foo should not show the source code or at least not all of it. Is there a way to do this ? I have searched the mailing list and used google, and have found something like [R] Hiding internal package functions for the doc. pkg-internal.Rd but this seems different since it seems that the keyword internal just hides the function from showing in the index and hides documentation, not the function itself. Can someone help? Thanks -- 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 __ 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 -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ 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
[R] multiple scale
Hi all
i need to put on one graph 2 functions who's x axis is the same and y not.
I mean on horizontal the time, and on vertical left: pressure, on vertical
right: rpm of a motor, is R able to do that?
i've found this that i could adapt maybe (i don't need time series really?) :/ :
(http://tolstoy.newcastle.edu.au/R/help/04/03/1456.html)
##
## Description: A simple function which plots two time series on one plot where
## the series can have different value intervals over the same time interval.
## Usage: ts.plot.2Axis(xleft, xright)
## Arguments: xleft is the time series for the left vertical axis and xright
## is for the right axis. xleft and xright are defined as time series with
## the 'ts' function in package ts.
## ts.plot function must be available, do library(ts) to ensure this if
## necessary.
## In addition the usual 'ts.plot' and 'plot' parameters can be set
## directly (mar, main, xlab, ylab, lwd) or through gpars as in ts.plot.
## Also parameter digits is the preferred number of decimal digits on right
## axis and ticks is the preferred number of tick marks on right axis.
## Details: The time series for the right vertical axis is scaled with a simple
## rule of thumb scaling.
## The ts.plot function is used to plot the series.
## Value: None.
## Note: When scaling is not acceptable try switching the series parameters.
## If a ylabel is to be set it is here only possible for the left axis.
## See also: 'ts.plot', 'ts', 'legend'.
## Author and date: Hauksson, Bjorn Arnar. March 2004.
## Example:
## First paste this function into the R console or use 'source'.
#library(ts)
#data(UKLungDeaths)
#x - ldeaths
#y - fdeaths/mdeaths
#ts.plot.2Axis(x, y)
#legTxt - c(UK lung deaths, UK female/male deaths (rhs))
#legend(1976.5, 3950, legTxt, lty=c(1:2), col=c(1:2), lwd=2, bty=n)
##
ts.plot.2Axis - function(xleft, xright, digits=1, ticks=5,
mar=(c(4,4,4,4)+0.1), main=,
xlab=, ylab=, lwd=2, gpars=list()) {
# Settings for other parameters than those in the function parameter
list
par(mar=mar) # Margins
k - ncol(as.matrix(xleft)) # Number of time series on left vertical
scale
lty - c(1:(k+1)) # Line types
col - c(1:(k+1)) # Line colors
# Scale time series on right vertical axis
scale - (max(xleft)-min(xleft))/(max(xright)-min(xright))
xright2 - xright*scale
meanScale - mean(xleft) - mean(xright2)
xright2 - xright2 + meanScale
# Plot the series
ts.plot(xleft, xright2, lty=lty, col=col, main=main, ylab=ylab,
xlab=xlab,
lwd=lwd, gpars=gpars)
# Add the right vertical axis labels
lab - seq(round(min(xright), digits), round(max(xright), digits),
length=ticks)
labAt - seq(min(xright2), max(xright2), length=ticks)
axis(side=4, labels=lab, at=labAt)
}
are there a better way to plot what i want?
thks.
guillaume.
// Webmail Oreka : http://www.oreka.com
__
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 print a data.frame without row.names
Heinz == Heinz Tuechler [EMAIL PROTECTED] on Tue, 02 Aug 2005 17:46:07 +0200 writes: ... Heinz I tried this, but then the column headers and column Heinz contents are not aligned. Use the tabulator if you need them aligned : write.table(USArrests, row.names = FALSE, sep = \t) __ 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] can we manage memory usage to increase speed?
On 8/2/05, Spencer Graves [EMAIL PROTECTED] wrote: And you can identify inefficient code fairly easily taking snapshots from proc.time and computing elapsed time for sections of your code. spencer graves Using Rprof may be a better choice. See ?Rprof Tuszynski, Jaroslaw W. wrote: If you have a code that takes 2 weeks to run, than it might be a case of inefficient algorithm design. I was able to go from overnight runs (SELDI data analysis) to 20 minute runs by identifying single inefficient function that took most of the time, and writing it in C. Jarek \=== Jarek Tuszynski, PhD. o / \ Science Applications International Corporation \__,| (703) 676-4192 \ [EMAIL PROTECTED] `\ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zhilin Liu Sent: Monday, August 01, 2005 8:28 PM To: r-help@stat.math.ethz.ch Subject: [R] can we manage memory usage to increase speed? Hi, Thanks for reading. I am running a process in R for microarray data analysis. RedHat Enterprise Linux 4, dual AMD CPU, 6G memory. However, the R process use only a total of 200M memory. And the CPU usage is total to ~110% for two. The program takes at least 2 weeks to run at the current speed. Is there some way we can increase the usage of CPUs and memories and speed up? Any suggestion is appreciated. Thanks again. Zhilin [[alternative HTML version deleted]] __ 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 __ 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 -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ 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 __ 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] multiple scale
Hi,
Search the list, you might be able to find the message but here it is.
Copied From Dr. Brian Ripley's post
x - 1:10
y - rnorm(10)
z - runif(10, 1000, 1)
par(mar=c(5,4,4,4) + 0.1) # Leave space for z axis
plot(x, y)
par(new=T)
plot(x, z, type=l, axes=F, bty=n, xlab=, ylab=)
axis(4, at=pretty(range(z)))
mtext(z, 4, 3)
change last line to mtext(z, 4, 3).
J.
On Tue, 2005-08-02 at 17:18 +0100, [EMAIL PROTECTED] wrote:
Hi all
i need to put on one graph 2 functions who's x axis is the same and y not.
I mean on horizontal the time, and on vertical left: pressure, on vertical
right: rpm of a motor, is R able to do that?
i've found this that i could adapt maybe (i don't need time series really?)
:/ :
(http://tolstoy.newcastle.edu.au/R/help/04/03/1456.html)
##
## Description: A simple function which plots two time series on one plot
where
## the series can have different value intervals over the same time interval.
## Usage: ts.plot.2Axis(xleft, xright)
## Arguments: xleft is the time series for the left vertical axis and xright
## is for the right axis. xleft and xright are defined as time series with
## the 'ts' function in package ts.
## ts.plot function must be available, do library(ts) to ensure this if
## necessary.
## In addition the usual 'ts.plot' and 'plot' parameters can be set
## directly (mar, main, xlab, ylab, lwd) or through gpars as in ts.plot.
## Also parameter digits is the preferred number of decimal digits on right
## axis and ticks is the preferred number of tick marks on right axis.
## Details: The time series for the right vertical axis is scaled with a
simple
## rule of thumb scaling.
## The ts.plot function is used to plot the series.
## Value: None.
## Note: When scaling is not acceptable try switching the series parameters.
## If a ylabel is to be set it is here only possible for the left axis.
## See also: 'ts.plot', 'ts', 'legend'.
## Author and date: Hauksson, Bjorn Arnar. March 2004.
## Example:
## First paste this function into the R console or use 'source'.
#library(ts)
#data(UKLungDeaths)
#x - ldeaths
#y - fdeaths/mdeaths
#ts.plot.2Axis(x, y)
#legTxt - c(UK lung deaths, UK female/male deaths (rhs))
#legend(1976.5, 3950, legTxt, lty=c(1:2), col=c(1:2), lwd=2, bty=n)
##
ts.plot.2Axis - function(xleft, xright, digits=1, ticks=5,
mar=(c(4,4,4,4)+0.1), main=,
xlab=, ylab=, lwd=2, gpars=list()) {
# Settings for other parameters than those in the function parameter
list
par(mar=mar) # Margins
k - ncol(as.matrix(xleft)) # Number of time series on left vertical
scale
lty - c(1:(k+1)) # Line types
col - c(1:(k+1)) # Line colors
# Scale time series on right vertical axis
scale - (max(xleft)-min(xleft))/(max(xright)-min(xright))
xright2 - xright*scale
meanScale - mean(xleft) - mean(xright2)
xright2 - xright2 + meanScale
# Plot the series
ts.plot(xleft, xright2, lty=lty, col=col, main=main, ylab=ylab,
xlab=xlab,
lwd=lwd, gpars=gpars)
# Add the right vertical axis labels
lab - seq(round(min(xright), digits), round(max(xright), digits),
length=ticks)
labAt - seq(min(xright2), max(xright2), length=ticks)
axis(side=4, labels=lab, at=labAt)
}
are there a better way to plot what i want?
thks.
guillaume.
// Webmail Oreka : http://www.oreka.com
__
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
--
Jeanie (Jie) Na
Programmer Analyst II _ _____ _
Department of Quantitative Health Sciences [_]-[_] / - \ | |_| | (_(_
Cleveland Clinic Foundation | | ( |_| ) ) _ ( _| )
Tel: (216)4451369 [_]-[_] \_\_\ |_| |_| (___/
__
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 print a data.frame without row.names
Martin Maechler [EMAIL PROTECTED] writes: Heinz == Heinz Tuechler [EMAIL PROTECTED] on Tue, 02 Aug 2005 17:46:07 +0200 writes: ... Heinz I tried this, but then the column headers and column Heinz contents are not aligned. Use the tabulator if you need them aligned : write.table(USArrests, row.names = FALSE, sep = \t) Unless a column or a header is 8 chars or wider (and UrbanPop is!). This seems to do it: x - as.matrix(format(USArrests)) rownames(x) - rep(, nrow(x)) print(x, quote=FALSE, right=TRUE) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
[R] problem using evaluating a formula
##data
y1 - matrix(c(3,1,0,1,0,1,1,0,0,0,1,0,0,0,1,1,0,1,1,1),
nrow = 5, byrow = TRUE)
y2 - matrix(c
(3,0,10,3,3,0,0,1,1,0,0,0,0,0,1,0,1,0,0,2,1,0,1,1,0,2,1,1,4,1),
nrow = 5, byrow = TRUE)
y1 - as.data.frame(y1)
y2 - as.data.frame(y2)
rownames(y1) - rownames(y2) - paste(site, 1:5, sep = )
colnames(y1) - paste(spp, 1:4, sep = )
colnames(y2) - paste(spp, 1:6, sep = )
##code
coca.formula - function(formula, data, ...)
{
##cat(\nusing formula method\n)
##browser()
if (missing(data)) {
data - parent.frame()
}
m - match.call(expand.dots = FALSE)
m$... - NULL
m[[1]] - as.name(model.frame)
## the next line fails
m - eval(m, sys.parent())
Terms - attr(m, terms)
Response - model.extract(m, response)
attr(Terms, intercept) - 0
Predictor - model.matrix(Terms, m)
retval - list(m = m, Terms = Terms, Response = Response,
Predictor = Predictor)
return(retval)
}
coca(y1 ~ y2, method = symmetric, symmetric= TRUE)
gives:
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames, :
invalid variable type
when executing the indicated line
now both y1 and y2 are data.frames - this is the natural way of
specifying the model I have in mind - and I think this is the problem as
it seems to be the rhs of the formula that is causing the error.
Is there an alternative way of handling and evaling formulae if the rhs
is a data.frame (if my assumption is correct of course)? I would like,
eventually, to have the option of specifying the predictors as either a
data.frame or via named variables found in the variable passed to data.
A simple alternative would be to do the following:
predictor - get(as.character(formula[[3]]))
response - get(as.character(formula[[2]]))
Would I be missing something vital that I'm not appreciating if I used
this simple method?
Any other suggestions gratefully received.
Many thanks in advance,
Gav
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Gavin Simpson [T] +44 (0)20 7679 5522
ENSIS Research Fellow [F] +44 (0)20 7679 7565
ENSIS Ltd. ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk
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.
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
__
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
[R] simplifying a lmer model
I have been using lmer in lme4() to analyse the effect of dropping a term from the model as below anova.name-anova(m1,m2) Where m1 is an original model and m2 has one term removed. I can then create my own type III tables for each variable in the model. However with many variables this becomes exceedingly time consuming! anova.lme in nlme() and Anova() in car dont seem to work for lme objects created with lmer? Is there any other way to create type III tables? Any help much appreciated. Simon P Simon Pickett Centre for Ecology and Conservation Biology University of Exeter in Cornwall Tremough Campus Penryn Cornwall TR10 9EZ UK Tel: 01326371852 __ 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] simplifying a lmer model
sp219 [EMAIL PROTECTED] writes: I have been using lmer in lme4() to analyse the effect of dropping a term from the model as below anova.name-anova(m1,m2) Where m1 is an original model and m2 has one term removed. I can then create my own type III tables for each variable in the model. However with many variables this becomes exceedingly time consuming! anova.lme in nlme() and Anova() in car dont seem to work for lme objects created with lmer? Is there any other way to create type III tables? Any help much appreciated. Simon P I haven't played nearly as much with lme4 as I perhaps should have, but my first try would be to see whether drop1 works on lmer models. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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
[R] Help with sas.get
I am running R 2.0.1 on Windows trying to import a SAS dataset into R using sas.get. It is a small SAS dataset, but when I write the command, the SAS window opens but never appears to complete. Am I doing something wrong? Here is an example of my command: temp - sas.get(J:/blah,name) Jorge [[alternative HTML version deleted]] __ 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] problem using evaluating a formula
On Tue, 2005-08-02 at 18:27 +0100, Gavin Simpson wrote: ##data snip coca(y1 ~ y2, method = symmetric, symmetric= TRUE) sorry, this should have been: coca.formula(y1 ~ y2, method = symmetric, symmetric= TRUE) gives: Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid variable type snip G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] gavin.simpsonATNOSPAMucl.ac.uk 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. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] can we manage memory usage to increase speed?
On Tue, 2 Aug 2005, Spencer Graves wrote: And you can identify inefficient code fairly easily taking snapshots from proc.time and computing elapsed time for sections of your code. Or use the profiler, which makes it much easier. There was a Programmers' Niche article about it in one of the first R Newsletters. -thomas spencer graves Tuszynski, Jaroslaw W. wrote: If you have a code that takes 2 weeks to run, than it might be a case of inefficient algorithm design. I was able to go from overnight runs (SELDI data analysis) to 20 minute runs by identifying single inefficient function that took most of the time, and writing it in C. Jarek \=== Jarek Tuszynski, PhD. o / \ Science Applications International Corporation \__,| (703) 676-4192 \ [EMAIL PROTECTED] `\ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zhilin Liu Sent: Monday, August 01, 2005 8:28 PM To: r-help@stat.math.ethz.ch Subject: [R] can we manage memory usage to increase speed? Hi, Thanks for reading. I am running a process in R for microarray data analysis. RedHat Enterprise Linux 4, dual AMD CPU, 6G memory. However, the R process use only a total of 200M memory. And the CPU usage is total to ~110% for two. The program takes at least 2 weeks to run at the current speed. Is there some way we can increase the usage of CPUs and memories and speed up? Any suggestion is appreciated. Thanks again. Zhilin [[alternative HTML version deleted]] __ 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 __ 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 -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ 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 Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ 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
[R] reading in and mps file
Hi all: How does one read in an mps file and store it in a matrix as is. I have pasted the format of the file. I have implemented an mps writer but would like to have the capability to read in an mps file as well and store it in a matrix with out using the 'linprog' routines in R. Is there are way to use read.table or scan on the file below. Your help will be greatly appreciated. -Dhiren NAME test.2005-08-02.Tue ROWS N obj L CPA E ass1 E ass2 E ass3 COLUMNS 982323.1 obj 7.12279694339023 CPA -0.300433084368706 ass1 1 982323.2 obj -8.41320485916529 CPA 0.603671897647387 ass1 1 982323.41 obj 0 CPA 0 ass1 1 982351.1 obj -21.4471176117659 CPA 1.80909823649563 ass2 1 982351.22 obj -32.9606785054072 CPA 3.23030611400710 ass2 1 982351.41 obj 0 CPA 0 ass2 1 982554.1 obj 1.66536080466821 CPA -0.107303781434894 ass3 1 982554.23 obj -1.07268986390231 CPA 0.100720627703143 ass3 1 982554.41 obj 0 CPA 0 ass3 1 RHS rhs ass1 1 rhs ass2 1 rhs ass3 1 ENDATA __ 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
[R] Hmisc / Design question
All, I have been reading Dr. Harrell's excellent Regression Modeling Strategies book and trying out the exercises. I understand that contrast( ) is used to obtain contrasts between two variables for given levels of other nuisance variables; is there a way to use contrast( ) to obtain, for example, Scheffe confidence intervals / hypothesis tests for many post hoc contrasts at once? Any help would be much appreciated, Greg __ 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
[R] Loop problem
Dear everyone I am a new user,would like to combine these code together by using a loop,each function has three value as Tr = 1 - 3,how can i combine together? logitTr1 -logit[logit[,Study]logit[,Tr]==1,] (number of row in each group (1-3) is difference but equal in colume) fnTr1 - function (p) sum( n/2*log(2*pi)+log(1/logitTr1$sd)+1/2*(logitTr1$logitp*logitTr1$logitp-2*logitTr1$logitp*p+p^2) *1/logitTr1$sd*logitTr1$sd ) (maximum likelyhood function) outTr1- nlm (fnTr1,p=c(10),hessian=TRUE) minimumTr1 - outTr1$minimum valueTr1 - outTr1$estimate (estimate the value) The problem is the program couldn't work by using logitTr[i],fnTr[i] outTr[i],minimumTr[i],value[i] in a loop. The function logitTr[i] is the data matrix which is not equal each group, fnTr[i] is the maximumlikelyhood function for estimation in next step; outTr[i],minimumTr[i],valueTr[i]. Has anyone got any idea to help me?,thank you very much. Hathaikan __ 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
[R] memory limit
Hi, is it possible to increase the memory limit to infinite so that I don't need to worry about whether it is enough or not? In S-plus, you can do this by setting: options( memory = as.integer( Inf ) ) is it possible to do this in R? __ 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
[R] parallel computing in R
Hi, is there an excellent source of documentation for installation, configuration of R packages (Rmpi,snow,rsprng etc.) for parallel computing on linus system? Thanks __ 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] memory limit
array chip wrote: Hi, is it possible to increase the memory limit to infinite so that I don't need to worry about whether it is enough or not? In S-plus, you can do this by setting: options( memory = as.integer( Inf ) ) is it possible to do this in R? You are on Windows, right? See ?memory.limit You cannot say Inf, but memory.limit(4000) sets it to 4Gb which you won't reach with a 32bit machine anyway. Say you are on a 32bit machine with 512Mb of RAM, you certainly do not want that R accesses much more than 512Mb for itself, in order to prevent too much swapping. And that's what R chooses for you. Uwe Ligges __ 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 __ 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] Hmisc / Design question
Greg Tarpinian wrote:
All,
I have been reading Dr. Harrell's excellent
Regression Modeling Strategies book and trying out
the exercises. I understand that contrast( ) is used
to obtain contrasts between two variables for given
levels of other nuisance variables; is there a way
to use contrast( ) to obtain, for example, Scheffe
confidence intervals / hypothesis tests for many
post hoc contrasts at once?
Any help would be much appreciated,
Greg
Steven Novick (cc'd) has written some nice code that I regret I haven't
had time to add into contrast.Design for doing simulation-based
adjustment for multiple comparisons. Below is the code he sent me.
## Program: multiple.adjustment.R
## Version: 1
## Author: Steven Novick
## Date:May 21, 2004
## Purpose: Compute the exact T-critical value for multiple
comparisons based on the paper
## Don Edwards and Jack Berry (1987). The Efficiency of
Simulation-Based Multiple Comparison.
## Biometrics 43, pp913-928.
multiple.adjustment = function(fit, cont1, cont2, alpha=.05, m=7)
{
## fit = object of class ols from library Design
## cont1, cont2 = data.frame with elements to be contrasted. See
function contrast in Design.
## alpha = test significance level
## m = number of monte-carlo runs
V=fit$var/fit$stats[Sigma]^2 ## Var( coef(fit) ) = sigma^2 * V
C=contrast(fit, cont1, cont2)$X ## Contrast matrix
df = fit$df## Error degrees of freedom
r = (m+1)*(1-alpha) # P( W w[r] ) = alpha
if ( floor(r) != ceiling(r) )
stop((m+1)*(1-alpha) must be an integer.)
## Create random numbers
n.contrast=nrow(C)
n.coef=length(coef(fit))
G=chol(V)
U=apply(C, 1, function(ctr){( G%*%ctr
)/as.vector(sqrt(t(ctr)%*%V%*%ctr)) })
W = sort(sapply(1:m, function(i){ z=rnorm(n.coef); y=sqrt(rchisq(1,
df)/df); w=abs(t(U)%*%z)/y; return(max(w)) }))
w.alpha = W[r] ## Cut-off value for testing; 95% CI = beta.hat +
c(-1, 1)*w.alpha* SE(beta.hat)
alpha.star = 2*(1-pt(w.alpha, df)) ## What is alpha if using
T-statistic ?
return(list(w.alpha=w.alpha, alpha.star=alpha.star))
}
--
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
[R] cut.Date functionality for chron date/time objects
Hello, I've encountered the need to cut some chron objects of the form: R mychron - chron(sort(runif(10, 0, 10))) R mychron [1] (01/01/70 16:36:20) (01/02/70 00:08:46) (01/03/70 16:54:49) [4] (01/04/70 06:45:00) (01/07/70 06:21:24) (01/07/70 18:28:44) [7] (01/08/70 00:47:05) (01/08/70 05:11:44) (01/10/70 01:07:53) [10] (01/10/70 17:46:53) into arbitrary (e.g. a given number of minutes, seconds, etc.) units. Basically, I'm searching for the functionality of cut.Date, which has a nice 'breaks' argument: ,-[ *help[R](cut.Date)* (lines: 23 - 30) ] | breaks: a vector of cut points _or_ number giving the number of | intervals which 'x' is to be cut into _or_ an interval | specification, one of 'sec', 'min', 'hour', 'day', | 'DSTday', 'week', 'month' or 'year', optionally | preceded by an integer and a space, or followed by 's'. | For 'Date' objects only 'day', 'week', 'month' and | 'year' are allowed. `- 'cut.dates' (from chron itself) allows for cut'ing into months, years, etc., but not any fractions or multiples of these. Converting the chron objects to POSIXct (via 'as.POSIXct') and then using cut.Date works, but is inconvenient, as it introduces time zone information. Is there a better way to deal with this? Thanks in advance, -- Sebastian P. Luque __ 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 with sas.get
Jorge, My understanding about sas.get is that it actually runs SAS in the backend, output the SAS data, and then import it into R again. It might be better to convert SAS to csv format and read it into R. On 8/2/05, Jorge Sirgo [EMAIL PROTECTED] wrote: I am running R 2.0.1 on Windows trying to import a SAS dataset into R using sas.get. It is a small SAS dataset, but when I write the command, the SAS window opens but never appears to complete. Am I doing something wrong? Here is an example of my command: temp - sas.get(J:/blah,name) Jorge [[alternative HTML version deleted]] __ 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 -- WenSui Liu, MS MA Senior Decision Support Analyst Division of Health Policy and Clinical Effectiveness Cincinnati Children Hospital Medical Center __ 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
[R] breaking command in command line in R for Mac Aqua
I'm using R for Mac Aqua version 2.1.1 If at the command line, I type: ls( and then a return, the command line prompt changes to a plus sign indicating that the command has not been completed. How do I break, or kill, the partial command? Sometimes, I type a long command but miss a bracket or parenthesis. On a unix or linux version of R, I can type ctrl-c. On the Mac, ctrl-c, command-(dot), and escape do not work. Any solutions? Mike __ 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 with sas.get
Wensui Liu wrote: Jorge, My understanding about sas.get is that it actually runs SAS in the backend, output the SAS data, and then import it into R again. He has SAS running locally. It might be better to convert SAS to csv format and read it into R. For that, the Hmisc package's sasxport.get(..., method='csv'...) can help. Frank On 8/2/05, Jorge Sirgo [EMAIL PROTECTED] wrote: I am running R 2.0.1 on Windows trying to import a SAS dataset into R using sas.get. It is a small SAS dataset, but when I write the command, the SAS window opens but never appears to complete. Am I doing something wrong? Here is an example of my command: temp - sas.get(J:/blah,name) Jorge [[alternative HTML version deleted]] __ 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 -- 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
Re: [R] can we manage memory usage to increase speed?
Hi, Thank you all for the kind reply. I recompiled R as the previous one turned profiling off. I am using package MAANOVA, running the matest function which is a permutation test. The author did warn that it takes a long time to run. Here is one of the test results: [ Rdata]# ./R CMD Rprof maanovatest.out Each sample represents 0.02 seconds. Total run time: 905.95999466 seconds. Total seconds: time spent in function and callees. Self seconds: time spent in function alone. % total % self totalseconds selfsecondsname 100.00905.94 0.00 0.00 matest 80.18726.40 0.25 2.30 fitmaanova 79.37719.04 0.19 1.72 mixed 68.34619.16 1.05 9.50 pinv 64.33582.78 0.88 7.96 La.svd 55.51502.90 55.51502.90 .Call 38.47348.54 1.58 14.28 makeHq 34.50312.60 0.13 1.18 solveMME 19.80179.42 0.18 1.60 matest.engine 10.19 92.30 10.19 92.30 %*% .. The other part are not pasted as they are almost the same everytime we check the profiling. Only the parts above changes. For example, here is another output: 100.00 1411.02 0.00 0.02 matest 82.88 1169.40 0.24 3.40 fitmaanova 82.22 1160.18 0.19 2.74 mixed 68.82971.02 1.06 14.90 pinv 64.84914.94 0.85 11.98 La.svd 56.10791.64 56.10791.64 .Call 39.13552.10 1.55 21.84 makeHq 36.77518.82 0.13 1.88 solveMME 31.40443.04 0.00 0.00 matest.perm 17.10241.32 0.16 2.28 matest.engine 10.15143.24 10.15143.24 %*% I run this with a permutation of 2 times and it is still running. So it is not possible to run 1000 permutations with this kind of speed. And here is the output of TOP for R: PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 15250 liuz 0 -20 218m 136m 2556 R 72.3 2.5 29:05.20 R Any suggestion to improve the performance is highly appreciated. Thanks a lot. Zhilin --- Douglas Bates [EMAIL PROTECTED] wrote: On 8/2/05, Spencer Graves [EMAIL PROTECTED] wrote: And you can identify inefficient code fairly easily taking snapshots from proc.time and computing elapsed time for sections of your code. spencer graves Using Rprof may be a better choice. See ?Rprof Tuszynski, Jaroslaw W. wrote: If you have a code that takes 2 weeks to run, than it might be a case of inefficient algorithm design. I was able to go from overnight runs (SELDI data analysis) to 20 minute runs by identifying single inefficient function that took most of the time, and writing it in C. Jarek \=== Jarek Tuszynski, PhD. o / \ Science Applications International Corporation \__,| (703) 676-4192 \ [EMAIL PROTECTED] `\ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Zhilin Liu Sent: Monday, August 01, 2005 8:28 PM To: r-help@stat.math.ethz.ch Subject: [R] can we manage memory usage to increase speed? Hi, Thanks for reading. I am running a process in R for microarray data analysis. RedHat Enterprise Linux 4, dual AMD CPU, 6G memory. However, the R process use only a total of 200M memory. And the CPU usage is total to ~110% for two. The program takes at least 2 weeks to run at the current speed. Is there some way we can increase the usage of CPUs and memories and speed up? Any suggestion is appreciated. Thanks again. Zhilin [[alternative HTML version deleted]] __ 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 __ 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 -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ 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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting
Re: [R] parallel computing in R
Steve Adams steve_adams_sd at yahoo.com writes: Hi, is there an excellent source of documentation for installation, configuration of R packages (Rmpi,snow,rsprng etc.) for parallel computing on linus system? In case you want it ready-to-run, Rmpi, SNOW, Rsprng, ... work out of the box under Quantian, which would give you openMosix to boot which can make scheduling MPI/PVM easier. For more about Quantian, see the pages at http://dirk.eddelbuettel.com/quantian All three are also part of Debian so you could add them (pre-built, no less) to a regular Debian system, and possibly a derived system such as Ubuntu. Sprng was a bit tricky to build, the others are pretty standard. I talked about it a little at Usenix last year and intend to revisit this for DSC 2005 in a couple of days. Hope this helps, Dirk __ 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 print a data.frame without row.names
Thanks to all of you for your help. As far as I see, the solution of Peter Dalgaard works exactly as I want. All other solutions have limitations. Heinz At 19:19 02.08.2005 +0200, Peter Dalgaard wrote: Martin Maechler [EMAIL PROTECTED] writes: Heinz == Heinz Tuechler [EMAIL PROTECTED] on Tue, 02 Aug 2005 17:46:07 +0200 writes: ... Heinz I tried this, but then the column headers and column Heinz contents are not aligned. Use the tabulator if you need them aligned : write.table(USArrests, row.names = FALSE, sep = \t) Unless a column or a header is 8 chars or wider (and UrbanPop is!). This seems to do it: x - as.matrix(format(USArrests)) rownames(x) - rep(, nrow(x)) print(x, quote=FALSE, right=TRUE) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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] cut.Date functionality for chron date/time objects
Assuming, as in your post: set.seed(123) mychron - chron(sort(runif(10, 0, 10))) breaks - quantile(mychron) # is one of these adequate? cut(mychron, breaks) cut(unclass(mychron), unclass(breaks), lab = FALSE) On 8/2/05, Sebastian Luque [EMAIL PROTECTED] wrote: Hello, I've encountered the need to cut some chron objects of the form: R mychron - chron(sort(runif(10, 0, 10))) R mychron [1] (01/01/70 16:36:20) (01/02/70 00:08:46) (01/03/70 16:54:49) [4] (01/04/70 06:45:00) (01/07/70 06:21:24) (01/07/70 18:28:44) [7] (01/08/70 00:47:05) (01/08/70 05:11:44) (01/10/70 01:07:53) [10] (01/10/70 17:46:53) into arbitrary (e.g. a given number of minutes, seconds, etc.) units. Basically, I'm searching for the functionality of cut.Date, which has a nice 'breaks' argument: ,-[ *help[R](cut.Date)* (lines: 23 - 30) ] | breaks: a vector of cut points _or_ number giving the number of | intervals which 'x' is to be cut into _or_ an interval | specification, one of 'sec', 'min', 'hour', 'day', | 'DSTday', 'week', 'month' or 'year', optionally | preceded by an integer and a space, or followed by 's'. | For 'Date' objects only 'day', 'week', 'month' and | 'year' are allowed. `- 'cut.dates' (from chron itself) allows for cut'ing into months, years, etc., but not any fractions or multiples of these. Converting the chron objects to POSIXct (via 'as.POSIXct') and then using cut.Date works, but is inconvenient, as it introduces time zone information. Is there a better way to deal with this? Thanks in advance, -- Sebastian P. Luque __ 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 __ 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
[R] Trouble with SciViews-R 0.7-3, SciViews R 0.8-7, and Tinn-R 1.16.1.5
Hello everybody, I am new to using Windows and R, and have been experimenting with various packages. I recently installed R 2.1.1 under Windows XP SP2, and tried installing the latest versions of SciViews (0.7-6, and R package 0.8-7 found on the sciviews.org website), and also Tinn-R 1.16.1.5 stable. I have also been experimenting with R Commander 0.9-14 stable, 1.0-2 stable, and also tried 1.1 unstable (along with dependent packages). Oddly, although the installer for SciViews says version 0.7-3, the About dialog box says 0.7.6. I am not certain which is the correct version. I have confirmed incompatibility with the latest stable and unstable R Commander and SciViews (recently noted by Grosjean in R-help). R Commander 0.9-14 does work with SciViews 0.7.6 (.3?), but also produces the previously reported error that R Commander is not installed (answering No to installing, will allow the correct dialog box to open). I have noticed the following additional two behaviours which have consistently been produced. 1. After installing SciViews 0.8-7 package from the SciViews website, the call-tip functionality is broken in Tinn-R 1.16.1.5 stable. Downgrading, or installing, the SciViews 0.8-6 from CRAN restores, or enables, this functionality. 2. The Packages menu in SciViews-R 0.7.3 is hopelessly broken for me (at least under R 2.1.1). The only menu option that works sometimes, for reasons I am unable to elucidate, is Load packages (the first option); however, many times Rconsole crashes altogether. The other menu choices result in nothing happening. I am able to replicate this behaviour with multiple fresh installs of R 2.1.1, SciViews 0.7-6 (3?) (and SciViews 0.8.7 package), and tcltk2 0.7-4. I am not sure that these reports matter since it appears that SciViews will shortly be updated, but since I found no mention of these issues, I am hopeful that the next version may fix them. __ 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] cut.Date functionality for chron date/time objects
Gabor Grothendieck [EMAIL PROTECTED] wrote: Assuming, as in your post: set.seed(123) mychron - chron(sort(runif(10, 0, 10))) breaks - quantile(mychron) # is one of these adequate? cut(mychron, breaks) cut(unclass(mychron), unclass(breaks), lab = FALSE) Thank you Gabor, that showed me I really needed to be more creative with the 'breaks' argument. So what I needed was (with mychron as above): breaks - seq(min(mychron, na.rm = TRUE), ceiling(max(mychron, na.rm = TRUE)), by = 1/2) cut(unclass(mychron), unclass(breaks), include.lowest = TRUE, labels = FALSE) in order to cut the chron object into 1/2 day units. Thanks so much, -- Sebastian P. Luque __ 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] cut.Date functionality for chron date/time objects
How about the following: set.seed(123) mychron - chron(sort(runif(10, 0, 10))) (breaks - chron(pretty(quantile(mychron [1] 01/01/70 01/03/70 01/05/70 01/07/70 01/09/70 01/11/70 spencer graves Sebastian Luque wrote: Gabor Grothendieck [EMAIL PROTECTED] wrote: Assuming, as in your post: set.seed(123) mychron - chron(sort(runif(10, 0, 10))) breaks - quantile(mychron) # is one of these adequate? cut(mychron, breaks) cut(unclass(mychron), unclass(breaks), lab = FALSE) Thank you Gabor, that showed me I really needed to be more creative with the 'breaks' argument. So what I needed was (with mychron as above): breaks - seq(min(mychron, na.rm = TRUE), ceiling(max(mychron, na.rm = TRUE)), by = 1/2) cut(unclass(mychron), unclass(breaks), include.lowest = TRUE, labels = FALSE) in order to cut the chron object into 1/2 day units. Thanks so much, -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ 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
[R] prcomp eigenvalues
Hello, Can you get eigenvalues in addition to eigevectors using prcomp? If so how? I am unable to use princomp due to small sample sizes. Thank you in advance for your help! Rebecca Young -- 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 __ 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] prcomp eigenvalues
I donn't think you can get it directly from prcomp ,but you can get it though svd.In fact,the prcomp use the svd to do the principal components analysis . === 2005-08-03 10:06:56 您在来信中写道：=== Hello, Can you get eigenvalues in addition to eigevectors using prcomp? If so how? I am unable to use princomp due to small sample sizes. Thank you in advance for your help! Rebecca Young -- 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 __ 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 = = = = = = = = = = = = = = = = = = = = 2005-08-03 -- Deparment of Sociology Fudan University Blog:http://sociology.yculblog.com __ 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] prcomp eigenvalues
Rebecca Young wrote: Hello, Can you get eigenvalues in addition to eigevectors using prcomp? If so how? I am unable to use princomp due to small sample sizes. Thank you in advance for your help! Rebecca Young Hi, Rebecca, From ?prcomp: The calculation is done by a singular value decomposition of the (centered and possibly scaled) data matrix, not by using 'eigen' on the covariance matrix. This is generally the preferred method for numerical accuracy. ... So you can get the singular values, but not the eigenvalues. You could use ?princomp if you really want the eigenvalues. In either case, you read the code to see how this is done. x - matrix(rnorm(1000), 100, 10) # eigenvalues v - cov.wt(x) ev - eigen(v$cov * (1 - 1/v$n.obs), symmetric = TRUE)$values ev[ev 0] - 0 princomp(x)$sdev sqrt(ev) # singular values sv - svd(scale(x, center = TRUE, scale = FALSE), nu = 0) prcomp(x)$sdev sv$d/sqrt(max(1, nrow(x) - 1)) HTH, --sundar __ 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] cut.Date functionality for chron date/time objects
Spencer Graves [EMAIL PROTECTED] wrote: How about the following: set.seed(123) mychron - chron(sort(runif(10, 0, 10))) (breaks - chron(pretty(quantile(mychron [1] 01/01/70 01/03/70 01/05/70 01/07/70 01/09/70 01/11/70 I was looking for a way to cut it into specified units of time, rather than quantiles. Anyway, both your suggestions show one can go very far with the breaks arg. Thank you! -- Sebastian P. Luque __ 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
[R] hash code for arbitrary object
Can anyone suggest a simple way to calculate a 'hash code' from an arbitrary R object? hash(x) should return an integer or string with the property that if hash(x) != hash(y) then x and y are not identical and the time to compute hash(x) should be quite short. Any suggestions welcome thanks Adrian Baddeley __ 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] hash code for arbitrary object
On Wed, 2005-08-03 at 12:05 +0800, Adrian Baddeley wrote: Can anyone suggest a simple way to calculate a 'hash code' from an arbitrary R object? hash(x) should return an integer or string with the property that if hash(x) != hash(y) then x and y are not identical and the time to compute hash(x) should be quite short. Any suggestions welcome thanks Adrian Baddeley Take a look at Dirk Eddelbuettel's digest() function in the package of the same name on CRAN. Be sure to read the details section for caveats regarding collisions. HTH, Marc Schwartz __ 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
[R] regexpr and portability issue
Dear all-- I am still forging my first arms with R and I am fighting with regexpr() as well as portability between unix and windoz. I need to extract barcodes from filenames (which are located between a double and single underscore) as well as the directory where the filename is residing. Here is the solution I came to: aFileName - /Users/marco/Desktop/diagnosticAnalysis/test/MA__251329410021_S01_A01.txt t - regexpr(__\\d*_,aFileName, perl=T) t.dir - regexpr(^.*/, aFileName, perl=T) base.name - substr(aFileName, t+2, t-2 + attr(t,match.length)) base.dir - substr(aFileName, t.dir, attr(t.dir,match.length)) My questions are: 1) Is there a more elegant way to deal with regular expressions (read here: more easier, more like perl style). 2) I have a portability problem when I extract the base.dir Windoz is using '\' instead of '/' to separate directories. Any suggestions/comments Many Tx Marco Blanchette, Ph.D. [EMAIL PROTECTED] Donald C. Rio's lab Department of Molecular and Cell Biology 16 Barker Hall University of California Berkeley, CA 94720-3204 Tel: (510) 642-1084 Cell: (510) 847-0996 Fax: (510) 642-6062 __ 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
[R] how to test this
Dear there, I am wondering how to test whether a simple linear regression model (e.g. y=1.05x) is significantly different from a 1 to 1 line (i.e. y=x). Thanks. Regards, Jin [[alternative HTML version deleted]] __ 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] regexpr and portability issue
Try this. The regular expression says to match - anything - followed by a double underscore - followed by one or more digits - followed by an underscore - followed by anything. The digits have been parenthesized so that they can be referred to in the backreference \\1.Also use the R function dirname rather than regular expressions. base.name - sub(.*__([[:digit:]]+)_.*, \\1, aFileName, ext = TRUE) base.dir - dirname(aFileName) On 8/3/05, Marco Blanchette [EMAIL PROTECTED] wrote: Dear all-- I am still forging my first arms with R and I am fighting with regexpr() as well as portability between unix and windoz. I need to extract barcodes from filenames (which are located between a double and single underscore) as well as the directory where the filename is residing. Here is the solution I came to: aFileName - /Users/marco/Desktop/diagnosticAnalysis/test/MA__251329410021_S01_A01.txt t - regexpr(__\\d*_,aFileName, perl=T) t.dir - regexpr(^.*/, aFileName, perl=T) base.name - substr(aFileName, t+2, t-2 + attr(t,match.length)) base.dir - substr(aFileName, t.dir, attr(t.dir,match.length)) My questions are: 1) Is there a more elegant way to deal with regular expressions (read here: more easier, more like perl style). 2) I have a portability problem when I extract the base.dir Windoz is using '\' instead of '/' to separate directories. Any suggestions/comments Many Tx Marco Blanchette, Ph.D. [EMAIL PROTECTED] Donald C. Rio's lab Department of Molecular and Cell Biology 16 Barker Hall University of California Berkeley, CA 94720-3204 Tel: (510) 642-1084 Cell: (510) 847-0996 Fax: (510) 642-6062 __ 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 __ 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
[R] Multilevel logistic regression using lmer vs glmmPQL vs. gllamm in Stata
Dear all, I am trying to replicate some multilevel models with binary outcomes using R's lmer and glmmPQL and Stata's gllmm, respectively. The data can be found at http://www.uni-koeln.de/~ahf34/xerop.dta. The relevant Stata output can be found at http://www.uni- koeln.de/~ahf34/stataoutput.txt. First, you will find the unconditional model, i.e. no level1- or 2-predictor variables. The second model contains some level 1-predictor variables My R file can be found at http://www.uni-koeln.de/~ahf34/xerop.R. Beside the fact that there is a difference between the estimates of the intercept (unconditional model: R: -2.76459 and Stata: -2.698923) I am especially interested in the level 2 variance. In Stata the level 2 variance is about 1.03, while in R it is 4.68. Using glmmPQL from package MASS again gives different results for the level 2 variance component. What is meant by Residual? I thought the level 1 variance is fixed to (pi^2)/3. I am a beginner in multilevel modeling so I assume I made some mistake either in interpreting the output or specifying the models. I would appreciate any help. Bernd __ 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
