[R] [R-pkgs] proftools package now available from CRAN

to be worse). More careful design of the data structures and memoizing calculations that are now repeated is likely to improve performance substantially. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa

Re: [R] clusterCall with replicate function

__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial

Re: [R] Suspected memory leak with R v.2.5.x and large matrices with dimnames set

and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319

Re: [R] makeSOCKcluster

- socketConnection(port = port, server=TRUE, blocking=TRUE, open=a+b) can someone please tell me what exactly could be the problem? Thank you, Rishi -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences

Re: [R] How to properly finalize external pointers?

mingw32 system i386, mingw32 status major 2 minor 5.1 year 2007 month 06 day27 svn rev42083 language R version.string R version 2.5.1 (2007-06-27) -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham

Re: [R] simultaneous computing

/biopara.html) Are there other possibilities? Are there special groups working on simultaneous computing with R? Thanks Markus -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335

Re: [R] Parallel processes

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386

[R] Subject: useR! 2007 --- programming competition

R Users and Developers, The first North American useR! to be held at Iowa State University, Ames, Iowa, August 8-10, 2007, will include a programming competition. The challenge: Develop a package useful for the analysis of large data sets. Your package could augment an existing

Re: [R] snow parLapply standard output

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics

Re: [R] can't load just saved R object ReadItem: unknown type 65

2.9.13 1.13.14 1.3.3 1.13.39 -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017

Re: [R] Snow Package and SPRNG: Will it solve my problem?

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics

Re: [R] question on suppressing error messages with Rmath library

guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386

Re: [R] Scoping issue?

read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone

Re: [R] how much performance penalty does this incur, scalar as a vector of one element?

. Overflows automatically get promoted to ordinary Double's, which are pointers to objects holding real IEEE doubles. Luke Tierney [EMAIL PROTECTED] writes: Systems that support integer scalars often represent them as immediate values within pointers by sacrificing one or two bits

Re: [R] how much performance penalty does this incur, scalar as a vector of one element?

-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E

Re: [R] features of save and save.image (unexpected file sizes)

-- Doctorate student, http://www.mif.vu.lt/katedros/eka/katedra/zemlys.php Vilnius University -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics

Re: [R] wrapping mle()

On Sat, 30 Dec 2006, Sebastian P. Luque wrote: On Sat, 30 Dec 2006 15:46:01 -0600 (CST), Luke Tierney [EMAIL PROTECTED] wrote: It is much cleaner to do this sort of thing with lexical scope. For example, mkll - function(x, y) { function(ymax=15, xhalf=6) { -sum

Re: [R] wrapping mle()

- function(ymax=15, xhalf=6) { -sum(stats::dpois(y, lambda=ymax/(1+x/xhalf), log=TRUE)) } fit.mle - function(FUN, x, y) mle(proto(FUN = match.fun(FUN))[[FUN]], method=L-BFGS-B, lower=c(0, 0)) fit.mle(ll, x=0:10, y=c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)) On 12/30/06, Luke Tierney [EMAIL

Re: [R] wrapping mle()

-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241

Re: [R] snow's makeCluster hanging (using Rmpi)

-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone

Re: [R] Rmpi performance

/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax

Re: [R] Evaluation of defaults in functions

code is in http://www.stat.uiowa.edu/~luke/R/lazy/. This is out of date but not too hard to fix. Insuring memory efficiency is still a bit tricky; some comments are int he notes at this site. Best, luke -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor

Re: [R] Evaluation of defaults in functions

with this for fun a one point. Some code is in http://www.stat.uiowa.edu/~luke/R/lazy/. This is out of date but not too hard to fix. Insuring memory efficiency is still a bit tricky; some comments are int he notes at this site. Thanks, I will take a look at that. Regards, Hadley -- Luke

Re: [R] makeSOCKcluster

state. It cannot run the next command which is con - socketConnection(port = port, server=TRUE, blocking=TRUE, open=a+b) can someone please tell me what exactly could be the problem? Thank you, Rishi -- Luke Tierney Chair, Statistics and Actuarial

Re: [R] increasing the # of socket connections

asked that question if the answer had been options(max.connections=100)? I for one would not. Best, luke -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department

[R] [R-pkgs] misc3d_0.4-0 now available on CRAN

to represent 3D structure. The examples in example(contour3d) example(parametric3d) demo(lighting) demo(teapot) illustrate some of the features. Dai Feng and Luke Tierney -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences

Re: [R] How to get the namespace of a function?

at the console. There's an article by Luke Tierney in one of R News 3/1 that explains the search order when namespaces are involved. Duncan Murdoch FS On 2/2/06, Duncan Murdoch [EMAIL PROTECTED] wrote: On 2/2/2006 10:56 AM, Fernando Saldanha wrote: I declared the environment of the function

Re: [R] repeat { readline() }

__ 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 -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences

Re: [R] Broken tkrplot on Mac OS X

, because I don't see any .C/.Call in the tkrplot R code. I have to run now, but I can have a closer look later this week if it's of interest. Cheers, Simon -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa

Re: [R] Chemoinformatic people

://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386

Re: [R] when can we expect Prof Tierney's compiled R?

On Wed, 20 Apr 2005, Peter Dalgaard wrote: Luke Tierney [EMAIL PROTECTED] writes: Vectorized operations in R are also as fast as compiled C (because that is what they are :-)). A compiler such as the one I'm working on will be able to make most difference for non-vectorizable or not very

RE: [R] when can we expect Prof Tierney's compiled R?

-project.org/posting-guide.html -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241

RE: [R] when can we expect Prof Tierney's compiled R?

as C. It requires explicit variable declaration. Jason --- Luke Tierney [EMAIL PROTECTED] wrote: I hope to be making some substantial progress on this over summer. But I would not hold up any projects in anticipation of major R changes--the current recommended strategy of first writing something

Re: [R] static analysis tools for R code?

__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa

Re: [R] workload of R

efforts underway for compiling R and also for parallel computing in R. If you could ask a clearer question we might be able to help and cooperate. luke -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa

Re: [R] tkRplot under macos x

mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial

RE: [R] Do environments make copies?

-guide.html -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http

Re: [R] socket problems (maybe bugs?)

. With the current implementation this ensures that the read completely empties the buffer and so this problem does not bite. It sounds like the same stategy should allow you to work with the current implementation. Best, luke -- Luke Tierney University of Iowa Phone: 319-335-3386

Re: [R] socket problems (maybe bugs?)

On Sat, 19 Feb 2005, Luke Tierney wrote: On Thu, 17 Feb 2005, Christian Lederer wrote: Dear R Gurus, for some purpose i have to use a socket connection, where i have to read and write both text and binary data (each binary data package will be preceeded by a header line). When experimenting, i

Re: [R] Parallel computations using snow: how to combine boot objects?

/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall

Re: [R] Errors while compiling packages with namespace?

/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall

Re: [R] interpreting profiling output

. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http

Re: [R] mkChar can be interrupted

/posting-guide.html -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW

RE: [R] mkChar can be interrupted

On Mon, 14 Jun 2004, Vadim Ogranovich wrote: -Original Message- From: Luke Tierney [mailto:[EMAIL PROTECTED] Sent: Monday, June 14, 2004 1:30 PM To: Vadim Ogranovich Cc: R-Help Subject: Re: [R] mkChar can be interrupted Not sure why you think this suggest mkChar can

RE: [R] mkChar can be interrupted

Thanks, Vadim From: Luke Tierney [mailto:[EMAIL PROTECTED] On Mon, 14 Jun 2004, Vadim Ogranovich wrote: From: Luke Tierney [mailto:[EMAIL PROTECTED] ... Not sure why you think this suggest mkChar can be interrupted. ... by calls to this function. I don't

RE: [R] mkChar can be interrupted

, which will result in a non-local exit. If the allocation succeeds, you are responsable for calling Free. luke -Original Message- From: Luke Tierney [mailto:[EMAIL PROTECTED] Sent: Monday, June 14, 2004 5:43 PM To: Vadim Ogranovich Cc: R-Help Subject: RE: [R] mkChar can

Re: [R] nls and R scoping rules

the environment of the functions in the structure). Since environment sharing is preserved within a serialization, this means the change would only alter the parent of the env environment, not add anything extra. Best, luke -- Luke Tierney University of Iowa Phone

Re: [R] tryCatch() and preventing interrupts in 'finally'

-guide.html -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http

Re: warnings and tryCatch() (Was: RE: [R] catching the warnings)

/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Luke Tierney University of Iowa Phone

Re: [R] looking for a tutorial on exception handling

be nice if there was one online, but references to books would also be appreciated. Thanks, Tamas -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall

Re: [R] socket clusters on snow dies easily

? Any comments or suggestion are welcome :) Regards, Rong-En Fan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Luke Tierney

Re: [R] snow documentation comments

that the master process uses. So there are a total of three processes. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email

Re: [R] Status of Rmpi

I suppose we could switch to rpvm, so I'll probably keep fiddling with it. I'm using LAM 6.5.8-2. Footnote: Does anyone know if the serialize that comes with R 1.8.1 is compatible with the serialize package? Should the latter be unnecessary? -- Luke Tierney University of Iowa

Re: [R] Porting let* from Common LISP to R

-- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http

Re: [R] Implementating streams in R

/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall

RE: [R] performance gap between R 1.7.1 and 1.8.0

__ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall

Re: [R] Persistent state of R

(installed.packages(priority=base)[,Package])) { cat(paste(converting, p, ...)) makeLazyLoading(p) cat(done\n) } The rev() is a quick and dirty way to get stepfun done before modreg, since modreg imports from stepfun. -- Luke Tierney University of Iowa Phone

Re: [R] signalCondition

will transfer control to that handler and the default code is not reached. Hope that helps, luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall

Re: [R] query on proxy settings for R.

/pipermail/r-help/2003-July/035410.html luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242

Re: [R] Help needed: plotting with no device

https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED

Re: [R] R on Linux/Opteron?

and in R Sys.info()[machine] machine x86_64 .Machine$sizeof.pointer [1] 8 So it looks like a functional 64-bit setup so far. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial

Re: [R] R on Linux/Opteron?

: This e-mail message, together with any attachments,...{{dropped}} __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- Luke Tierney University of Iowa Phone: 319-335-3386 Department

RE: [R] R won't connect to the internet on SUSE Linux 8.1

__ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- Luke Tierney University of Iowa Phone

Re: [R] namespaces not available

there is something more complicated going on. Does a traceback() tell you anything? Otherwise, can you send me your .RData file and I will try to track this down. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax

[R] SNOW: Simple Parallel Computing in R

as a technical report at http://www.bepress.com/uwbiostat/paper193. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email

Re: [R] getMethod in a setMethod context

for A calls generics for which the class of the original obj would be more relevant. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall

Re: [R] R (external ?) reference

-- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http

Re: [R] Lexical scoping question

of the evaluation befoe the change, then you have to force the evaluation to occur before the change. You can do force-function(z) z f - function(y) { force(y) g - function(x) x + y g } which will work as you expect. IIRC Luke Tierney has added force

Re: [R] data manipulation function descriptions

justifialy proud as well as ...] luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242

Re: [R] Memory allocation, IBM-AIX and R-1.6.2 - addendum

will be different in detail but the basic issue is the same: 2^32 = 4G only leave you so much room to do the things the OS needs to do. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial

Re: [R] interaction of options(error=) and try()

option is to disable your error handler around the try. luke -- Luke Tierney University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED