On Thu, 15 Mar 2012, Bert Gunter wrote:
Bill et. al:
1. This is new to me. Thanks.
2. As I read the man page, this is not guaranteed to work if the model
fitting function does not contain sufficient interrupts. Is that
correct?
Yes. If someone wrote a model fitting package in Fortran with no
callbacks then it is not interruptible, including not by timers. In
that case all you can do is to kill the R session.
The author of setTimeLimit()
-- Bert
On Thu, Mar 15, 2012 at 4:14 PM, William Dunlap <wdun...@tibco.com> wrote:
There is a setTimeLimit function in base. It could be encapsulated into
the following to limit the time spent on an expression:
timeOut <- function (expr, ...) {
on.exit(setTimeLimit())
setTimeLimit(...)
expr
}
Using setTimeLimit(transient = TRUE) is slightly simpler here.
E.g., with the following slow way to compute Euler's phi
f <- function(n) sum(sapply(seq_len(n), function(i)1/i)) - log(n)
I get
> timeOut(f(1e5), elapsed=1)
[1] 0.5772207
> timeOut(f(1e6), elapsed=1)
Error in FUN(1:1000000[[711624L]], ...) : reached elapsed time limit
Use try() or tryCatch() to check for the error. E.g.,
> sapply(1:7, function(n)tryCatch(timeOut(f(10^n), elapsed=1),
error=function(e)-1))
[1] 0.6263832 0.5822073 0.5777156 0.5772657 0.5772207 -1.0000000
-1.0000000
You could look at 'e' in the error handler to see if it is a time out problem.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-----Original Message-----
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf
Of Bert Gunter
Sent: Thursday, March 15, 2012 3:05 PM
To: Ramiro Barrantes
Cc: r-help@r-project.org
Subject: Re: [R] Timer on a function
On Thu, Mar 15, 2012 at 2:24 PM, Ramiro Barrantes
<ram...@precisionbioassay.com> wrote:
Hello,
I have a program that consists of a loop fitting a function over many
models. Sometimes the fitting on a particular model takes minutes to converge.
Is there
a way that I can limit the amount of time that R spends on a given model:
AFAIK, no -- this is an OS level issue.
Of course, most iterative fitting procedures have controls for the
number of iterations, convergence criteria, etc. , but there is no
awareness of timing except when the OS is interrogated, e.g. by
?proc.time or ?system.time . Such calls would have to be built into
the fitting function or OS level services would have to be invoked to
run the R process with timing limitations built in. See e.g. ?Rscript
for one possible approach.
Corrections or clever tricks to get around these perceived limitations
welcomed, of course.
-- Bert
Cheers,
Bert
say if my line is:
fittingFunction( func, model.1)
can I have some function:
stopIfUnderTime( fittingFunction( func, model.1) , 5 )
where stopIfUnderTime will return the result if it finishes under 5 seconds, or
NA
otherwise.
Is there anything like this? (just looked through the web but did not find
anything)
Thanks,
Ramiro
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-
biostatistics/pdb-ncb-home.htm
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
