[R] Timer on a function
Bert Gunter
gunter.berton at gene.com
Fri Mar 16 01:18:56 CET 2012
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?
-- Bert
On Thu, Mar 15, 2012 at 4:14 PM, William Dunlap <wdunlap at 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
> }
>
> 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-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On Behalf
>> Of Bert Gunter
>> Sent: Thursday, March 15, 2012 3:05 PM
>> To: Ramiro Barrantes
>> Cc: r-help at r-project.org
>> Subject: Re: [R] Timer on a function
>>
>> On Thu, Mar 15, 2012 at 2:24 PM, Ramiro Barrantes
>> <ramiro at 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 at 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 at 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
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