Hello,
I'm following this, since it seems I'm having to try to get C code going in
order to estimate dynamic models from biological data.Without saying
that gsl and related packages are proving to be obdurate, and knowing that R
is proving to be an excellent solution to the widest range of statistical
problems, is there a way to estimate dynamic/ode models from biological data
that uses R?
regards,
Alexander(I add that my attempts with James W. Haefner's c programming
course from "Modeling Biological Systems" is the precursor here.)
On Sat, Apr 17, 2010 at 3:56 AM, Prof Brian Ripley <rip...@stats.ox.ac.uk>wrote:
> On Fri, 16 Apr 2010, Charles C. Berry wrote:
>
> On Fri, 16 Apr 2010, J. Sebastian Tello wrote:
>>
>> Dear fellow R users,
>>>
>>> I am now investing time in learning how to use compiled C code to
>>> produces functions that can be used in R. I am just starting, and there is
>>> much that I need to learn, so I have a question that might be straight
>>> forward. I am
>>>
>>
> See the posting guide: this is not the list advised for non-R programming
> questions.
>
>
> learning how to use function in the C library GSL (gnu scientific
>>> library), to write C code, that I then plant to use in R. Is there any
>>> problem in doing this? I mean, using functions of GSL to write C funtions to
>>> then use them in R? I just want to make sure that this approach is correct,
>>> before I invest more time trying to figure out how to include GSL functions
>>> into my C functions. Any commentaries, insights or advice will be highly
>>> appreciated.
>>>
>>
>>
>> per the posting guide ("Do Your Homework" section), you should do this:
>>
>> RSiteSearch("GSL")
>>
>> If you are considering doing something that might be submitted to
>> BioConductor, you should read up on what they require:
>>
>> http://wiki.fhcrc.org/bioc/Package_Guidelines
>>
>> IIRC, they tend to discourage the use of external libraries.
>>
>
> Maybe they do, but at least one package, GLAD, requires gsl in a rather
> non-standard way and several others have really arcane requirements for
> external libraries, some of which will not install on any of my systems.
>
> There are I believe 3 CRAN packages (gsl, BayesPanel, segclust) make use of
> gsl.
>
>
> The R API is rich with functions that provide a lot of what GSL has, so you
>> might want to study that before committing to GSL.
>>
>
> I agree: people who use gsl to do things R already does have caused
> problems in the past.
>
> If you want to distribute your package you should be aware that gsl is not
> written with any concessions to portability. It is a real pain to port to
> Windows (but I have managed with some versions and 32- and 64-bit builds as
> used for CRAN are at http://www.stats.ox.ac.uk/pub/Rtools/).
>
> HTH,
>>
>> Chuck
>>
>>
>>> Sebastian
>>>
>>> J. Sebasti?n Tello
>>>
>>>
>>>
>>> Department of Biological Sciences
>>> 285 Life Sciences Building
>>> Louisiana State University
>>> Baton Rouge, LA, 70803
>>> (225) 578-4284 (office and lab.)
>>>
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>>
>>>
>> Charles C. Berry (858) 534-2098
>> Dept of Family/Preventive
>> Medicine
>> E mailto:cbe...@tajo.ucsd.edu UC San Diego
>> http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
>> 92093-0901
>>
>>
>>
> --
> 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
>
>
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
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>
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