Re: [R] GSL in C code for R
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.ukwrote: 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, UKFax: +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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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.
Re: [R] GSL in C code for R
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 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. 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. 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 __ 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.
Re: [R] GSL in C code for R
Hi Sebastian, 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 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. It may or may not be relevant to your query, but there is a GSL wrapper package available on CRAN which might be instructive or even used directly for your purposes. http://cran.r-project.org/web/packages/gsl/index.html Best, Tobias __ 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.
Re: [R] GSL in C code for R
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, UKFax: +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.
