Hi, Not an expert R user, something of a novice - please be gentle with me! I have a particular interest in generalised linear models (GLMs) and I'm experienced in fitting them using other bits of software. R can fit GLMs of course, using the glm() command. I have some large multivariate data sets I'd like to fit GLMs to, ideally using R. Two concerns though: Firstly, I'm told that R isn't especially fast at fitting GLMs, especially if the data files are too large to fit into RAM. Can anyone advise if there are alternatives to glm() around which might cope better. For example, I've heard that RevolutionR is available, and claims to fit GLMs faster in these cases. Might it be possible, alternatively, to write some very quick code using C (for example) and to get R to invoke this instead? Has anyone tried to do this? Secondly, I might like to create some kind of GUI so that I can have a nice interface for viewing data, specifying models, showing graphical model outputs, etc. Is there a preferred way to do this? The only GUI builder I know of is Shiny - http://www.rstudio.com/shiny/ - is this a good way to go? What alternatives might I consider? My IT/coding skills are limited. I'm hoping at some point to find an R expert to collaborate with, but in the mean time, a few pointers would be appreciated. Thanks! [[alternative HTML version deleted]]
Alan, I can't answer your first question, but as far as the second question goes, have you examined RStudio? http://www.rstudio.com/ Rstudio is a free, nice, IDE (I think this stands for integrated development environment that facilitates working in R. I provides very very basic sytax help (i.e. makes sure parenthesis are balanced), but more importantly allows for viewing plots generated by code more easily. John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) >>> Alan Sausse <alansausse at gmail.com> 8/11/2013 7:47 AM >>> Hi, Not an expert R user, something of a novice - please be gentle with me! I have a particular interest in generalised linear models (GLMs) and I'm experienced in fitting them using other bits of software. R can fit GLMs of course, using the glm() command. I have some large multivariate data sets I'd like to fit GLMs to, ideally using R. Two concerns though: Firstly, I'm told that R isn't especially fast at fitting GLMs, especially if the data files are too large to fit into RAM. Can anyone advise if there are alternatives to glm() around which might cope better. For example, I've heard that RevolutionR is available, and claims to fit GLMs faster in these cases. Might it be possible, alternatively, to write some very quick code using C (for example) and to get R to invoke this instead? Has anyone tried to do this? Secondly, I might like to create some kind of GUI so that I can have a nice interface for viewing data, specifying models, showing graphical model outputs, etc. Is there a preferred way to do this? The only GUI builder I know of is Shiny - http://www.rstudio.com/shiny/ - is this a good way to go? What alternatives might I consider? My IT/coding skills are limited. I'm hoping at some point to find an R expert to collaborate with, but in the mean time, a few pointers would be appreciated. Thanks! [[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. Confidentiality Statement: This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message.
1. For RevolutionR capabilities, contact them (mailing lists, website, etc.) 2. CRAN has a whole section on GUI's. You should consult it: http://www.sciviews.org/_rgui/ 3. Your GUI query would be more appropriate on the R-sig-gui list. Cheers, Bert On Sun, Aug 11, 2013 at 4:47 AM, Alan Sausse <alansausse at gmail.com> wrote:> Hi, > > Not an expert R user, something of a novice - please be gentle with me! > > I have a particular interest in generalised linear models (GLMs) and I'm > experienced in fitting them using other bits of software. > > R can fit GLMs of course, using the glm() command. I have some large > multivariate data sets I'd like to fit GLMs to, ideally using R. Two > concerns though: > > Firstly, I'm told that R isn't especially fast at fitting GLMs, especially > if the data files are too large to fit into RAM. Can anyone advise if > there are alternatives to glm() around which might cope better. For > example, I've heard that RevolutionR is available, and claims to fit GLMs > faster in these cases. Might it be possible, alternatively, to write some > very quick code using C (for example) and to get R to invoke this instead? > Has anyone tried to do this? > > Secondly, I might like to create some kind of GUI so that I can have a nice > interface for viewing data, specifying models, showing graphical model > outputs, etc. Is there a preferred way to do this? The only GUI builder I > know of is Shiny - http://www.rstudio.com/shiny/ - is this a good way to > go? What alternatives might I consider? > > My IT/coding skills are limited. I'm hoping at some point to find an R > expert to collaborate with, but in the mean time, a few pointers would be > appreciated. > > Thanks! > > [[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
Steve Lianoglou
2013-Aug-11 20:48 UTC
[R] Advice on use of R for Generalised Linear Modelling
Hi, On Sun, Aug 11, 2013 at 4:47 AM, Alan Sausse <alansausse at gmail.com> wrote:> Hi, > > Not an expert R user, something of a novice - please be gentle with me! > > I have a particular interest in generalised linear models (GLMs) and I'm > experienced in fitting them using other bits of software. > > R can fit GLMs of course, using the glm() command. I have some large > multivariate data sets I'd like to fit GLMs to, ideally using R. Two > concerns though: > > Firstly, I'm told that R isn't especially fast at fitting GLMs, especially > if the data files are too large to fit into RAM. Can anyone advise if > there are alternatives to glm() around which might cope better. For > example, I've heard that RevolutionR is available, and claims to fit GLMs > faster in these cases. Might it be possible, alternatively, to write some > very quick code using C (for example) and to get R to invoke this instead? > Has anyone tried to do this?Likely not -- you'll need to have RevolutionR around for that, and if you've have RevoR, then just use RevoR -- not sure what the point would be call RevoR-specific functionality from R. Perhaps the biglm package can help you from R, though, as it provides a bigglm function that can do GLMs with out-of-memory data -- no idea how well/fast it works, though. You should also consider that your data may not require that, though -- glmnet, for instance, works incredibly fast on large data. If your data can actually be loaded (perhaps via a sparse matrix), then you can try that. HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech
Yvonnick Noel
2013-Aug-12 16:15 UTC
[R] Advice on use of R for Generalised Linear Modelling
Alan, You might want to have a look to the R2STATS package on CRAN. It is a GUI for GLM and GLMM written in GTK (with the use of the nice RGtk2 and gWidgets packages by Michael Lawrence and John Verzani). Don't expect any gain in performance on large datasets though. But at least the use of GLM is quite intuitive. HTH, Yvonnick Noel Psychology and Statistics University of Britanny, Rennes France