Cody_Hamilton at Edwards.com
2007-Jun-11 18:52 UTC
[R] R vs. Splus in Pharma/Devices Industry
Following up to some extent on Friday's discussion regarding the 'validation' of R, could I ask the list group's opinion on possible advantages of R over Splus from a pharma/devices perspective? I wish to exclude the obvious price difference, which doesn’t seem to carry as much weight as I would have thought. Besides, I have noticed many former Splus users gravitating towards R, and I suspect that the reasons are not purely economic. I can think of a few advantages of Splus: 1. SeqTrial (of course that means more $) 2. Tech support 3. The warm fuzzies that management seems to get from proprietary software I can also think of a few advantages of R: 1. Based on my personal experiences, simulations requiring a lot of looping seem to run faster. 2. R interfaces with BUGS, for example through BRUGS. 3. The wonderful help list! As always, I am speaking for myself and not necessarily for Edwards Lifesciences. Regards, -Cody Cody Hamilton, PhD Edwards Lifesciences [[alternative HTML version deleted]]
Cody_Hamilton at Edwards.com wrote:> Following up to some extent on Friday's discussion regarding the > 'validation' of R, could I ask the list group's opinion on possible > advantages of R over Splus from a pharma/devices perspective? I wish to > exclude the obvious price difference, which doesn???t seem to carry as much > weight as I would have thought. Besides, I have noticed many former Splus > users gravitating towards R, and I suspect that the reasons are not purely > economic. > > I can think of a few advantages of Splus: > 1. SeqTrial (of course that means more $) > 2. Tech support > 3. The warm fuzzies that management seems to get from proprietary software > > I can also think of a few advantages of R: > 1. Based on my personal experiences, simulations requiring a lot of looping > seem to run faster. > 2. R interfaces with BUGS, for example through BRUGS. > 3. The wonderful help list! > > As always, I am speaking for myself and not necessarily for Edwards > Lifesciences. > > Regards, > -Cody > > Cody Hamilton, PhD > Edwards Lifesciences > [[alternative HTML version deleted]]A big one for us is plotmath (for clinical trial reports we put a lot of greek letters and subscripts on plots), and later we will consider migrating a lot of our stuff to the ggplot package which I don't think is available in S-Plus. Lexical scoping is another advantage of R as is the ability to reference files on the internet. Frank> > > > ------------------------------------------------------------------------ > > ______________________________________________ > R-help at stat.math.ethz.ch 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.-- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University
Cody_Hamilton at Edwards.com
2007-Jun-13 22:07 UTC
[R] R vs. Splus in Pharma/Devices Industry
I should have also noted that Sweave is available for use with R. This is offset, however, by the fact that I will probably never be able to convince anyone to use Latex. This is a pity as I often find myself admiring reports done in Latex as opposed to the ones I have worked on in MS Word. Cody Hamilton, PhD Edwards Lifesciences As always, I am speaking for myself and not necessarily for Edwards Lifesciences. Cody_Hamilton@Edwards.com wrote:> Following up to some extent on Friday's discussion regarding the > 'validation' of R, could I ask the list group's opinion on possible > advantages of R over Splus from a pharma/devices perspective? I wish to > exclude the obvious price difference, which doesn’t seem to carry asmuch> weight as I would have thought. Besides, I have noticed many formerSplus> users gravitating towards R, and I suspect that the reasons are notpurely> economic. > > I can think of a few advantages of Splus: > 1. SeqTrial (of course that means more $) > 2. Tech support > 3. The warm fuzzies that management seems to get from proprietarysoftware> > I can also think of a few advantages of R: > 1. Based on my personal experiences, simulations requiring a lot oflooping> seem to run faster. > 2. R interfaces with BUGS, for example through BRUGS. > 3. The wonderful help list! > > As always, I am speaking for myself and not necessarily for Edwards > Lifesciences. > > Regards, > -Cody > > Cody Hamilton, PhD > Edwards Lifesciences > [[alternative HTML version deleted]][[alternative HTML version deleted]]
Cody_Hamilton at Edwards.com
2007-Jun-14 20:19 UTC
[R] R vs. Splus in Pharma/Devices Industry
Greg, This is very interesting. Perhaps something similar could be worked out here. Do you have to get MS Word users to work only with the template you provide, or can they provide you any old MS Word document? Regards, -Cody Cody Hamilton, PhD Edwards Lifesciences But sweave is expanding. There is a driver for HTML sweaving in the R2HTML package and the odfWeave package allows you to sweave with open office docs (which can be converted to/from MS word). I personally like using LaTeX and the original sweave, but I work with people who want everything in MS word or similar, so for them I will create a template file in open office, odfWeave that, convert to MS word and send that to them. I think the offset is more that S-PLUS 8 is supposed to implement many of the things that R does now (I don't know which, I'm waiting for my copy of 8), so soon it may be possible to sweave in both. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.snow@intermountainmail.org (801) 408-8111> -----Original Message----- > From: r-help-bounces@stat.math.ethz.ch > [mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of > Cody_Hamilton@edwards.com > Sent: Wednesday, June 13, 2007 4:07 PM > To: r-help@stat.math.ethz.ch > Subject: Re: [R] R vs. Splus in Pharma/Devices Industry > > > I should have also noted that Sweave is available for use > with R. This is offset, however, by the fact that I will > probably never be able to convince anyone to use Latex. This > is a pity as I often find myself admiring reports done in > Latex as opposed to the ones I have worked on in MS Word. > > Cody Hamilton, PhD > Edwards Lifesciences > > As always, I am speaking for myself and not necessarily for > Edwards Lifesciences.[[alternative HTML version deleted]]
I am happy to say nice things about odfWeave. Before it was released I was looking at the RTF spec to see if I could write an RTF driver for sweave. But the task was a bit daunting and I doubt that I would have had time for it. So, I was (and still am) exited when odfWeave came out. It is a big time saver for me and I have shown it to several other people as well. I have looked at ooconvert, but unfortunately the current version is limited to *nix, and I am currently in a MS windows world. I tried getting it to run under cygwin at one point, but did not succeed at the time. Once it is available more generally, I will just set up Makefiles so that I can automatically produce either .doc or .pdf documents from my templates and data. Thanks for the great package, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.snow at intermountainmail.org (801) 408-8111> -----Original Message----- > From: Kuhn, Max [mailto:Max.Kuhn at pfizer.com] > Sent: Thursday, June 14, 2007 3:11 PM > To: Greg Snow; Cody_Hamilton at edwards.com; r-help at stat.math.ethz.ch > Subject: RE: [R] R vs. Splus in Pharma/Devices Industry > > Greg, > > Thanks for the kind words about odfWeave. > > > These reports are usually put out as internal webpages for various > > people in the organization to look at, so we could either go the > > odfWeave approach and generate pdf files (not as automated > as I would > > like) > > I agree that automating the conversion should be easier. My > wish would be that the OO binary had a flag to convert from > one format to another. > > On Linux, there is a bash script that uses the open office > binaries to do the conversion at the command line by Nathan Coulter at > > http://sourceforge.net/projects/ooconvert/ > > Also, there is a Java class called jooconvert out there (if memory > serves) that has similar functionality. > > Max > > > > ---------------------------------------------------------------------- > LEGAL NOTICE > Unless expressly stated otherwise, this message is > confidential and may be privileged. It is intended for the > addressee(s) only. Access to this E-mail by anyone else is > unauthorized. If you are not an addressee, any disclosure or > copying of the contents of this E-mail or any action taken > (or not taken) in reliance on it is unauthorized and may be > unlawful. If you are not an addressee, please inform the > sender immediately. >
Greg,> I have looked at ooconvert, but unfortunately the current version is > limited to *nix, and I am currently in a MS windows world. I tried > getting it to run under cygwin at one point, but did not succeed atthe> time. Once it is available more generally, I will just set upMakefiles> so that I can automatically produce either .doc or .pdf documents from > my templates and data.I found the Java tool at http://www.artofsolving.com/opensource/jodconverter (they changed the name). I just tried it on my Windows machine and it worked. You have to start a headless soffice process (see the readme file) and then it is a simple command line away. Max ---------------------------------------------------------------------- LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}
Hi, I just saw this thread. This issue, and the larger scale issue of open source in industry is being addressed. One has to realize that the behemoth that is the clinical aperatus of the pharma industry is very conservative and very slow to change. In many cases switching to R would meean changing a great many processes all based on legacy code. One of the big issues is that the industry demands consistency not necessarily correctness. All that said there are a great many areas where R could be used that would not impact regulatory submission, data security etc. Many in pharma are quietly working on this, but steps are small and incremental. Development takes time in industry because of the amount of documentation necessary. All this impacts the "free" nature of R and cost and risk (From the industries perspective) need to be justified. Probably when the statistical community is using Z big pharma will be ready to use R. %P Nicholas
Cody_Hamilton at Edwards.com
2007-Jun-15 19:21 UTC
[R] R vs. Splus in Pharma/Devices Industry
Nicholas, You're making me depressed! Cody Hamilton, PhD Edwards Lifesciences Hi, I just saw this thread. This issue, and the larger scale issue of open source in industry is being addressed. One has to realize that the behemoth that is the clinical aperatus of the pharma industry is very conservative and very slow to change. In many cases switching to R would meean changing a great many processes all based on legacy code. One of the big issues is that the industry demands consistency not necessarily correctness. All that said there are a great many areas where R could be used that would not impact regulatory submission, data security etc. Many in pharma are quietly working on this, but steps are small and incremental. Development takes time in industry because of the amount of documentation necessary. All this impacts the "free" nature of R and cost and risk (From the industries perspective) need to be justified. Probably when the statistical community is using Z big pharma will be ready to use R. %P Nicholas ______________________________________________ R-help@stat.math.ethz.ch 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. [[alternative HTML version deleted]]
On 6/15/07, Nicholas Lewin-Koh <nikko at hailmail.net> wrote:> Hi, > I just saw this thread. This issue, and the larger scale issue of open > source in industry > is being addressed. One has to realize that the behemoth that is the > clinical aperatus > of the pharma industry is very conservative and very slow to change. In > many cases > switching to R would meean changing a great many processes all based on > legacy code. One > of the big issues is that the industry demands consistency not > necessarily correctness. > > All that said there are a great many areas where R could be used that > would not impact > regulatory submission, data security etc. Many in pharma are quietly > working on this, > but steps are small and incremental. Development takes time in industry > because of the amount of > documentation necessary. All this impacts the "free" nature of R and > cost and risk (From the industries > perspective) need to be justified.> Probably when the statistical community is using Z big pharma will be > ready to use > R. %PI think you mean A, not Z. First there was S, then there was R.