I hope that Marc doesn't mind, but I felt that part of his recent post was important enough to deserve it's own subject line rather then being lost in a 60-msg-long thread... On Sun, Jan 11, 2009 at 10:08 AM, Marc Schwartz <marc_schwartz at comcast.net> wrote: ... I strongly believe that the comments regarding R and the FDA are overly negative and pessimistic. The hurdles to the use of R for clinical trials are shrinking. There has been substantive activity over the past several years, both internally at the FDA and within the R community to increase R's acceptance in this domain. At the Joint Statistical Meetings in 2006, Sue Bell from the FDA spoke during a session with a presentation entitled Times 'R' A Changing: FDA Perspectives on Use of "Open Source". A copy of this presentation is available here: http://www.fda.gov/cder/Offices/Biostatistics/Bell.pdf In 2007, during an FDA committee meeting reviewing the safety profile of Avandia (Rosiglitazone), the internal FDA meta-analysis performed by Joy Mele, the FDA statistician, was done using R. A copy of this presentation is available here: http://www.fda.gov/ohrms/dockets/ac/07/slides/2007-4308s1-05-fda-mele.ppt Given the high profile nature of drug safety issues today, that R was used for this analysis by the FDA itself speaks volumes. Also in 2007, at the annual R user meeting at Iowa State University, I had the pleasure and privilege of Chairing a session on the use of R for clinical trials. The speakers included Frank Harrell (well known to R users here), Tony Rossini and David James (Novartis Pharmaceuticals) and Mat Soukup (FDA statistician). Copies of our presentations are available here, a little more than half way down the page: http://user2007.org/program/ At that meeting, we also introduced a document that has been updated since then and approved formally by the R Foundation for Statistical Computing. The document provides guidance for the use of R in the regulated clinical trials domain, addresses R's compliance with the relevant regulations (eg. 21 CFR 11) as well as describing the development, testing and quality processes in place for R, also known as the Software Development Life Cycle. That document is available here: http://www.r-project.org/doc/R-FDA.pdf I have heard directly from colleagues in industry that this document has provided significant value in their internal discussions regarding implementing the use of R within their respective environments and assuaging many fears regarding R's use. Additionally, presentations regarding the use of open source software and R specifically for clinical trials have been made at DIA and other industry meetings. This fall, there is a session on the use of R scheduled for the FDA's Industry Statistics Workshop in Washington, D.C. For those unfamiliar, I would also point out the membership and financial donors to the R Foundation for Statistical Computing and take note of the plethora of large pharma companies and clinical research institutions: http://www.r-project.org/foundation/memberlist.html The use of R within this domain is increasing and will only continue to progress as R's value becomes increasingly clear to even risk averse industry decision makers. Regards, Marc Schwartz
I don't mind at all. Very kind of you Kingsford. Thanks, Marc on 01/11/2009 01:05 PM Kingsford Jones wrote:> I hope that Marc doesn't mind, but I felt that part of his recent post > was important enough to deserve it's own subject line rather then > being lost in a 60-msg-long thread... > > > > On Sun, Jan 11, 2009 at 10:08 AM, Marc Schwartz > <marc_schwartz at comcast.net> wrote: > > ... > > I strongly believe that the comments regarding R and the FDA are overly > negative and pessimistic. > > The hurdles to the use of R for clinical trials are shrinking. There has > been substantive activity over the past several years, both internally > at the FDA and within the R community to increase R's acceptance in this > domain. > > At the Joint Statistical Meetings in 2006, Sue Bell from the FDA spoke > during a session with a presentation entitled Times 'R' A Changing: FDA > Perspectives on Use of "Open Source". A copy of this presentation is > available here: > > http://www.fda.gov/cder/Offices/Biostatistics/Bell.pdf > > In 2007, during an FDA committee meeting reviewing the safety profile of > Avandia (Rosiglitazone), the internal FDA meta-analysis performed by Joy > Mele, the FDA statistician, was done using R. A copy of this > presentation is available here: > http://www.fda.gov/ohrms/dockets/ac/07/slides/2007-4308s1-05-fda-mele.ppt > > Given the high profile nature of drug safety issues today, that R was > used for this analysis by the FDA itself speaks volumes. > > Also in 2007, at the annual R user meeting at Iowa State University, I > had the pleasure and privilege of Chairing a session on the use of R for > clinical trials. The speakers included Frank Harrell (well known to R > users here), Tony Rossini and David James (Novartis Pharmaceuticals) and > Mat Soukup (FDA statistician). Copies of our presentations are available > here, a little more than half way down the page: > > http://user2007.org/program/ > > At that meeting, we also introduced a document that has been updated > since then and approved formally by the R Foundation for Statistical > Computing. The document provides guidance for the use of R in the > regulated clinical trials domain, addresses R's compliance with the > relevant regulations (eg. 21 CFR 11) as well as describing the > development, testing and quality processes in place for R, also known as > the Software Development Life Cycle. > > That document is available here: > > http://www.r-project.org/doc/R-FDA.pdf > > I have heard directly from colleagues in industry that this document has > provided significant value in their internal discussions regarding > implementing the use of R within their respective environments and > assuaging many fears regarding R's use. > > Additionally, presentations regarding the use of open source software > and R specifically for clinical trials have been made at DIA and other > industry meetings. This fall, there is a session on the use of R > scheduled for the FDA's Industry Statistics Workshop in Washington, D.C. > > For those unfamiliar, I would also point out the membership and > financial donors to the R Foundation for Statistical Computing and take > note of the plethora of large pharma companies and clinical research > institutions: > > http://www.r-project.org/foundation/memberlist.html > > The use of R within this domain is increasing and will only continue to > progress as R's value becomes increasingly clear to even risk averse > industry decision makers. > > > Regards, > > Marc Schwartz >
On Sun, Jan 11, 2009 at 11:05 AM, Kingsford Jones <kingsfordjones at gmail.com> wrote:> I hope that Marc doesn't mind, but I felt that part of his recent post > was important enough to deserve it's own subject line rather then > being lost in a 60-msg-long thread...I also wanted to thank Marc for this wealth of information on using R in clinical trials. I particularly want to recommend the "R: Regulatory Compliance and Validation Issues" document at http://www.r-project.org/certification.html . Even if you're not looking to validate R for 21CFR11 compliance, this document is an excellent description of R's world-class software development process. With this, and the documented use of R by the FDA itself and within pharma companies for clinical trials, I hope we can settle the "Is R Validated?" question at long last. Thanks go to the authors (Marc Schwartz, Frank Harrell, Tony Rossini and Ian Francis) and the R Foundation generally for putting this together. By the way, if (or a skeptical colleague) needs a more detailed answer to the "Is R Validated?" question, I expand upon the information Marc provided here: http://blog.revolution-computing.com/2009/01/analyzing-clinical-trial-data-with-r.html # David Smith -- David M Smith <david at revolution-computing.com> Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (Seattle, USA)