[R] SAS or R software

Austin, Matt maustin at amgen.com
Sat Dec 18 01:49:27 CET 2004

One point that is missing in this discussion is ease of review by the
statistician at the FDA.  As a statistician in clinical trials, you want to
make it as easy as possible for your colleague at the FDA to do their job,
so you put the programs in a format that they are more likely to find
useful.  As more reviewing statisticians are familiar with SAS than with
other statistical packages/languages, I feel more comfortable sending a
submission in SAS. 

Reviewers do use the programs in a filing that were written for creation of
data sets and analysis to check for correct variable definitions and
appropriate analyses.  If the programs are written in a package/language
that the reviewer understands they can get their job done easier.

Given this, I have used S-Plus in regulatory work where it was clearly
stronger--at some point I hope to use R where it adds a clear benefit.  Of
course 95% of the statistical analyses that are performed for regulatory
submission can probably be done just as well with any of the major
statistical package/languages available.



Matt Austin

One Amgen Center Drive
M/S 24-2-C
Thousand Oaks CA 93021
(805) 447 - 7431

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch
> [mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of Marc Schwartz
> Sent: Friday, December 17, 2004 16:19 PM
> To: Alexander C Cambon
> Cc: R-Help; Douglas Bates
> Subject: Re: [R] SAS or R software
> On Fri, 2004-12-17 at 17:11 -0500, Alexander C Cambon wrote: 
> > I apologize for adding this so late to the "SAS or R software "
> > thread.
> > This is a question, not a reply, but it seems to me to fit in well
> > with
> > the subject of this thread.
> > 
> > I would like to know anyone's experiences in the following two areas
> > below.  I should add I have no experience myself in these areas:
> > 
> > 1) Migrating from SAS to R in the choice of statistical 
> software used
> > for FDA  reporting.
> You will find that to be a non-issue from the FDA's perspective. This
> has been discussed here with some frequency.  If you search 
> the archives
> you will find comments from Frank Harrell and others.
> The FDA does not and cannot endorse a particular software product. Nor
> does it validate any statistical software for a specific purpose. They
> do need to be able to reproduce the results, which means they need to
> know what software product was used, which version and on 
> what platform,
> etc.
> The SAS XPORT Transport Format (which is openly defined and 
> documented),
> has been used for the transfer of data sets and has been available in
> many statistical products.
> There have been a variety of activities (CDISC, HL-7, etc) 
> regarding the
> electronic submission of data to the FDA. Some additional 
> information is
> here:
> http://www.fda.gov/cder/regulatory/ersr/default.htm
> and here:
> http://www.cdisc.org/news/index.html
> Any other issues impacting the selection of a particular statistical
> application are more likely to be political within your working
> environment and FUD. 
> As you are likely aware, other statistically relevant issues are
> contained in various ICH guidance documents regarding GCP 
> considerations
> and principles for clinical trials:
> http://www.ich.org/UrlGrpServer.jser?@_ID=475&@_TEMPLATE=272
> Keep in mind also that one big advantage R has (in my mind) is the use
> of Sweave for the reproducible generation of reports, which 
> to an extent
> are self-documenting. 
> >  (For example, was there more effort involved in areas of
> > documentation, revision tracking,  or validation of software codes?
> Since the FDA's role with computer software and validation has been
> raised before, the following documents cover many of these areas. The
> list is not meant to be exhaustive, but should give a flavor in this
> domain.
> There are specific guidance documents by the FDA pertaining 
> to software
> that is contained in a medical device (ie. the firmware in a pacemaker
> or medical monitoring equipment) or is used to develop a 
> medical device.
> The current guidance in this case is here:
> http://www.fda.gov/cdrh/comp/guidance/938.html
> Other guidance pertains to 21 CFR 11, which addresses data management
> systems used for clinical trials and covers issues such as electronic
> signatures, audit trails and the like. A guidance document for that is
> here:
> http://www.fda.gov/cder/guidance/5667fnl.htm
> Keep in mind, from a perspective standpoint, that even MS Excel and
> Access can be made to be 21 CFR 11 compliant and there are companies
> whose business is focused on just that task.
> There is also a general guidance document for computer systems used in
> clinical trials here:
> http://www.fda.gov/ora/compliance_ref/bimo/ffinalcct.htm
> Though it is to be superseded by a draft document here:
> http://www.fda.gov/cder/guidance/6032dft.htm 
> > 2) Migrating from SAS to R in the choice of statistical 
> software used
> > for NIH reporting  (or other US or non-US) government agencies) .
> Same here to my knowledge.
> As I was typing this, I see Frank just responded.
> I also just noted Doug's post, so perhaps some of the above 
> information
> will be helpful in clarifying some of his questions as well.
> I believe that the above is factually correct, but if someone knows
> anything to not be so, please correct me.
> HTH,
> Marc Schwartz
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