[R] SAS or R software

[Marc Schwartz]

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