[R] R and FDA trials

[Marc Schwartz]

On Sun, 2007-10-07 at 21:25 -0500, Frank E Harrell Jr wrote:
> Ricardo Pietrobon wrote:
> > Yesterday I just noticed the new document on R and regulatory aspects
> > for biomedical research posted at
> > http://www.r-project.org/doc/R-FDA.pdf
> > 
> > Coming from an institution that performs a large number of clinical
> > trials for FDA and being an advocate of R myself, I have found that
> > the following issues usually come up when discussing the use of R for
> > FDA trials:
> > 
> > 1. Most FDA submissions come down to a series of r x k tables, and it
> > is hard to claim that one system is better than another for that.
> > 
> > 2. Data is to be submitted to the FDA in SAS (considered by many as
> > the industry standard) or CDISC XML formats (http://www.cdisc.org/);
> > there are pretty good SAS tools for that;  does R have comparable?
> > 
> > 3. Some packages in R provide acknowledgedly better functionality than
> > their SAS-equivalent, but an entire FDA validation would have to occur
> > each time an enhancement is made to the R package because often an
> > enhancement breaks something else or the syntax would change from one
> > release to another.
> 
> Your item 3. is up to the company's policy.  FDA does not require it and 
> the word "validation" is not well defined in this context.  No package 
> does a complete validation any time any piece of the package is enhanced.
> 
> Frank

Just to augment Frank's response:

With respect to point number 2, I believe the only R based package that
offers the ability to write SAS XPORT format files at this point is the
SASxport CRAN package by Greg Warnes et al. There are several, including
Frank's Hmisc package and the standard foreign package that will read
XPORT files.

Keep in mind that it is the SAS XPORT files, not the proprietary SAS
files, that the FDA wants, since the XPORT format is openly documented.

There are other third party packages, such as DBMS/Copy and
Stat/Transfer, that will also write XPORT format files.

At some point, CDISC based exports will likely need to be looked at by
one or more folks motivated to do so. In the mean time, you would need
to consider third party tools for that. My recollection of Mat Soukup's
comments from our panel at useR back in August, is that the FDA itself
is not yet at the point where CDISC based file exchanges are without
issue.

Finally, bear in mind that the document to which you refer covers
specifically listed packages released via the R Foundation. See Section
2 of the document. Other CRAN/non-CRAN R packages are not covered. In
either case, you would need to engage in appropriate risk mitigation
processes when using those and as Frank notes, these would be internal
procedures and policies as deemed appropriate within the GxP framework.

HTH,

Marc Schwartz