RE: [Rd] Problem with read.xport() from foreigh package (PR#7389)

From: Werner Engl <englw_at_gmx.net>
Date: Fri 10 Dec 2004 - 00:33:07 EST


Dear R-devel list,

This is to confirm Prof. Ripley's analysis of the read.xport issue.

The section on missing data in TS140 is pertinent to numeric variables only. In SAS, character variables are of fixed length (between 1 and 200 for the xport format). Shorter strings are padded with trailing blanks when assigned to a variable.

An uninitialized character variable is stored as all blanks in the xport format file. This is the only representation of 'missing' data for SAS character variables. 'Special missing' codes (.A to .Z and ._) are available for numeric variables only.

Please find enclosed a patch to the
R-2.0.1/src/library/Recommended/foreign/SASxport.c file and a xport file that I used for testing. The xport file was created by SAS V8.2 on Linux, but should be plattform and version independent (except for the header information). I have simply commented out the code lines that try to detect missing character values.

The code in SASxport.c already does a good job in removing trailing blanks from character values. For missing character data (all blanks) the result is the empty string (""), which is fine for me. There is no equivalent to the R missing character representation in SAS (as far as I know).

The enclosed gzipped tar file contains:

diff_SASxport_c.txt	diff for SASxport.c
xptchar1.xpt	test file in xport format
xptchar.sas	trivial SAS program used to 
	generate xptchar1.xpt
xptchar_SAS_System_Viewer9_1.csv	xptchar1.xpt 
	converted to comma separated file using SAS 
	System Viewer 9.1 (on Win XP)

With the patch applied, read.xport produces the same data frame from xptchar1.xpt as read.csv does from xptchar_SAS_System_Viewer9_1.csv (tested on i386 Linux with R Version 2.0.1) except that read.csv converts empty strings to NAs. As explained above, the empty string is closer to the meaning of an all-blanks value in SAS.

There is renewed interest in this old data format in the pharmaceutical industry, because the US Food and Drug Administration requests clinical and pre-clinical data to be submitted in this format. I spent some time analyzing the xport file format to be sure of what is actually submitted to FDA with these files.

Thank you for considering this patch (and for the great R system, of course)!

Best regards,

Werner Engl


Werner Engl, PhD, CStat            
Senior Manager, Biostatistics                             
Baxter AG, Vienna, Austria
e-mail: werner_engl@baxter.com
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Received on Fri Dec 10 00:39:49 2004

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