The project in question had used a negative binomial regression function from the MASS package, but colleague had omitted any reference to it. In this case, a citation would provide both credit to the authors and a useful guide to anyone wanting to replicate our approach. It would also allow readers to consider whether changes in the package might affect the results observed. A call to citation(package="MASS") will provide the preferred citation here. (Any package name can be inserted, or course, though some authors may not have provided a full citation.)
Similarly, while SAS authors are rarely identified by name and presumably get a salary from SAS, it's preferable to identify the version of the software and where it can be obtained. In medical research this is usually done by an in-text reference. For example: "Analyses were performed in SAS 9.3 (SAS Institute, Cary NC)."
For complex analyses, it is also best to mention the SAS procedure used. As with the R package, this can help readers plan similar analyses, and may inform interpretation.
So a multi-software analysis section might end with the following statement: Analyses were performed in R 2.14.2  using the MASS package  glm.nb() function for negative binomial regression and in SAS 9.3 (SAS Institute, Cary NC) using the MCMC procedure for negative binomial mixture models." The references to  and  would be found using the citation() function.
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