I overlooked blogging about this at the time, but Jari released a minor update to our Vegan package to fix a few issues following release of R 2.13-0. As far as the user is concerned, this mainly affects capscale(). metaMDSrotate(), a helper function for rotating nMDS solutions from function metaMDS() can now handle missing values via argument na.rm = TRUE. The relevant section of the NEWS file is reproduced below.

                   CHANGES IN VEGAN 1.17-10

- This is minor revision that mainly fixes vegan with respect to
changes in the currently released R 2.13.0. Most importantly,
cmdscale() output changed in R 2.13.0 and because of this
capscale() could fail in some rare situations with argument 'add
= TRUE'. This vegan bug made BiodiversityR package fail its
tests in R 2.13.0.

- metaMDSrotate: gained argument na.rm = TRUE.

R

R
vegan