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
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.