The mefa 2.0 is available on CRAN. I have completely revised the code to speed up data processing. In addition, many new methods are available for manipulating the community data matrix and related data tables for samples and taxa as well. A new vignette will be available soon.

Some further paragraphs on the project are available in my R-Forge dairy:
http://r-forge.r-project.org/developer/diary.php?diary_user=459