Roy,
Did the referee say *which* species to remove?
The selection of a species to be removed will influence the results, so it is
crucial to pick the "correct" species. Conclusion: the referee got it wrong.
There is a special theory of PCA of proportional data, but only removing one
species d
If by CA you mean Correspondence Analysis then see the Environmetrics
Task View which list several potential options with an ecological bent:
http://cran.r-project.org/web/views/Environmetrics.html
You might also consider the Multivariate Task View for a wider
selection:
http://cran.r-project.or
