While vegan and other packages offer many powerful tools for analyzing
species composition data, there's a fair bit available that is more
directly aimed at using aquatic biotic data for water quality monitoring
and assessment.  I suggest spending some time with r-seek (www.rseek.org)
to find out what's available, as quite a few water quality & monitoring
folks use R, and many of the US Government folks make their code available
as downloads or sometimes packages.

EPA has quite a bit of relevant R code available: spsurvey for GRTS sample
draws & analyses is on CRAN, but they also have code for RIVPACS and other
approaches available on their websites:
http://www.epa.gov/wed/pages/models/rivpacs/rivpacs.htm
(it appears that the port-to-a-new-content-system bug bit EPA, so you may
have to search their site for the download).

You might find what you need in package bio.infer: it has functions for
cleaning taxonomic names, pooling within-site duplicates, mapping taxa to
feeding groups based on Vieira et al., and calibrating and computing some
indices.

Package analogue does weighted averaging and similarity and other
approaches for inferring environmental conditions from taxonomic
composition (e.g., paleohydrology from diatoms).

There's also a package for Functional Diversity:
https://r-forge.r-project.org/projects/fdiversity/

I am not expressing my opinion on the appropriateness of any of these
approaches to monitoring of biotic responses to water quality and habitat
conditions.

Tom 2



-------------------------------------------
Tom Philippi, Ph.D.
Quantitative Ecologist & Data Therapist
Inventory and Monitoring Program
National Park Service
(619) 523-4576
Tom_Philippi@nps.gov
http://science.nature.nps.gov/im/monitor
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