Hi Rich,

Theres a book coming out next May by Otto Wildi called "Data Analysis in
Vegetation Ecology" 2nd Edition which includes a lot of R code. While its
aimed at vegetation ecology, a lot of the principles in the book can be
generalised to community analysis in whatever form. It covers ordination,
cluster analysis, some basic GLM and numerous other topics.

It takes the topics in the 1st Ed and adds R code to redo the analyses, and
adds a few other methods not covered in the 1st Ed, the main difference
will be the code though.

Book:
http://eu.wiley.com/WileyCDA/Section/id-302479.html?query=Otto+Wildi

1st Ed website:
http://www.wsl.ch/info/mitarbeitende/wildi/data_analysis_book/index_EN

HTH

Alan


--------------------------------------------------
Email: aghaynes@gmail.com
Mobile: +41794385586
Skype: aghaynes



On 6 December 2012 04:59, alfredo tello <alfredotello@gmail.com> wrote:

> Hi Rich,
>
> Check out the R package Vegan tutorial by Jari Oksanen:
> http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf. Vegan has
> several
> functions which I believe should allow you to address some of your
> questions. I have not worked with functional groups, but I'm guessing you
> could treat them as you would treat taxa for statistical purposes (?). I
> think Vegan's function 'adonis' might be of interest to you. It allows you
> to partition variation in a data/distance matrix according to specified
> factors (e.g., water chemistry).
>
> Hopet this helps!
>
> Best,
>
> A
>
>
> On Wed, Dec 5, 2012 at 10:26 PM, Rich Shepard <rshepard@appl-ecosys.com
> >wrote:
>
> >   I left academia and basic ecological research decades ago and now work
> > with environmental data collected by companies in compliance with
> > regulatory
> > permit requirements. I've bought and read (mostly) all the books I could
> > find on ecological analyses using R (all but one of Alain Zuur's books,
> > Legendre & Legendre's 2nd English edition, Mike McCarthy's Bayesian
> methods
> > book, and Ben Bolker's book) but cannot find any references to
> > 'communities'
> > in the indices. I'd greatly appreciate pointers to sources appropriate
> for
> > environmental data (which is much sloppier than ecological research
> data).
> >
> >   The last time I addressed community analyses was my post-doc research
> > which I published in Freshwater Biology in 1984. Only within the past
> year
> > have my clients needed to address issues using benthic macroinvertebrate
> > assemblages (and fish) in streams. And, since I work by myself, I've no
> one
> > with whom to share ideas and discuss approaches; perhaps there's a better
> > forum than this mail list for this.
> >
> >   The available benthic data has little taxonomic consistency below the
> > family level. I want to use functional feeding groups rather than taxa as
> > the basis of comparison because those better reflect conditions in each
> > stream (collections of biota are made only once per year), and I want to
> > examine correlations and cause-and-effect relations between biotic
> > assemblages and water chemistry. There are only a few fish collections,
> > tool, in the available data.
> >
> >   All ideas are certainly welcome!
> >
> > TIA,
> >
> > Rich
> >
> > --
> > Richard B. Shepard, Ph.D.          |   Integrity - Credibility -
> Innovation
> > Applied Ecosystem Services, Inc.   |
> > <http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax:
> > 503-667-8863
> >
> > ______________________________**_________________
> > R-sig-ecology mailing list
> > R-sig-ecology@r-project.org
> > https://stat.ethz.ch/mailman/**listinfo/r-sig-ecology<
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology>
> >
>
>
>
> --
> Alfredo Tello (http://alfredotello.com)
> Sustainable Aquaculture Group
> Institute of Aquaculture
> University of Stirling
> Scotland, UK.
>
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>
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