[R-sig-eco] Applied Environmental Data Analyses: Water Chemistry and Biota

[Ian R Waite]

Rich,

I would suggest checking out the following book -- I find it very useful
and well written, using good case studies and all with R.

 Environmental and Ecological Statistics with R (Chapman & Hall/CRC Applied
 Environmental Statistics) [Paperback]
 Song S. Qian (Author)
 › Visit Amazon's Song S. Qian Page


Not to start  a debate, but I would suggest considering using
macroinvertebrate metrics such as EPT Richness or Ave. Tolerant Richness or
NonInsect Richness, etc. as your response measures instead of functional
feeding groups but this requires the user to come to a common taxonomic
resolution level -- for each major group make sure all samples have data
aligned at the same level if the taxa occur in those samples. Example, all
Ephemeroptera are ID'd to Genus or Family level for all samples, higher
level specimens are either removed or proportioned into their children.
(See Cuffney's paper on this subject -- attached below).

With the data resolved for taxonomic issues, you can then also use specie
matrix methods of similarity indices such as Bray-Curtis and others that
then allow you to try a variety of multivariate methods -- cluster
analysis, ordinations, ANOSIM, etc.

Just my two cents, HTH

Ian


(See attached file: Cuffney-2007_Ambiguous Taxa_JNABS.pdf)


~^^~~^^^~~~^^~~~^^^^~~~^~~^~~^~~^^~~~^^^~~~^^^^~~^~~^~~^~~~~~^^^^~
Ian R. Waite, Ph.D.
Aquatic Ecologist
USGS - OWSC
2130 SW 5th Avenue
Portland, OR 97201
email: iwaite at usgs.gov

                   "Sometimes your joy is the source of your smile, but
                         sometimes your smile can be the source of your
joy."
Thich Nhat Hanh
"We may search the world over for joy but
  unless we carry it within us, we will not find it."
                                                Ralph Waldo Emerson
~^^^~~~^^^~~~~^^^~~^^^~~~~^^~~~^~^^^~~~^^^^~~~~~~^^^^^~~~~^^^^~~~~~~


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  |Rich Shepard <rshepard at appl-ecosys.com>                                                                                                           |
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  |r-sig-ecology at r-project.org                                                                                                                       |
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  |12/06/2012 06:12 AM                                                                                                                               |
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  |Re: [R-sig-eco] Applied Environmental Data Analyses: Water Chemistry and Biota                                                                    |
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  |r-sig-ecology-bounces at r-project.org                                                                                                               |
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On Thu, 6 Dec 2012, alfredo tello wrote:

> 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.

Alfredo,

   I will certainly do this.

> I have not worked with functional groups, but I'm guessing you could
treat
> them as you would treat taxa for statistical purposes(?)

   For benthic macroinvertebrates I'll strongly argue that functional
feeding
groups are better than the mixed taxonomic levels that are usually given
equal weights. So yes, statistical models should work equally well,
particularly if the methods will work with percentages (proportions) which
normalize for different numbers of individuals in the different streams.

> 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!

   I'm sure it will.

Thanks very much,

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

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