Hi Travis, I concur with using PRIMER ver 6 and the two manuals that come
with it for the proposed analysis. Further to this, I highly recommend using
PERMANOVA+, an add-on to Primer ver 6, and its manual. It accommodates very
complex designs and any number of factors and should be well suited for your
purpose.
Dr. Isabelle Wolf
*********************************************************************
Research and Analysis Officer
Parks and Wildlife Group
Department of Environment, Climate Change and Water (NSW)
Level 2, Hurstville, NSW 2220
[email protected]
Ph: 02 9585 6672
Fax: 02 9585 6601
----- Original Message -----
From: "Liz Pryde" <[email protected]>
To: <[email protected]>
Sent: Wednesday, March 30, 2011 8:01 PM
Subject: Re: [ECOLOG-L] Community Analysis Hypothesis Tests
Hi Travis,
As it is a community comparison I think ANOSIM is still widely accepted to
test for differences between treatments/time, particularly in the marine
literature. Manuel is correct, it will not tell you the biological reason
behind a difference and cannot really give a magnitude of difference per se
(depending on the design of the study) but it does give a meaningful p value
based on permutations of configurations of the presence-absence matrix. In
this way its limitations are analogous with ANOVAs. As this is a comparative
study I would think that a statistically significant p value would be
meaningful.
However, teasing out the question "why the difference" requires closer
examination and comparisons between the community matrices and say,
environmental variables. Examples of these types of further analyses can be
found in the PRIMER manuals (ver 6) and in the extensive literature that can
be found on the PRIMER-E website.
Hope that helps,
Liz
On Tue, Mar 29, 2011 at 11:12 PM, Manuel Spínola
<[email protected]>wrote:
Hi Travis,
I don't think that a p-value is going to tell you if there is a biological
meaningful difference between community.
What will be the metrics that you are planning to use with ANOSIM ?
Without seeing the data I can tell you that there is a difference between
communities, but the important question is how different they are, so you
can assess a practical or biological significance and a p-value is not
going
to tell you that.
Best,
Manuel
On 28/03/2011 07:14 a.m., T. Travis Brown wrote:
Hello, I am trying to determine the best way to test for a difference in
the overall mussel community found in a stream between 1980 and 2008. I
have seven sites with presence/absence data. In addition to various
descriptive statistics and graphs (nonmetric multidimensional scaling) I
would like to use ANOSIM because it offers a P-value, and answers the
question: "well, is there a difference or not?". I am not as up-to-date
on
this literature as I would like to be. Does anyone know if this is still
an
accepted test? Would some type of multi-response permutation procedure
be
better?
T. Travis Brown
[email protected]
--
*Manuel Spínola, Ph.D.*
Instituto Internacional en Conservación y Manejo de Vida Silvestre
Universidad Nacional
Apartado 1350-3000
Heredia
COSTA RICA
[email protected]
[email protected]
Teléfono: (506) 2277-3598
Fax: (506) 2237-7036
Personal website: Lobito de río <
https://sites.google.com/site/lobitoderio/>
Institutional website: ICOMVIS <http://www.icomvis.una.ac.cr/>
--
Liz Pryde
PhD Candidate (off-campus)
School of Earth and Environmental Sciences
James Cook University
Thornbury, Melbourne
0418551570
