Travis, Note that partial Canonical Correspondence Analysis and partial Redundancy Analysis are ideal for this sort of a hypothesis test (especially if the permutations are set up correctly). Also note that it is not 'ordination vs. MRPP', because these direct gradient analysis techniques, when applied to categories, can be considered special cases of MRPP: Palmer, M.W., D.J. McGlinn, L. Westerberg, and P. Milberg. 2008. Indices for detecting changes in species composition: some simplifications. Ecology. 89:1769-1771. Direct gradient analysis such as pCCA or pRDA yields diagnostics for species and samples, and allows graphical representation of results. You get far more than just a p-value. While the job of interpreting results is always up to the interpreter, these diagnostics can help get you on a solid footing. I suggest avoiding NMDS, as this technique collapses information about species identity - and not being a direct gradient analysis technique, it is of questionable value when you have clean hypothesis tests. ---Mike Palmer ________________________________________ From: Ecological Society of America: grants, jobs, news [[email protected]] On Behalf Of Liz Pryde [[email protected]] Sent: Wednesday, March 30, 2011 4:01 AM To: [email protected] 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
