[R] indicator value in labdsv

Dave Roberts droberts at montana.edu
Mon Sep 19 18:00:23 CEST 2005


     As Jari indicated, it depends on which function you meant in you 
inquiry.  The duleg() function implements the Dufrene-Legendre 
algorithm, where "indicator" species are indicative of a priori 
communities.  It this requires a classification, and is biased to find 
species which occur in the dataset approximately as often as the mean 
cluster size.

     The indpsc() function calculates the mean similarity of all samples 
a species occurs in.  This is slightly biased because  we know that the 
samples being used to calculate the mean share at least the species that 
defines them, but it is still possible to compare those values to the 
mean similarity of the whole matrix, or to an expectation of maximum 
similarity.  Obviously, as species occur more frequently, the harder it 
is to have a really high similarity (indicator value), with the extreme 
case that a species that occurs in every sample must have the same value 
as the mean of the whole matrix.

     To tell the truth, I forgot that indspc() was included in the 
current version of labdsv.  In the new version (due to be released any 
day), I have included a permutation test that estimates quantiles of 
expected values for different numbers of occurrences.  It works, but is 
pretty slow.  Jari has created a version that uses parametric statistics 
to estimate the same envelope, but I haven't had a chance to try it yet.

     What research are you doing, and what are you really trying to 
determine?  Perhaps something altogether different will work better.

Thanks, Dave Roberts

> On Mon, 2005-09-19 at 09:41 +0200, astrzelczak at ps.pl wrote:
>>I'm trying to find out what threshold of indicator value in labadsv should be
>>used to accept a specie as an indicator one? So far I assumed that indval=0.5
>>is high enough to avoid any mistakes but it was based only in my intuition.
>>I'd be greatful for any advise
>>best regards
> Agnieszka,
> R mailing list software appends the following to your message:
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
> Then about indicator value analysis. You should be more specific: there
> seem to be three alternatives functions for "indicator species" in
> labdsv. Which did  you mean? At least two of these return an item called
> "indval", and these two alternative "indvals" are very different. For
> the Dufrêne-Legendre indvals, you should check the original paper (see
> references in the help page), and there you even have an associated "P
> value". In indspc, the variance of the indval clearly is dependent on
> species frequency. Moreover, in indspc the expected indval (and its
> variance) are dependent on the whole set of sites you have: these
> reflect the general "homogeneity" of your data set. Therefore you cannot
> say there that any certain value would mean that a species is a good
> indicator. However, it would be easy to work out standard errors for
> indspc indvals.
> I think it would be more useful to post to some other mailing group
> where people are more concerned about indicator species, or to contact
> the package author directly (I CC this message to him).
> cheers, jari oksanen

David W. Roberts                                     office 406-994-4548
Professor and Head                                      FAX 406-994-3190
Department of Ecology                         email droberts at montana.edu
Montana State University
Bozeman, MT 59717-3460

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