[R] indicator value in labdsv

astrzelczak@ps.pl astrzelczak at ps.pl
Mon Sep 19 18:25:00 CEST 2005


I was uclear before, I'm sory about it. I forgot to add that I'm using duleg...

I used mvpart for multivariate regression trees. My input variables are
environmental parameters, output variables are macrophyte species
(presence=1,absence=0 in conecutive cases=lakes). For obtained classes I used
duleg to find indicator species for every class. I checked the article Dufrene,
M. and Legendre, P. 1997. Species assemblages and indicator species: the need
for a flexible asymmetrical approach. Ecol. Monogr. 67(3):345-366. The authors
used the threshold of indval=0.25(25%) and that's the only hint I've found in
the literature. This threshod seems to reasonable, but still I have impression
that's too low...

best regards

> Agnieszka,

>      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!
>> 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ęne-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

Best regards,
                                                      mailto:astrzelczak at ps.pl

Agnieszka Strzelczak, Research Assistant
mailto:astrzelczak at ps.pl

Institute of Chemistry and Environmental Protection
Faculty of Chemical Engineering
Szczecin University of Technology
Aleja Piastow 42
71-065 Szczecin

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