indicator value in labdsv

Wow!  That was fast!

     Unfortunately, Agnieszka, I don't think you will find an objective
criterion for this.  Clearly, species which do not have a statistically
significant value are probably less useful, but of the many that are
significant, many may be marginal.

     Without knowing fully what you are hoping to achieve, I think I
would rank the species by indicator value, and establish the highest
threshold for indicator value that gives you a suitable number of
species for each type.  That way, if you are looking to write a field
key, for example, you would have sufficient values to identify every
type I suspect.

Good luck, Dave

astrzelczak at ps.pl wrote:

Hello,

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

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

M. and Legendre, P. 1997. Species assemblages and indicator species: the need
for a flexible asymmetrical approach. Ecol. Monogr. 67(3):345-366. The

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

that's too low...

best regards
Agnieszka

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:

Hi,

I'm trying to find out what threshold of indicator value in labadsv should

used to accept a specie as an indicator one? So far I assumed that

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:

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??ne-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