[R] indicator value in labdsv

[astrzelczak@ps.pl]

That's what I was afraid of.. I'm not a biologist, so I have to involve my
co-workes who are well-versed in biological issues. Thank you very, very much
for help!!!

best regards
Agnieszka


Monday, September 19, 2005, 6:38:35 PM, you wrote:

> 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
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
>>
>>
>>
>>>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
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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
>>
>>