[R-sig-eco] Difference between mantel test and adonis

[Jari Oksanen]

Hello all,
On 16/01/2013, at 09:35 AM, <v_coudrain at voila.fr>
 wrote:

> Dear Martin, 
> Tank you very much. I thought about constrained ordination, but the distance matrix I am using is not among the "usual" (Euclidian, Bray-Curtis,...). An option 
> would be to use distance-based RDA, which is almost the same as adonis, but I read that adonis should be even better (?

adonis() and db-RDA (capscale) are indeed very similar, but they differ in handling negative distances due to negative eigenvalues and complex eigenvectors. Briefly, adonis() handles them but capscale() does not. Otherwise the results are very similar. If you do not need a graphical presentation, I recommend you use adonis().

> ) Anyway I am mainly interested to 
> understand the difference between analyses based on distance matrix of the environemental gradient (Mantel test), or on the gradient directly. 

So would I. I'm working to improve my understanding, but this is a tricky issue. However, in *most* (but perhaps not in all) cases it is better to work via gradients directly, and via rectangular data instead of distances/dissimilarities. Method working with rectangular data and gradients in vegan include capscale(), adonis() and betadisper(). Methods that work with dissimilarities in vegan include mantel(), mantel.partial(), anosim(), bioenv(), mrpp() and meandist(). The former set is usually preferred.

Cheers, Jari Oksanen


> 
>> Message du 16/01/13 à 00h53
>> De : "Martin Weiser" 
>> A : v_coudrain at voila.fr
>> Copie à : r-sig-ecology at r-project.org
>> Objet : Re: [R-sig-eco] Difference between mantel test and adonis
>> 
>> v_coudrain at voila.fr píše v Út 15. 01. 2013 v 16:08 +0100:
>>> Dear sig-eco users,
>>> 
>>> I would like to investigate the changes in a species community along an ecological gradient. I first thought about performing a Mantel test and infer if 
> differences in 
>>> species composition are related to differences in the ecological gradient. I noticed that the function adonis (package vegan) could handle continuous 
> variables as 
>>> well. However, the ecological gradient is not entered as a distance matrix and therefore I don't understand exactly how to interpret the outcome of the adonis 
> test 
>>> and what is the difference to the Mantel test. Any help will be apprectiate.
>>> 
>>> Best wishes. Valerie
>>> ___________________________________________________________
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>> 
>> Dear Valerie,
>> I would go for constrained ordination: it is easily interpretable and
>> tailored exactly to your needs.
>> To do so, in R use ade4 or vegan (I am not familiar with ade4) and run
>> CCA or RDA (depends on data and taste). Plus, Jari Oksanen wrote
>> easy-to-understand tutorial:
>> http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf 
>> Another great free resources are Mike Palmer's website:
>> http://ordination.okstate.edu/ 
>> and ordnews mailinglist:
>> ordnews at colostate.edu
>> I hope this helps.
>> Best,
>> Martin W.
>> 
>> 
> 
> ___________________________________________________________
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-- 
Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
jari.oksanen at oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa