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

[syrovat at sci.muni.cz]

> Thank you very much for your explanations. So if I understood it
> correctly, a significant outcome from adonis() (or capscale()) should
> indicate me that my species community changes along the gradient?

Yes, you understand it correctly.

> Nice that you also mention
> betadisper, because I'd like also to look at variation in species
> composition within the
> factor levels and along the gradient and came about the same issue.

That's a good idea. Also note that adonis (PERMANOVA) "may confound
location and dispersion effects", as one may read in Note in adonis help
(?adnois). Thus, one might want to compare results obtained by adonis and
betadisper for the same model:
adonis(comm ~ factorX)
betadisper(comm, factorX)

Cheers,
Vit

> Best wishes
> Valérie
>
>
>> Message du 16/01/13 à 10h08
>> De : syrovat at sci.muni.cz
>> 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
>>
>> Hi Valérie,
>> adonis is analogous to RDA or CCA, as it directly estimates the variance
>> in the distance matrix attributable to an independent variables(s), with
>> the advantage that one may use any distance measure. It parallels r2 in
>> a
>> linear model.
>> Mantel test simply calculates the correlation between two distance
>> matrices (and tests it via permutations), thus, one gets the idea about
>> wthether there is a linear relationship between them at all.
>> Cheers,
>> Vit
>>
>> > 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 (?) 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.
>> > Best,
>> > Valérie
>> >
>> >
>> >> 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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>> >> > _______________________________________________
>> >> > R-sig-ecology mailing list
>> >> > R-sig-ecology at r-project.org
>> >> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>> >>
>> >> 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.
>> >>
>> >>
>> >
>> > ___________________________________________________________
>> > Les téléviseurs écrans plats sont en soldes sur le comparateur de prix
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>> > Voila.fr http://shopping.voila.fr/vitrine/televiseurs-ecran-plat
>> >
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>> >
>>
>>
>>
>
> ___________________________________________________________
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>