Dear Gian,
I'm still not quite sure about the functioning of adonis(). I made some
proofs and I don't understand how does it calculate the degrees of
freedom of a nested factor. But this is most probably due to my lack of
experience with this function (as I told you I usually work with the
PER
Hi Maria,
Yes, I think it's right, maybe now I did the correct function, It seems that
the "area" effect is also visible...
> adonis(ABCDsqrt ~ Host, method="bray", data=env.table, permutations=99,
strata=env.table$Community)
Call: adonis(formula = ABCDsqrt ~ Host, data = env.table, permutations
On Wed, 2009-12-09 at 10:25 +0100, gabriel singer wrote:
> Gian,
>
> You may also want to use betadisper() to check whether the host effect
> is due to differences in "location" or "dispersion" (or both). This is
> equivalent to checking homogeneity of variance when running a classical
> ANOVA.
Gian,
You may also want to use betadisper() to check whether the host effect
is due to differences in "location" or "dispersion" (or both). This is
equivalent to checking homogeneity of variance when running a classical
ANOVA.
cheers, g
Gian Maria Niccolò Benucci wrote:
Jari, Gavin, Chris
On Tue, 2009-12-08 at 20:27 +0100, Gian Maria Niccolò Benucci wrote:
> Jari, Gavin, Chris, Gabriel and Carsten...
> ...So, I would explain a little about my datasets:
>
> - the species matrix is done by roots samples in which were counted the
> ectomycorrhizal fungal species present (cells entiti
Hi Gian,
I've never used adonis() [I'm a R beginner] but I've been doing
multivariate analysis for some time: I usually use PRIMER with the
PERMANOVA add-in. nMDS followed by PERMANOVA works quite well for me in
experimental designs similar to yours. But it seems to me that you have
nestednes
Jari, Gavin, Chris, Gabriel and Carsten...
Many thank you all for your support and kindness... and for your competence
and experience that could not be ever comparized to mine at least in that
stuffs...
Gabriel said: .*..I found this mailing list very helpful many times for my
own questions, but
On Tue, 2009-12-08 at 17:09 +0100, Carsten Dormann wrote:
> Dear disputants.
I'm not sure anyone is disagreeing here?
>
> If this is a poll, I'd like to second Gabriel's email, with respect to
> his comments on the usefulness of the R-sig-ecology mailing list AND his
> comments on (n)MDS + ado
Dear disputants.
If this is a poll, I'd like to second Gabriel's email, with respect to
his comments on the usefulness of the R-sig-ecology mailing list AND his
comments on (n)MDS + adonis AND his point on slowly developing the
standard of your research field, rather than immediately dwarfing
Hi Gian and others,
I think we better stop worrying about subjective interpretations of
emotional backgrounds of what in other aspects are absolutely helpful
discussion threads... I guess part of the challenge on this mailing list
is to span the whole range of expertise with useful
discussion
On Mon, 2009-12-07 at 20:10 +0100, Gian Maria Niccolò Benucci wrote:
> Hi Gavin and Hi all,
>
> I will not go in front of a bus for sure, I not mad, at least I am not still
> mad... :)
>
> I would like to tell you that I am a Ph.D. student, and for what I know,
> Ph.D. student still have to under
Gian,,
I applaud your continued struggle to understand the best route of analysis.
If I were you, I would ignore the rude comments made by some and focus on
the constructive replies from others. Good luck!
Chris Habeck
Ph.D. Candidate
Department of Zoology
University of Wisconsin, Madison
http:
Hi Gavin and Hi all,
I will not go in front of a bus for sure, I not mad, at least I am not still
mad... :)
I would like to tell you that I am a Ph.D. student, and for what I know,
Ph.D. student still have to understand things studing those from whom wrote
before them...
Isac Newton became famou
On Sun, 2009-12-06 at 17:56 +0100, Gian Maria Niccolò Benucci wrote:
> Hi all again,
>
> And thank you all for the kind responses...
>
> I do not want to torture myself for sure... :) I red (lot of) publications
> about fungal community ecology studies (soil fungi), my research field
> indeed, an
Hi all again,
And thank you all for the kind responses...
I do not want to torture myself for sure... :) I red (lot of) publications
about fungal community ecology studies (soil fungi), my research field
indeed, and all uses NMDS or DCA as ordination techniques... So, I am only
trying to do my be
On Thu, 2009-12-03 at 19:27 +0100, Gian Maria Niccolò Benucci wrote:
> Jari,
>
> I am here again ... :)
> So, to try having a comparison of the real goodness of my metaMDS data I
> tried to perform a DCA (with same input table)
> Then please forgive me if I do somethign wrong with it... That's my
Jari,
I am here again ... :)
So, to try having a comparison of the real goodness of my metaMDS data I
tried to perform a DCA (with same input table)
Then please forgive me if I do somethign wrong with it... That's my R code:
>decorana(sqrtABCD, iweigh=0, ira=0) -> DCA.1
> DCA.1
Call:
decorana(ve
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