Re: Adonis for significance of clusteredness from, hclust (vegan package)

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Re: Adonis for significance of clusteredness from, hclust (vegan package)

Michael Marsh
hello Ansley,
You might want to look at the multi-respnse permutation procedure (mrpp
in R), which examines the difference among clusters, that is, how much
greater similarity the elements of cluster have to each other as
compared to the overall similarity of elements of the data. I am not
well enough informed to advise on how the outputs of this test satisfy
your requirements, but have used it myself to assess the degree of
difference among clusters created by hclust and the "significance" of
that difference.
Mike

On 10/5/2016 3:00 AM, [hidden email] wrote:
>   Re: [R-sig-eco] Adonis for significance of clusteredness from
> hclust (vegan package)
2016.10.03. 21:52 keltez?el, Ansley Silva ?a:

> Hello:
>
> I have created a dendrograms using hierarchical cluster analysis with the
> vegan package (function: hclust).
>
> By visually observing the dendrogram, I have determined that there are 3
> main clusters if I "cut" the tree at the height 0.25  (please see the
> dendrogram from the code).
> I then created a new dataset, which is essentially the same as the
> original, but I have added the categorical variable Group to represent
> these 3 main clusters.
> ST0 is group a, AP0 and AP100 is group b, and AP200 AP300 ST100 ST200 ST
> 300 is group c.
> I want to now if they are significantly different from each other.  I
> understand, from the output pasted below, that I can accept that there is a
> significant effect of Group.  Is this the only thing I can say from
> Permanova?  What would be the code for a follow up test to look at
> pair-wise significant differences?
> Thanks very much.


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