[R-sig-eco] Adonis for significance of clusteredness from hclust (vegan package)

[Zoltan Botta-Dukat]

Dear Ansley,

I cannot answer your question, I hope someone else will answer. I'd 
rather point out a problem in your approach. Statistical tests were 
developed for testing difference between a priori groups, thus estimated 
Type I error rate is valid only for this situation. When you calculates 
Type I error rate for comparison of groups created by cluster analysis 
of the SAME data, the calculated error rate will be lower than the valid 
error rate. So you cannot use the term "significant" in this situation.

Sorry for making you sadden by this information.

Zoltan

2016.10.03. 21:52 keltezéssel, Ansley Silva írta:
> 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.
>
> Call:
> adonis(formula = species ~ Group, data = environ, permutations = 999)
>
> Permutation: free
> Number of permutations: 999
>
> Terms added sequentially (first to last)
>
>            Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)
> Group      2   0.40244 0.201219   4.969 0.66528  0.007 **
> Residuals  5   0.20248 0.040495         0.33472
> Total      7   0.60492                  1.00000
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>
>
>
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-- 

Botta-Dukát Zoltán                                Zoltán BOTTA-Dukát
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Ökológiai és Botanikai Intézet                    Institute of Ecology and Botany
Magyar Tudományos Akadémia                        Hungarian Academy of Sciences
Ökológiai Kutatóközpont                           Centre for Ecological Research
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