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

[Graciliano Galdino]

pvclust is a good package to create and test significance of cluster groups.

2016-10-05 11:31 GMT-03:00 Pierre THIRIET <pierre.d.thiriet at gmail.com>:

> Dear Ansley,
>
> I agree with Zoltan.
>
> I suggest SIMPROF test in package "clustsig". A complimentary package
> for use with hclust; simprof tests to see which (if any) clusters are
> statistically different. The null hypothesis is that there is no a
> priori group structure.
> See Clarke, K.R., Somerfield, P.J., and Gorley R.N. 2008. Testing of
> null hypothesis in exploratory community analyses: similarity profiles
> and biota-environment linkage. J. Exp. Mar. Biol. Ecol. 366, 56-69
>
> HTH
> Pierre
>
> Le 04/10/2016 à 14:14, Zoltan Botta-Dukat a écrit :
> > 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 keltez�ssel, Ansley Silva �rta:
> >> 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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> >
> >
> >
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-- 
Graciliano Galdino A. dos Santos
Biólogo
Doutorando em Ciências Florestais - PPGCF
Universidade Federal Rural da Amazônia - UFRA

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