[R-sig-eco] negative F value in adonis()

[Jari Oksanen]

Adriano,

This seems to be a property of betadiver(..., index="sim"). I could confirm
this with the 'sipoo' data in vegan. Obviously the index is very nonmetric.
This also seems to happen with some other strongly non-metric indices, such
as Mountford index of vegdist(). We'll have a look at this: I don't know yet
if this is just like it should be or should we do something with this.

Cheers, Jari Oksanen


On 10/08/2010 1:21, "Adriano Melo" <grumicha at yahoo.com.br> wrote:

> Dear colleagues,
> I and a graduate student (Fabiana Schneck) are using the adonis() function in
> vegan to test for the effect of two treatments (homogenous and heterogenous
> substrate) on diatom species composition. Data resulted from a experiment
> carried out in 11 stream reaches. Data were obtained in six visits after
> colonization ceased and we opted to use the 66 combination of reaches and time
> as block (strata in the argument list of the function). We were able to run
> the function using the default 'bray' method. However, we get negative
> F-values when using a dissimilarity matrix obtained from simpson formulae.
> This is our code and result:
> bio.quali<-ifelse(bio>0, 1, 0)bio.quali.simp<-betadiver(bio.quali,
> "sim")adonis(bio.quali.simp~trat, strata=bloco, permutations = 9999)
> 
> Call:
> adonis(formula
> = bio.quali.simp ~ trat, permutations = 9999,      strata = bloco)
> 
>                                Df       SumsOfSqs    MeanSqs   F.Model   R2  
>   Pr(>F)
> trat         1.000000  -0.587663  -0.587663  -8.821903 -0.0728      1
> Residuals  130.000000  8.659838  0.066614  1.0728
> 
> Total      131.000000  8.072174  1.0000
> 
> 
> 
> 
> The reasoning to use the simpson dissimilarity was to assess whether
> differences among treatments observed with Sorensen (Bray-Curtis for p/a data)
> was due to differences in species richness (the simpson index is supposed to
> measure turnover and be robust to differences in species richness: Lennon et
> al. 2001: J.An.ECol 70:966-79).
> It is hard to imagine a negative F-value in a traditional univariate analysis,
> but I am not sure whether this is possible in adonis(). 
> Adriano Sanches Melo
> 
> Departamento de Ecologia - ICB
> 
> Universidade Federal de GoiásBrazil
> 
> 
>       
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> 
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