[R-sig-eco] Fwd: Fwd: how to calculate "axis variance" in metaMDS, pakage vegan?

[gabriel singer]

A difference between two communities within a host could still exist and 
could make perfect sense, too, when you regard "community" as a random 
factor. Then "community" may introduce some extra variation (compared to 
the within-community variation), experimentally seen interesting and 
important, because the replication of communities makes sure you are not 
pseudoreplicating. I am not sure however, how to declare the correct df 
for the random factor in adonis in this case... anybody knows better than I?



Gian Maria Niccolò Benucci wrote:
> Maria,
>
>
> *...Nevertheless you still do not know if your communities are significantly
> different between each other, within each host. Now it depends on the
> hypothesis you intend to test.*..
>
>
> I think no sense for "Community" inside "Host"... Couse A and B are from the
> same host "Corylus", and C and D are from host "Ostrya".
> So the effect between two host tree species is real, but difference between
> two community inside the same host (A vs B i.g.) could not be.
> That is also confirmed by my diversity indices data I got (see my lastest
> post), they show that A and B are alwasy different from C and D, but between
> A and B (and for sure also between C and D ) there are no statistical
> differences (ANOVA).
>
> I think both "host" and "community" effect and if use them separately I got
> :
>
>   
>> adonis(sqrtABCD ~ Host, method="bray", data=env.table, permutations=99)
>>     
>
> Call: adonis(formula = sqrtABCD ~ Host, data = env.table, permutations =
> 99,      method = "bray")
>
>                 Df SumsOfSqs  MeanSqs  F.Model     R2 Pr(>F)
> Host       1.00000   1.64429  1.64429  5.38984 0.1242   0.01 **
>
> Residuals 38.00000  11.59276  0.30507          0.8758
> Total     39.00000  13.23705                   1.0000
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
>
>   
>> adonis(sqrtABCD ~ Community, method="bray", data=env.table,
>>     
> permutations=99)
>
> Call: adonis(formula = sqrtABCD ~ Community, data = env.table, permutations
> = 99,      method = "bray")
>
>                 Df SumsOfSqs  MeanSqs  F.Model     R2 Pr(>F)
> Community  3.00000   2.43264  0.81088  2.70182 0.1838   0.01 **
>
> Residuals 36.00000  10.80441  0.30012          0.8162
> Total     39.00000  13.23705                   1.0000
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>   
>
>
> Thank you so much to all want to write any comments on that...
>
> Cheers,
>
>
> Gian
>
>
>
>
>   
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