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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