Hi Jari and hi all again,

The documentation is sintetic and clear... I don't know, maybe is rather
difficutl for me also because I am studing statistics since few time ago and
also maybe english lenguage didn't help me with that...
I would ask something about the permutation in adonis().
As every permutational tests do, also adonis() systematically recomputing
the statistic estimate leaving out one observation at a time from the data
set. The* F*-tests are then based on sequential data that are choosen from
the original one...

In this case what is the correct choice for the permutation number?

Why I obtain the same output when I try "Community" and "Host" interaction
and "Community" effect nested within "Host"???

> adonis(sqrtABCD ~ Community*Host, method="bray", data=env.table,
permutations=99)

Call:
adonis(formula = sqrtABCD ~ Community * Host, 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

> adonis(sqrtABCD ~ Community/Host, method="bray", data=env.table,
permutations=99)

Call:
adonis(formula = sqrtABCD ~ Community/Host, 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
>


Anyway, looking at the graph, that't great and I think I'll go for this one:


>
> NMS.2
Call:metaMDS(comm = sqrtABCD, distance = "bray", k = 2, trymax = 100,
autotransform = F)

Nonmetric Multidimensional Scaling using isoMDS (MASS package)

Data:     sqrtABCD
Distance: bray shortest

Dimensions: 2
Stress:     24.53723
Two convergent solutions found after 60 tries
Scaling: centring, PC rotation, halfchange scaling
Species: expanded scores based on ‘sqrtABCD’
>
>
> stressplot(NMS.2)
Using step-across dissimilarities:
Too long or NA distances: 230 out of 780 (29.5%)
Stepping across 780 dissimilarities..

Non-metric fit, R2=0.94
Linear fit, R2=0.719
>
> envfit(NMS.2, env.table, permu=1000) -> NMS.2ef
> NMS.2ef

***FACTORS:

Centroids:
              NMDS1   NMDS2
CommunityA   0.3268 -0.2131
CommunityB   0.2055 -0.2042
CommunityC  -0.2584  0.3133
CommunityD  -0.2738  0.1040
HostCorylus  0.2661 -0.2087
HostOstrya  -0.2661  0.2087

Goodness of fit:
              r2   Pr(>r)
Community 0.2061 0.006993 **
Host      0.1937 0.001998 **
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
P values based on 1000 permutations.
>
>
> adonis(sqrtABCD ~ Host*Community, method="bray", data=env.table,
permutations=99)
Call:adonis(formula = sqrtABCD ~ Host * Community, data = env.table,
permutations = 99, method = "bray")

                Df SumsOfSqs  MeanSqs  F.Model     R2 Pr(>F)
Host       1.00000   1.64429  1.64429  5.47874 0.1242   0.01 **
Community  2.00000   0.78834  0.39417  1.31337 0.0596   0.14
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
>
>


What do you think?

Cheers,

Gian



2009/12/13 Jari Oksanen <jari.oksanen@oulu.fi>

> On 13/12/09 12:44 PM, "Gian Maria Niccolò Benucci" <gian.benucci@gmail.com
> >
> wrote:
>
> > Does a better explanation of what adonis() do already exist?
>
> "In extreme cases, read the documentation" (Duncan Murdoch in R fortunes).
>
> > So briefly and to summerize... What are, at the end, the differences
> about
> > these different following functions?
> >
> > adonis(ABCDsqrt ~ Host, env.table)
> >
> ... by 'Host'
>
> > adonis(ABCDsqrt ~ Host/Community, env.table)
> >
>  ... by 'Host' nested within 'Community'.
>
> > adonis(ABCDsqrt ~ Host*Community, env.table)
> >
>  ... by 'Host' and 'Community' and their interaction.
>
> > adonis(ABCDsqrt ~ Host, strata = env.table$Community, env.table)
> >
>  ... by 'Host' but permutations statified within 'Community'. This makes no
> sense because you restrict your permutations within the only variable you
> use to explain the results.
>
> > Thank you,
> >
>
> Thanks, but which of these cases was *not* documented? Or alternatively, if
> you tried different formulae without reading the documentation of
> 'formula',
> which cases were not obvious from the output *when* you tried it? (Or did
> you try?)
>
> Cheers, jari oksanen
>
>


-- 
Dr. Gian Maria Niccolò Benucci
Ph.D. Candidate
Department of Applied Biology - University of Perugia
Borgo XX Giugno, 74
I-06121 - Perugia, ITALY
Email: gian.benucci@gmail.com
Tel: +39.075.5856433
http://www.unipg.it/

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