[R-sig-eco] interpreting adonis results

Jari Oksanen jari.oksanen at oulu.fi
Fri Nov 25 10:41:45 CET 2011 

On Fri, 2011-11-25 at 09:30 +0000, Gavin Simpson wrote:
> On Sun, 2011-11-20 at 03:37 +0000, yy.loh at york.ac.uk wrote:
> > Thanks all for your help on adonis！！！^_^
> > Thanks Kay too...;-)
> > 
> > 
> > So,I have moved on and currently working on betadisper and faced some 
> > problems.
> > 
> > 1.In vegatutor.pdf, betadisper (pg 33), "The function can only use one 
> > factor as an independent variable, and it does not know the formula 
> > interface,..."
> >  
> > mod <- with(dune.env, betadisper(betad, Management))
> > 
> > Let's say I need to investigate the interaction of factors: Management and 
> > USE. My question is: Can i create a new factor from the interaction of 
> > factor Management and USE then use it in betadisper()? E.g.
> > 
> > groupA<-interaction(dune.env$Management,dune.env$Use)
> > mod <- with(dune.env, betadisper(betad, groupA))
> > mod
> > 
> > Error in optim(apply(X, 2, median, na.rm = TRUE), fn = medfun, gr = 
> > dmedfun, :
> >   non-finite value supplied by optim
> 
> That interaction is generating groups with 1 or even 0 entries:
> 
> > table(groupA)
> groupA
> BF.Hayfield HF.Hayfield NM.Hayfield SF.Hayfield BF.Haypastu HF.Haypastu 
>           1           2           4           0           1           1 
> NM.Haypastu SF.Haypastu  BF.Pasture  HF.Pasture  NM.Pasture  SF.Pasture 
>           1           5           1           2           1           1
> 
> which will be the source of the error. I haven't tracked this through
> the code as yet, but we should be able to detect this and stop or even
> drop the empty levels if it is just those 0 groups that are causing the
> problem.
> 
Howdy Folks,

It seems that empty groups (count is zero) are the source of the
problem. You can drop them using factor() command for your interaction
-- this drops empty levels:

mod <- betadisper(betad, factor(groupA))

works for me.

However, like Gav said, this may not be a meaningful test (but still
calls for a fix in vegan). If I remember correctly, Marti Anderson had
interactions in her software, but that was dropped from current
versions. 

Cheers, jari oksanen

> > For the dune dataset, the above error occured. But for my data, the 
> > interaction works. I wonder if i continue to use the new factor generated 
> > from the factor-interaction for the betadisper, will it affects the 
> > results? If this is wrong, what would be the recommended function to use?
> 
> I would need to check more carefully, but this may not be what Marti
> Anderson's software would fit as an interaction model. I may be
> misremembering, but IIRC PERMDISP can handle two-way ANOVA type models
> within her framework and betadisper is not set-up for that. What you
> have done is look at whether certain combinations of your two factors of
> interest are more variable/dispersed than others. Which seems a
> reasonable hypothesis to me.
> 
> G
> 
> > Sincerely Yours,
> > J
> > 
> > On Nov 17 2011, Kay Cecil Cichini wrote:
> > 
> > >..to be save I would consider to exclude an effect due to different  
> > >multivariate spread. See chapter 5.2, Homogeneity of groups and beta  
> > >diversity, in the vegan tutorial at  
> > >http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf.
> > >
> > >best,
> > >kay
> > >
> > >
> > >Zitat von Gavin Simpson <gavin.simpson at ucl.ac.uk>:
> > >
> > >> On Wed, 2011-11-16 at 03:43 +0100, Gian Maria Niccolò Benucci wrote:
> > >>> Hi all,
> > >>>
> > >>> I had 84 samples collected in 7 different sites. In each sample were 
> > >>> individuated the different fungal species and recorded. I would test if 
> > >>> exist a real difference between the sites and if exist a sort of site 
> > >>> effect that structure the fungal communities... Then, I did adonis test
> > >>>
> > >>> > adonis(community.sq ~ location, data=env.table, permutations=999)
> > >>>
> > >>> Call: adonis(formula = community.sq ~ location, data = env.table, 
> > >>> permutations = 999)
> > >>>
> > >>>           Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)
> > >>> location   6    12.593 2.09886  6.8867 0.34922  0.001 ***
> > >>> Residuals 77    23.467 0.30477         0.65078
> > >>> Total     83    36.060                 1.00000
> > >>> ---
> > >>> Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1
> > >>>
> > >>>
> > >>>
> > >>> The significance is R2=0.349 at P=0.001 Can I assure that exist a 
> > >>> strong site effect in structuring the communities in each site?
> > >>
> > >> Depends. The test is one of no effect of `location`. You have found
> > >> evidence against this hypothesis and thus could reject this hypothesis,
> > >> instead accepting the alternative hypothesis that there is an effect of
> > >> `location`. As to the strength of this effect? ~35% of the sums of
> > >> squares can be explained by `location`. Substantially more of the
> > >> variance remains unexplained. As I know nothing about your subject area,
> > >> I am unable to comment further on the strength of the relationship.
> > >>
> > >> Seeing as many ecologists whose work I read would say an effect is
> > >> significant if the p-value was >= 0.05. Not that I subscribe to this way
> > >> or working, but by that criterion, you have identified a significant
> > >> `location` effect.
> > >>
> > >> HTH
> > >>
> > >> G
> > >>
> > >>>
> > >>> Thanks for helping,
> > >>>
> > >>> G.
> > >>>
> > >>> 	[[alternative HTML version deleted]]
> > >>>
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> > >>
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> > >>  Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
> > >>  ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
> > >>  Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
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