[R-sig-eco] interpreting adonis results
Gavin Simpson
gavin.simpson at ucl.ac.uk
Fri Nov 25 10:30:17 CET 2011
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.
> 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
> >> Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
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> >>
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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
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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