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
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?
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 <[email protected]>:
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]]
_______________________________________________
R-sig-ecology mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
_______________________________________________
R-sig-ecology mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
_______________________________________________
R-sig-ecology mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
--
Loh Yen Yee
Department of Biology (Area 18)
University of York
York, UK YO10 5DD
_______________________________________________
R-sig-ecology mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
