[R-sig-eco] Using adonis()
Gavin Simpson
gavin.simpson at ucl.ac.uk
Mon Nov 23 17:51:34 CET 2009
On Mon, 2009-11-23 at 10:33 -0600, Leigh Fall wrote:
> Dear all,
>
> After performing adonis(), how do you get the distribution of F values to
> decide whether to accept or reject your null hypothesis? In the help menu,
> I see there is a function 'f.perms', but I have been unsuccessful in using
> it. I can use the function 'terms' to get information on the components of
> the model.
Why do you want the distribution? The column marked 'Pr(>F)' gives you
the permutation-derived 'p'-value that is, the proportion of the
permuted F's (including the observed) greater than or equal to the
observed F.
> Here is my test:
>
> > bc <- adonis(bc2 ~samples, perm = 4999, method="jac")
> > bc
We can't run this as we don't have bc2 nor samples. Here is something we
can run (from ?adonis):
> data(dune)
> data(dune.env)
> mod <- adonis(dune ~ Management*A1, data=dune.env, permutations=99)
> mod
Call:
adonis(formula = dune ~ Management * A1, data = dune.env, permutations = 99)
Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
Management 3.00000 1.46859 0.48953 3.26288 0.3416 0.01 **
A1 1.00000 0.44089 0.44089 2.93867 0.1026 0.03 *
Management:A1 3.00000 0.58918 0.19639 1.30902 0.1370 0.26
Residuals 12.00000 1.80036 0.15003 0.4188
Total 19.00000 4.29902 1.0000
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> head(mod$f.perms)
[,1] [,2] [,3]
[1,] 0.5435436 0.8537530 0.9314347
[2,] 1.3900990 0.5298171 1.5712973
[3,] 1.4157505 0.5383744 0.7451193
[4,] 1.5889761 0.3698395 0.8468100
[5,] 0.9508102 0.2316184 0.7575177
[6,] 1.0072180 0.6972496 0.7375206
> nrow(mod$f.perms)
[1] 99
Here we have a model with 3 covariates (Management, A1, and their
interaction. Component 'f.perms' is the matrix of F.Model for the 99
permutations (rows) for the 3 covariates (columns). So the permutation F
distribution for Management is in mod$f.perms[,1], e.g.
> hist(mod$f.perms[,1], xlim = range(mod$f.perms[,1], 3.26288))
> abline(v = 3.26288, col = "red")
> box()
Does that help?
G
>
> Call:
> adonis(formula = bc2 ~ samples, permutations = 4999, method = "jac")
>
> Df SumsOfSqs MeanSqs F.Model R2
> Pr(>F)
> samples 3.00000 2.06676 0.68892 3.15012 0.1873 2e-04
> ***
> Residuals 41.00000 8.96657 0.21870 0.8127
> Total 44.00000 11.03334 1.0000
> ---
> Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
>
> Many thanks for the help in advance!
>
> Cheers,
> Leigh
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> 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
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
More information about the R-sig-ecology
mailing list