[R-sig-eco] adonis model specification

[Christine Griffiths]

Dear Jari and Peter

Thanks for the help. It works fine now. Glad it was that simple. :-)

I have a number of queries:
(1) I am a bit skeptical about the output in that if I run variations of 
the model, with treatment alone or treatment * block, with or without 
specifying month as strata, then I get the same p-values = 0.004975 for all 
factors. This is likely to be a foolish misinterpretation of the results or 
misspecification of the model. Should I be concerned about this?

Call:
adonis(formula = dataset.plot.count ~ treatment * month, data = 
dataset.plot.env,      permutations = 200, method = "morisita", strata = 
dataset.plot.env[,          "Month"])

                        Df  SumsOfSqs    MeanSqs    F.Model     R2   Pr(>F) 

treatment       2.0000e+00 1.5313e-01 7.6565e-02 1.1603e+01 0.1033 0.004975 
**
month           1.0000e+00 1.7446e-01 1.7446e-01 2.6439e+01 0.1177 0.004975 
**
treatment:month 2.0000e+00 5.3241e-02 2.6621e-02 4.0342e+00 0.0359 0.004975 
**
Residuals       1.6700e+02 1.1020e+00 6.5987e-03            0.7432 

Total           1.7200e+02 1.4828e+00                       1.0000 

---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1


(2) Is this the correct way to specify the null hypothesis: there is no 
difference between treatments over time? Can I account for block variation 
as a random effect?

(3) Because I am interested in testing if my blocks are reliable replicates 
of each other, ie have a similar species composition to start with. Do I 
need to specify this separately as below for time 1? I.e. not including the 
temporal pseudoreplication.
m1<-adonis(dataset.plot.count~treatment*block,data=dataset.time1,permutation=200,method="morisita")

I am aware that these are not purely R related questions, so if there is 
any  easily digestible literature describing the technique in depth, I 
would greatly appreciate being directed towards it.

Many thanks in advance,

Cheers
Christine

--On 29 September 2009 07:59 -0600 Peter Solymos <solymos at ualberta.ca> 
wrote:

> re right, you can supply raw data and use the method argument
> in adonis to define dissimilarity index (which is "bray" by default).
>