[R-sig-eco] Multivariate ANOVA/repeated measures

[Dr N.A. Cutler]

Dear All,

I have a query about multivariate analysis of community data.

In my experiment, 24 microbial communities in different locations were 
sampled using Sampling Technique 1 (ST1). A site X species matrix was then 
derived by molecular analysis.

The same 24 locations were then sampled again using a different sampling 
technique (ST2) and a second site X species matrix was derived. It is 
assumed that community structure remains intact after sampling by Technique 
1 i.e. the two techniques can sample from the same pool of organisms.

I want to compare the results of the two sampling exercises in order to 
test the performance of the two sampling techniques. My research question 
is: does Technique 1 produce a similar signal to Technique 2? Or do the 
different techniques give significantly different pictures of community 
structure? The null hypotheses is that there is no significant difference 
between the two sampling techniques i.e. they both capture community 
structure with the same degree of accuracy.

It occurred to be that I could use a multivariate ANOVA technique (e.g. 
Adonis) to distinguish between the results of the two sampling exercises, 
using sampling technique as a factor. But I am not sure how to deal with 
the obvious correlation between sample pairs. Should this situation be 
addressed as a repeated measures experiment with two time steps? If so, 
what is the best technique to use (a mixed model, perhaps?)

Any advice would be gratefully received.

Best wishes,

Nick Cutler