[R-sig-eco] split-split-plot design and adonis

[Arnaud Foulquier]

Dear colleagues,

I’m working on a data set in order to evaluate the impact of drying on
sediment microbial community structure. The objective is to determine if the
impact of drying varies among sediment types and/or depth within the
sediment.

The experimental design is as follows: The first factor *Sediment*
corresponds to three types of sediment (coded Sed1, Sed2, Sed3). For each
type of Sediment, sampling was carried out on three sites (3 sites for Sed1,
3 sites for Sed2, 3 sites for Sed3). *Site* is coded : Site1, Site2, ...,
Site9. The next factor is *Hydrology*: within each site, sampling is carried
out in a dry plot and in a wet plot (coded Dry /Wet). Within each of the
previous plot, sampling is carried out at two *Depths* (D1, D2) in
triplicate.

There are a total of n = 108 samples = 3 Sediment * 3 Sites * 2 Hydrology *
2 Depths * 3 Replicates.

I use the adonis function in the following way :

Sediment<-as.factor(rep(c("Sed1","Sed2","Sed3"),each=36))
Site<-as.factor(rep(c("Site1","Site2","Site3","Site4","Site5","Site6","Site7","Site8","Site9"),each=12))
Hydrology<-as.factor(rep(rep(c("Dry","Wet"),each=6),9))
Depth<-as.factor(rep(rep(c("D1","D2"),each=3),18))

adonis(community~Sediment*Hydrology*Depth,perm=999,strata=Site)

I need to specify strata=Site to account for the stratified structure of the
design.
However, I think it is incomplete and that I also should specify that
Hydrology is nested in Site (I use the lme function in the univariate case
as follows :
http://stats.stackexchange.com/questions/19818/split-split-plot-design-and-lme)

I tried the following :

Site_Hydro<-interaction(Site,Hydro)
adonis(community~Sediment*Hydrology*Depth,perm=999,strata=Site_Hydro)

Is it the correct way to account for the stratified structure of my data?

Any help on this question would be much appreciated.

Arnaud





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