I am trying to clarify whether I've structured my permutation restriction correctly based on my project design and application for permutation based hypothesis tests using permute::how() in R. I collected 10 replicate water samples and 8 sites and sequenced by metabarcoding. I would consider samples within sites to be exchangeable units. I would like to construct a restriction that allows free permutation of samples within but not across sites, or I think this means I would like to permutate all samples from a site together (?). I used the online documentation and textbook examples for guidance, but I'm still not sure if I've set up the argument properly for this objective, where permutations=CTRL:
CTRL <- how(within = Within(type = "free"), # freely permute samples within sites
plots = Plots(strata=as.factor(predictor.df$site.name),
type="free"), # restrict permutations to site
nperm=9999,
observed = TRUE)
Unclear if I've specified within, plots, and type correctly. I don't think the blocks argument applies to my experimental design, and I am considering sites to be plots in the context of the function (which may be wrong too). Thanks in advance for any help!