[R-sig-eco] Specifying contrasts for an interaction in mvabund/manyglm

[Kyle Tyler]

Dear list;

I am investigating how species assemblages of fish vary over space and time. I am performing a multivariate analysis using manyglm in mvabund, with the factors Site, Season and their interaction. Site has eight levels and Season 4. Each Site was sampled multiple times within each Season.

My model is:

full_mod <- manyglm(spp ~ Site + Season + Site:Season, offset=(log(Shot_L)), family="negative_binomial", data = Catch)

The offset is due to the linear length of each sampled �transect� varying between samples.

Using �anova.manyglm(full_mod, p.uni="adjusted"), I find that each factor, and the interaction, is highly significant. The next step is to then look at which pairs of factor levels differ. For the factors on their own, this is straightforward by again using �anova.manyglm� again, but with the �pairwise.comp =� specified for each factor.

In the case of the interaction, I do this with:

Catch$SiteSeason <- paste(Catch$SiteSeason, Catch$SiteSeason, sep=�_�)

anova.manyglm(full_mod, p.uni="adjusted�, pairwise.comp = Catch$SiteSeason)

However, for the interaction in my model, the number of comparisons really blows up and becomes impractical to manage, and even non-sensical in a lot of cases. This is because anova.manyglm will compare every possible combination, which in my case results in 496 comparisons for this interaction. This causes problems first due to so much multiple testing going on, but also because not all comparisons make sense, or at least I am not interested in them.

Ideally, I would like to restrict the contrasts to be only between seasons within each site, and between sites within a season, as these are the comparisons I am interested in. I don�t really care to know if the assemblage at site 1 in season 1 is different from that at site 8 in season 4 etc. In mvabund, is there a way to specify/restrict the contrasts to only those that I am interested in?

Thanks a lot for any help!
Kyle

Kyle J. Tyler
PhD Candidate � Aquatic Ecology
Charles Darwin University, Australia

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