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
[[alternative HTML version deleted]]
_______________________________________________
R-sig-ecology mailing list
R-sig-ecology@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
