Hello All, I have a large data set where I am interested in answering the question of whether initial conditions (i.e. our initial treatments) influenced the community composition over time. We have 10 replicates for each treatment and species abundances for 15+ species. My question is, I have seen approaches to use adonis and capscale to analyze the question of do sites change over time (omitting the treatment factor, as I have in my design). A summary of those codes can be found in this paper: http://www.esajournals.org/doi/full/10.1890/10-2138.1
However, my question is, is what I seek to do able to be properly done using adonis and/or capscale? In short, I am interested in the interactive treatment x time interaction. For example, Consider a case in which I expect to see no effect of time or treatment: #DATA speciesmatrix <- matrix(rnorm(3 * 6 * 20, 50, 10), nrow = 3 * 6, ncol = 20, dimnames = list(1:18, paste("Sp", 1:20, sep = ""))) #TIME AND TREATMENT VECTORS time <- as.ordered(rep(1:3, 6)) site <- gl(6, 3) treatment <- gl(3,6) #ADONIS adonis(speciesmatrix~treatment*time,permutations=1000, method="bray") Call: adonis(formula = speciesmatrix ~ treatment * time, permutations = 1000, method = "bray") Contrast this when I add an effect of treatment by adding 100 to each treatment 3: #Add 100 to each species in treatment 3 speciesmatrix[treatment==3,] <- speciesmatrix[treatment==3,] + 100 #Adonis adonis(speciesmatrix~treatment*time,permutations=1000, method="bray") After this, I see an effect of treatment. Great! Now let's add 50 to each species in time 2, and 75 to each species at time 3 (still having the effect of treatment by 100 being added to treatment 3 in the previous analysis) to see if this will produce a treatment x time effect speciesmatrix[time==2,] <- speciesmatrix[time==2,] + 50 speciesmatrix[time==3,] <- speciesmatrix[time==3,] + 75 adonis(speciesmatrix~treatment*time,permutations=1000, method="bray") According to this, I see the effect that I expected. However, my question is, is this the proper way to analyze this data? I have seen others treat each site as a strata, but when I incorporate those into my models the results I expect to see given my toy data fall apart. For example, I wouldn't see an effect of treatment after adding 100 to treatment 3. Any help would be very much appreciated because I have been struggling with this problem for a long time! [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology