Model structure and fit:
We ran HMSC models using the following setup: thin = 100, transient =
12,500, samples = 250. Using four chains to traverse parameter space and
sample the posterior distribution of estimates, we obtained a total of
1,000 samples from each species, which we used in downstream analysis
and interpretation. Gelman’s diagnostic scores were largely within the
range of acceptable values (98-99% of values were < 1.05),
suggesting that we had reached convergence of the model. Examination of
trace plots (not shown here) provided further support that chains were
well mixed.