Supplement 3. WinBUGS code for fitting a ZIP mixture model to estimate densities of animal guilds.

File List WinBUGS_ZIP_mixture_model.txt Description The WinBUGS_ZIP_mixture_model.txt file is code for fitting a zero-inflated Poisson (ZIP) mixture model to observations of animals to model densities of animal guilds. The code models the probability that an observation of zero comes from a Poisson distribution or alternatively as a structural zero, and then calculates the density of animal guilds with month and species as random effects. Parameters with the prefix b0 are effects of the absence part of the ZIP model quantifying the probability of a structural zero on the logit scale. Parameters with the prefix b are effects for the abundance part of the model: these effects are guild densities. Explanatory variables include: frt (fruit abundance); pca1 (PCA axis 1 – number of trees); pca2 (PCA axis 2 – number of lianas); pca3 (PCA axis 3 – understory); pco (canopy heterogeneity); site (different forest types) where [1] = logged, hunted forest, [2] = logged, unhunted forest, [3] = unlogged, unhunted forest. The standard deviation of the month × species random effect is sigma.mo. From the estimated explanatory variables and the data, we calculated: post.p as the probability that the observations along a transect come from a Poisson distribution for each site; post.lambda as the predicted guild density generated from a Poisson distribution for each site; and post.abund as the mean guild density for each site.