Example North American Breeding Bird Survey

We illustrate the multi-species occupancy model by fitting data collected from an avian community as part of the North American Breeding Bird Survey (BBS). We described the BBS earlier (see Chapters 4 and 8). Here we consider an analysis of detections of birds observed at 50 sampling locations along BBS route number 017 in New Hampshire. This route was visited by the same observer on 11 different days in June and early July of 1991.

During the 11 days of sampling, 99 distinct species of birds were detected. However, there is considerable variation among species in both apparent occurrence (proportion of 50 sites where a species was detected) and apparent detectability (relative frequency of detections within sites that appear to be occupied) (Figure 12.1).

We conducted a Bayesian analysis of these data using non-informative priors for the model's parameters (expit(a) ~ U(0,1), expit(ft) ~ U(0,1), au ~ U(0,10), <Jv ~ U(0,10), and p ~ U(-1,1) where p = auv/(<ruav)). Panel 12.1 contains WinBUGS code for implementing this model. The posterior summaries of these parameters, which are given in the first two columns of Table 12.1, indicate that logit-scale parameters for occurrence and detection vary quite a bit among species. In addition species occurrence and detection appear to be positively correlated (p = 0.42), which is to be expected because, for any species, both ft and p often increase as abundance of individuals increases (Royle and Nichols, 2003; Dorazio and Royle, 2005a; Dorazio et al., 2006).

The posterior summary in Table 12.1 also indicates that the average probability of occurrence is only 0.25 (=expit(-1.11)), so we might suspect that the avian community actually comprises additional species that were not detected. This situation is, by far, more common in natural systems. In the next section we consider elaborations of the model that can be used to estimate the number of species in the community that were missed during sampling.

Site number

Figure 12.1. Number of times that each bird species was detected in 11 visits to each site of BBS route 017 in New Hampshire, USA. Species are numbered from the most detectable to the least detectable. Gray scale indicates number of detections.

Table 12.1. Posterior summary statistics for two multi-species occupancy models fitted to the BBS data from route 017 in New Hampshire. In one model species richness N is assumed to equal the number of distinct species observed in the survey (i.e., N = n). In the other model species richness is estimated.

Table 12.1. Posterior summary statistics for two multi-species occupancy models fitted to the BBS data from route 017 in New Hampshire. In one model species richness N is assumed to equal the number of distinct species observed in the survey (i.e., N = n). In the other model species richness is estimated.

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