North American Breeding Bird Survey (BBS) uncertainty simulation code

The North American Breeding Bird Survey (BBS) (https://www.pwrc.usgs.gov/bbs/) has counted birds annually for over fifty-five years. Survey 'routes' each consist of 50 'stops' (point counts) placed along a route path. Inter-stop distances and stop locations can vary from route to route and from year to year, and precise locations of each stop are not typically recorded. Burner et al. (2024) quantified stop-level location uncertainty and the resulting uncertainty in land cover and developed a method to account for this uncertainty using informative Bayesian priors. This script conducts a robust simulation of this method by simulating BBS stop locations along routes in the upper Midwest, extracting land cover information using the National Land Cover Database (NLCD; https://www.usgs.gov/centers/eros/science/national-land-cover-database), and simulating bird communities. It then fits three alternative models to these simulated datasets: a ‘known’ model with true land cover, a ‘naive’ model assuming consistent 800-m stop spacing, and a ‘full’ model using informative priors to estimate land cover.

The repository supports the following publication(s):
Burner, R.C., Hostetler, J.A., and Kirschbaum, A. [In prep] Incorporating location uncertainty improves inference with stop-level North American Breeding Bird Survey (BBS) data. (for Ornithological Applications)

The repository requires the following USGS data release(s):
Burner, R.C., Kirschbaum, A., Anich, N.M., Niemuth, N.D., Striegel, E.D., and Thogmartin, W.E. 2024. Location and land cover uncertainty associated with stop-level data from the North American Breeding Bird Survey (BBS): U.S. Geological Survey data release. https://doi.org/10.5066/P1CLSQED.

The repository builds upon the following publication(s):
Burner, R.C., Kirschbaum, A., Hostetler, J.A., Ziolkowski Jr., D.J., Anich, N.M., Turek, D., Striegel, E.D., and Niemuth, N.D. 2024. Informative priors can account for location uncertainty in stop-level analyses of the North American Breeding Bird Survey (BBS), allowing fine-scale ecological analyses. Ornithological Applications 126:duae041 https://doi.org/10.1093/ornithapp/duae041.

The repository builds upon the following code repository:
Burner, R.C. 2024. North American Breeding Bird Survey (BBS) stop-level uncertainty code. U.S. Geological Survey code release. Reston, Va. https://doi.org/10.5066/P1HY6LDF.