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Data for: Occupancy–detection models with museum specimen data: Promise and pitfalls

Citation

Shirey, Vaughn; Khelifa, Rassim; M'Gonigle, Leithen; Guzman, Laura Melissa (2022), Data for: Occupancy–detection models with museum specimen data: Promise and pitfalls, Dryad, Dataset, https://doi.org/10.5061/dryad.s1rn8pk9q

Abstract

Historical museum records provide potentially useful data for identifying drivers of change in species occupancy. However, because museum records are typically obtained via many collection methods, methodological developments are needed in order to enable robust inferences. Occupancy-detection models, a relatively new and powerful suite of statistical methods, are a potentially promising avenue because they can account for changes in collection effort through space and time.

We use simulated datasets to identify how and when patterns in data and/or modelling decisions can bias inference. We focus primarily on the consequences of contrasting methodological approaches for dealing with species' ranges and inferring species' non-detections in both space and time. 

We find that not all datasets are suitable for occupancy-detection analysis but, under the right conditions (namely, datasets that are broken into more time periods for occupancy inference and that contain a high fraction of community-wide collections, or collection events that focus on communities of organisms), models can accurately estimate trends. Finally, we present a case-study on eastern North American odonates where we calculate long-term trends of occupancy by using our most robust workflow. 

These results indicate that occupancy-detection models are a suitable framework for some research cases and expand the suite of available tools for macroecological analysis available to researchers, especially where structured datasets are unavailable.

Methods

We simulated multiple unstructured datasets to test the behavior of occupancy-detection models when applied to natural history museum data. Also included are data from the Global Biodiversity Information Facility for eastern North American odonates.

Usage Notes

We strongly recommend using a computing cluster to reproduce this analysis.

Funding

Simon Fraser University

Natural Sciences and Engineering Research Council of Canada

Liber Ero Foundation

Georgetown University

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: P2ZHP2-175028

National Science Foundation, Award: 1937959

Compute Canada