Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders

Johnson, Josh; Jones, Jay E.; Rochelle, Michael; Brintz, Ben; Garcia, Tiffany S.; Peterman, Summer; Kroll, Andrew J.; Dugger, Katie; Murden, Blake

Citeable URL: http://ir.library.oregonstate.edu/concern/articles/pc289k897

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Supporting information available online at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142903#sec012

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Creator	Johnson, Josh Jones, Jay E. Rochelle, Michael Brintz, Ben Garcia, Tiffany S. Peterman, Summer Kroll, Andrew J. Dugger, Katie Murden, Blake
Abstract or Summary	Plethodontid salamanders are diverse and widely distributed taxa and play critical roles in ecosystem processes. Due to salamander use of structurally complex habitats, and because only a portion of a population is available for sampling, evaluation of sampling designs and estimators is critical to provide strong inference about Plethodontid ecology and responses to conservation and management activities. We conducted a simulation study to evaluate the effectiveness of multi-scale and hierarchical single-scale occupancy models in the context of a Before-After Control-Impact (BACI) experimental design with multiple levels of sampling. Also, we fit the hierarchical single-scale model to empirical data collected for Oregon slender and Ensatina salamanders across two years on 66 forest stands in the Cascade Range, Oregon, USA. All models were fit within a Bayesian framework. Estimator precision in both models improved with increasing numbers of primary and secondary sampling units, underscoring the potential gains accrued when adding secondary sampling units. Both models showed evidence of estimator bias at low detection probabilities and low sample sizes; this problem was particularly acute for the multi-scale model. Our results suggested that sufficient sample sizes at both the primary and secondary sampling levels could ameliorate this issue. Empirical data indicated Oregon slender salamander occupancy was associated strongly with the amount of coarse woody debris (posterior mean = 0.74; SD = 0.24); Ensatina occupancy was not associated with amount of coarse woody debris (posterior mean = -0.01; SD = 0.29). Our simulation results indicate that either model is suitable for use in an experimental study of Plethodontid salamanders provided that sample sizes are sufficiently large. However, hierarchical single-scale and multi-scale models describe different processes and estimate different parameters. As a result, we recommend careful consideration of study questions and objectives prior to sampling data and fitting models.
Resource Type	Article
DOI	10.1371/journal.pone.0142903
Date Available	2016-01-13T20:17:35+00:00
Date Issued	2015-11-30
Citation	Kroll, A. J., Garcia, T. S., Jones, J. E., Dugger, K., Murden, B., Johnson, J., ... & Rochelle, M. (2015). Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders. PLoS ONE, 10(11), e0142903. doi:10.1371/journal.pone.0142903
Series	PLoS ONE Vol. 10 no. 11
Rights Statement	In Copyright
Funding Statement (additional comments about funding)	Oregon State University Fish and Wildlife in Managed Forests Program, Oregon Forest Industries Council, Port Blakely Tree Farms, and Weyerhaeuser provided funding to collect empirical data. The funders provided support in the form of salaries for authors [AJK, TG, JJ, KD, BM, JJ, SP, MR].
Publisher	Public Library of Science
Peer Reviewed	Yes
Language	English [eng]
Replaces	http://hdl.handle.net/1957/58073
Additional Information	description.provenance : Submitted by Patricia Black (patricia.black@oregonstate.edu) on 2016-01-13T20:17:14Z No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) GarciaTiffanyFishWildlifeEvaluationMultiLevelModels.pdf: 936969 bytes, checksum: d1cec78fd5abb559c71c0c62cb778ca7 (MD5) GarciaTiffanyFishWildlifeEvaluationMultiLevelModels(Correction).pdf: 113721 bytes, checksum: 9648db0bef97bbb70fceb2f3d4eaef36 (MD5) description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2016-01-13T20:17:35Z (GMT) No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) GarciaTiffanyFishWildlifeEvaluationMultiLevelModels.pdf: 936969 bytes, checksum: d1cec78fd5abb559c71c0c62cb778ca7 (MD5) GarciaTiffanyFishWildlifeEvaluationMultiLevelModels(Correction).pdf: 113721 bytes, checksum: 9648db0bef97bbb70fceb2f3d4eaef36 (MD5) description.provenance : Made available in DSpace on 2016-01-13T20:17:35Z (GMT). No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) GarciaTiffanyFishWildlifeEvaluationMultiLevelModels.pdf: 936969 bytes, checksum: d1cec78fd5abb559c71c0c62cb778ca7 (MD5) GarciaTiffanyFishWildlifeEvaluationMultiLevelModels(Correction).pdf: 113721 bytes, checksum: 9648db0bef97bbb70fceb2f3d4eaef36 (MD5) Previous issue date: 2015-11-30

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