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ayebare_etal_2023_procb

An environmental habitat gradient and within-habitat segregation enable co-existence of ecologically similar bird species

bahlai_zipkin_2020_ploscomputbiol

Bahlai, C. A., Zipkin, E. F. 2020. The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations. PLoS Comput Biol 16(1): e1007542.

blommel

brodie_etal_2018_biotropica

Brodie J.E., Helmy O., Mohd-Azlan J., Granados A., Bernard H., Giordano A., and Zipkin E.F. 2018. Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment. Biotropica. 50: 5-15.

cabodevilla_etal_2022_agee

Cabodevilla, X., Wright, A. D., Villanua, D., Arroyo, B., and Zipkin, E. F. (2022). The implementation of irrigation leads to declines in farmland birds. Agriculture, Ecosystems, and Environment 323 (2022) 107701. https://doi.org/10.1016/j.agee.2021.107701

community_model_examples-basic_model

Example model code to run a basic version of the community hierarchical model with data augmentation

community_model_examples-covariate_model

Example code to run a covariate version of the community hierarchical model with data augmentation

danaus

This repository contains all necessary materials for a 'Math & Monarchs Module' to be used for K-12 educational purposes. This work is a product of @lxwrght with major contributions from @farrmt & @saund123. The published version of the app can be found at: https://danaus.shinyapps.io/Danaus/.

davis_etal_2022_ecolandevol

Davis, K. L., Silverman, E. D., Sussman, A. L., Wilson, R. R., Zipkin, E. F. (2022). Errors in aerial survey count data: Identifying pitfalls and solutions. Ecology and Evolution 12:e8733.

davis_etal_2023_biocons

Davis, K.L., S.P. Saunders, S. Beilke, E.R. Ford, J. Fuller, A. Landgraf, E.F. Zipkin. (2023). Breeding season management is unlikely to improve population viability of a data-deficient migratory species in decline. Biological Conservation 283:110104.

direnzo_etal_2018_ecoapps

DiRenzo, G. V., E. Zipkin, E. C. Grant, J. A. Royle, A. V. Longo, K. Z. Zamudio, and K. R. Lips. 2018. Eco-evolutionary rescue promotes host-pathogen coexistence. Ecological Applications 28: 1948-1962.

direnzo_etal_2019_ecolandevol

DiRenzo G. V., Che‐Castaldo C., Saunders S. P., Campbell Grant E. H., Zipkin E. F. 2019. Disease‐structured N‐mixture models: A practical guide to model disease dynamics using count data. Ecology and Evolution 9: 899–909.

doser_et_al_2024_mee

Doser, J. W., Finley, A. O., Kéry, M., & Zipkin, E. F. (2024). spAbundance: An R package for single-species and multi-species spatially-explicit abundance models. Methods in Ecology and Evolution.

doser_etal_2021_ecoapps

Doser, J. W., A. S. Weed, E. F. Zipkin, K. M. Miller, and A. O. Finley. 2021. Trends in bird abundance differ among protected forests but not bird guilds. Ecological Applications 00(00):e02377. 10. 1002/eap.2377

doser_etal_2021_mee

Doser, J. W., Finley, A. O., Weed, A. S., & Zipkin, E. F. (2021). Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance. Methods in Ecology and Evolution, 12(6), 1040-1049.

doser_etal_2022_mee

Doser, J. W., Leuenberger, W., Sillett, T. S., Hallworth, M. T., & Zipkin, E. F. (2022). Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.13811

doser_etal_2022_mee_a

Doser, J. W., Finley, A. O., Kéry, M., & Zipkin, E. F. (2022). spOccupancy: An R package for single-species, multi-species, and integrated spatial occupancy models. Methods in Ecology and Evolution. DOI: https://doi.org/10.1111/2041-210X.13897

doser_etal_2024_geb

doser_etal_2024_jabes

farr_etal_2019_ecoapps

Farr, M.T., Green, D.S., Holekamp, K.E., Roloff, G.J., & Zipkin, E.F. 2019. Multi-species hierarchical modeling reveals variable responses of African carnivores to management alternatives. Ecological Applications 9(2): e01845.

farr_etal_2021_ecol

Farr, M. T., D. S. Green, K. E. Holekamp, and E. F. Zipkin. 2021. Integrating distance sampling and presence-only data to estimate species abundance. Ecology 102(1):e03204. 10.1002/ecy.3204

farr_etal_2022_consbiol

M.T. Farr, T. O’Brien, C.B. Yackulic, and E.F. Zipkin. (2022). Quantifying the conservation status and abundance trends of wildlife communities with detection-nondetection data. Conservation Biology e13934.

farr_etal_2024_mee

gilbert_etal_2024_ecol

gilbert_etal_2024_tbd

green_etal_2019_ptrs

Green, D.S., Farr, M.T., Holekamp, K.E., Strauss, E.D., & Zipkin, E.F. 2019. Can hyena behavior predict abundances of sympatric carnivores? Philosophical Transactions of the Royal Society 374(1781): 20180052.

policies

Lab policies and operating procedures

ribeiro_etal_2018_ecoapps

Ribeiro, J.W., Siqueira, T., Brejão, G.L., & Zipkin E.F. 2018. Effects of agriculture and topography on tropical amphibian species and communities. Ecological Applications. 28: 1554-1564.

rossman_etal_2016_ecol

Rossman R., Yackulic C., Saunders S.P., Reid J., Davis R., and Zipkin E.F. 2016. Dynamic N-occupancy models: estimating demographic rates and local abundances from detection-nondetection data. Ecology. 97: 3300-3307.

rossman_etal_2016_ecolandevol

Rossman S., Ostrom P.H., Gordon F., and Zipkin E.F. 2016. Beyond carbon and nitrogen: guidelines for estimating three‐dimensional isotopic niche space. Ecology and Evolution 6: 2405-2413.