Repositories list

• zipkinlab.github.io

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  http://zipkinlab.github.io - Code aggregation site for projects in the Zipkin lab

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  Mozilla Public License 2.0

  •1•4•1•0•Updated Aug 27, 2025Aug 27, 2025

• PenguinChallenge

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  In this activity, students will learn about a method for surveying wild populations of penguins, and they will get to practice this method by counting colonies of stuffed penguins using clickers.

  0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• Danaus

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  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/.

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  •2•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• ButterflyCountsOutreach

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  •1•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• Leuenberger_etal_2025_PNAS

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  Leuenberger, W., J. W. Doser, M. W. Belitz, L. Ries, N. M. Haddad, W. E. Thogmartin, and E. F. Zipkin. 2025. Three decades of declines restructure butterfly communities in the Midwestern United States. Proceedings of the National Academy of Sciences 122:e2501340122 doi: 10.1073/pnas.2501340122

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  MIT License

  •1•0•0•0•Updated Aug 8, 2025Aug 8, 2025

• GitHub_HPCC_Tutorial

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  A tutorial on how to use GitHub and the HPCC through RStudio.

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  •10•1•0•0•Updated Jul 28, 2025Jul 28, 2025

• Davis_etal_2025_EcoApps

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  •1•0•0•0•Updated Jul 15, 2025Jul 15, 2025

• Gilbert_etal_2025_Ecography

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  •1•0•0•0•Updated Jul 15, 2025Jul 15, 2025

• Ayebare_etal_2025_Ecosphere

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  Improving population analysis using indirect count data: A case study of chimpanzees and elephants

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  MIT License

  •1•0•0•0•Updated Jul 15, 2025Jul 15, 2025

• Policies

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  Lab policies and operating procedures

  14•5•0•0•Updated May 23, 2025May 23, 2025

• Doser_et_al_2024_MEE

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  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.

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  MIT License

  •1•0•0•0•Updated May 9, 2025May 9, 2025

• Williams_etal_2024_NatComm

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  Code and data for Williams, Zipkin, and Brodie (in review)

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  MIT License

  •1•0•0•0•Updated May 9, 2025May 9, 2025

• Gilbert_etal_2024_Ecol

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  •1•0•0•0•Updated May 9, 2025May 9, 2025

• Gilbert_etal_2024_Ecol_A

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  •1•0•0•0•Updated Sep 13, 2024Sep 13, 2024

• Doser_etal_2024_GEB

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  MIT License

  •2•1•0•0•Updated Mar 22, 2024Mar 22, 2024

• Doser_etal_2024_JABES

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  MIT License

  •1•0•0•0•Updated Mar 22, 2024Mar 22, 2024

• Ayebare_etal_2023_ProcB

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

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  •1•0•0•0•Updated Mar 18, 2024Mar 18, 2024

• Davis_etal_2022_EcolAndEvol

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  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.

  abundancecount-dataimperfect-detection+ 5study-designaerial-surveycounting-errornondetectionspecies-misidentification

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  MIT License

  •1•1•0•0•Updated Mar 17, 2024Mar 17, 2024

• Zipkin_etal_2023_JAE

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  Zipkin E.F. , Doser J.W., Davis C.L., Leuenberger W., Ayebare S., Davis K.L., (2023) Integrated community models: A framework combining multi-species data sources to estimate the status, trends, and dynamics of biodiversity. Journal of Animal Ecology.

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  •2•1•0•0•Updated Mar 9, 2024Mar 9, 2024

• Farr_etal_2024_MEE

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  •1•0•0•0•Updated Mar 8, 2024Mar 8, 2024

• Doser_etal_2022_MEE

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  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

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  •1•0•0•0•Updated Nov 20, 2023Nov 20, 2023

• Doser_etal_2022_MEE_A

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  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

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  •2•0•0•0•Updated Sep 11, 2023Sep 11, 2023

• Davis_etal_2023_BioCons

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  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.

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  MIT License

  •1•0•0•0•Updated Sep 11, 2023Sep 11, 2023

• Zylstra_etal_2022_GCB

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  Zylstra, E. R., Neupane, N., & Zipkin, E. F. (2022). Multi-season climate projections forecast declines in migratory monarch butterflies. Global Change Biology.

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  •2•1•0•0•Updated Sep 8, 2022Sep 8, 2022

• Farr_etal_2022_ConsBiol

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  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.

  community-ecologydemographic-ratesmultiple-species-modeling+ 2population-viabilityunmarked-modeling

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  •2•3•0•0•Updated Sep 8, 2022Sep 8, 2022

• Wright_etal_2022_EcoApps

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  Wright, A. D., Grant, E. H. C., Zipkin, E. F. (2022). A comparison of monitoring designs to assess wildlife community parameters across spatial scales. Ecological Applications e2621

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  MIT License

  •1•0•0•0•Updated Jun 9, 2022Jun 9, 2022

• Cabodevilla_etal_2022_AgEE

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  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

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  MIT License

  •0•0•0•0•Updated Feb 11, 2022Feb 11, 2022

• Zylstra_etal_2021_NEE

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  •3•3•0•0•Updated Aug 30, 2021Aug 30, 2021

• Doser_etal_2021_EcoApps

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  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

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  •1•0•0•0•Updated Jun 17, 2021Jun 17, 2021

• Doser_etal_2021_MEE

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  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.

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  •3•0•0•0•Updated May 4, 2021May 4, 2021