Zipkin Quantitative Ecology Lab's repositories
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.
Sussman_etal_2019_MEE
Sussman A.L., Gardner B., Adams E.M., Salas L., Kenow K.P., Luukkonen D.R., Monfils M.J., Mueller W.P., Williams K.A., Leduc-Lapierre M., & Zipkin E.F. 2019. A comparative analysis of common methods to identify waterbird hotspots. MEE 10(9): 1454-1468.
Zipkin_etal_2014_EcolAndEvol
Zipkin, E.F., Sillett, T.S., Grant, E.H.C., Chandler, R.B., and Royle, J.A. (2014) Inferences from count data using multi-state population models: a comparison to capture-recapture approaches. Ecology and Evolution. 4: 417-426.
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.
Saunders_etal_2016_GEB
Saunders, S.P., Ries, L., Oberhauser, K.S., & Zipkin, E.F. (2016) Evaluating confidence in climate-based predictions of population change in a migratory species. GEB. 25: 1000-1012.
Saunders_etal_2018_Ecography
Saunders S.P., Ries L., Oberhauser K.S., Thogmartin W.E., & Zipkin E.F. (2018) Local and cross-seasonal effects of climate and land-use on migratory monarch butterflies. Ecography. 41: 278-290.
Saunders_etal_2018_JAE
Saunders, S.P., Cuthbert, F.J., & Zipkin, E.F. (2018) Evaluating population viability and efficacy of conservation management using integrated population models. JAE. 55: 1380-1392.
Saunders_etal_2019_Ecol
Saunders, S.P., Farr, M.T., Wright, A.D., Bahlai, C.A., Ribeiro, J.W., Rossman, S., Sussman, A.L., Arnold, T.W., & Zipkin, E.F. 2019. Disentangling data discrepancies and deficiencies with integrated population models. Ecology 100(6): e02714.
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.
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.
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.
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/.
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.
Saunders_etal_2019_PNAS
Saunders, S. P., Ries, L., Neupane, N., Ramirez, M. I., Garcia-Serrano, E., Rendon-Salinas, E., Zipkin, E. F. 2019. Multiscale seasonal factors drive the size of winter monarch colonies. Proceedings of the National Academy of Sciences 116: 8609-8614.
Zipkin_etal_2014_Ecol
Zipkin E.F., Thorson J.T., See K., Lynch H.J., Grant E.H.C., Kanno Y., Chandler R.B., Letcher B.H., and Royle J.A. 2014. Modeling structured population dynamics using data from unmarked individuals. Ecology. 95: 22-29.
Zipkin_etal_2017_Ecol
Zipkin E.F., Rossman S., Yackulic C., Wiens J.D., Thorson J.T., Davis R.J., and Grant E.H.C. 2017. Integrating count and detection-nondetection data to model population dynamics. Ecology. 98: 1640-1650.