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references.bib
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@misc{nykamp,
title = {The idea of a dynamical system},
author = {Nykamp, DQ},
url = {https://mathinsight.org/dynamical_system_idea}
}
@book{sayama2015,
title = {Introduction to the modeling and analysis of complex systems},
author = {Sayama, Hiroki},
year = {2015},
date = {2015},
publisher = {SUNY Geneseo},
series = {Open SUNY textbooks},
url = {https://math.libretexts.org/Bookshelves/Scientific_Computing_Simulations_and_Modeling/Book%3A_Introduction_to_the_Modeling_and_Analysis_of_Complex_Systems_(Sayama)},
note = {Citation Key: sayama2015},
address = {Albany},
langid = {eng}
}
@article{sugihara1990,
title = {Nonlinear forecasting as a way of distinguishing chaos from measurement error in time series},
author = {Sugihara, George and May, Robert M.},
year = {1990},
month = {04},
date = {1990-04},
journal = {Nature},
pages = {734--741},
volume = {344},
number = {6268},
doi = {10.1038/344734a0},
url = {https://www.nature.com/articles/344734a0},
note = {Number: 6268
Publisher: Nature Publishing Group},
langid = {en}
}
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title = {Trophic cascades promote threshold-like shifts in pelagic marine ecosystems},
author = {Casini, Michele and Hjelm, Joakim and Molinero, Juan-Carlos and {Lövgren}, Johan and Cardinale, Massimiliano and Bartolino, Valerio and Belgrano, Andrea and Kornilovs, Georgs},
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url = {https://www.pnas.org/doi/full/10.1073/pnas.0806649105},
note = {Publisher: Proceedings of the National Academy of Sciences}
}
@article{deyle2016,
title = {Tracking and forecasting ecosystem interactions in real time},
author = {Deyle, Ethan R. and May, Robert M. and Munch, Stephan B. and Sugihara, George},
year = {2016},
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date = {2016-01-13},
journal = {Proceedings of the Royal Society B: Biological Sciences},
pages = {20152258},
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number = {1822},
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url = {https://royalsocietypublishing.org/doi/10.1098/rspb.2015.2258},
note = {Publisher: Royal Society}
}
@article{chang2017,
title = {Empirical dynamic modeling for beginners},
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url = {https://doi.org/10.1007/s11284-017-1469-9},
langid = {en}
}
@article{ye2015,
title = {Equation-free mechanistic ecosystem forecasting using empirical dynamic modeling},
author = {Ye, Hao and Beamish, Richard J. and Glaser, Sarah M. and Grant, Sue C. H. and Hsieh, Chih-hao and Richards, Laura J. and Schnute, Jon T. and Sugihara, George},
year = {2015},
month = {03},
date = {2015-03-31},
journal = {Proceedings of the National Academy of Sciences},
volume = {112},
number = {13},
doi = {10.1073/pnas.1417063112},
url = {https://pnas.org/doi/full/10.1073/pnas.1417063112},
langid = {en}
}
@article{sugihara1994,
title = {Nonlinear forecasting for the classification of natural time series},
author = {Sugihara, George},
year = {1994},
date = {1994},
journal = {Philosophical Transactions of the Royal Society of London. Series A: Physical and Engineering Sciences},
pages = {477--495},
volume = {348},
number = {1688},
doi = {10.1098/rsta.1994.0106},
url = {https://royalsocietypublishing.org/doi/10.1098/rsta.1994.0106},
note = {Publisher: Royal Society}
}
@article{deyle2018,
title = {Ecosystem-based forecasts of recruitment in two menhaden species},
author = {Deyle, Ethan and Schueller, Amy M and Ye, Hao and Pao, Gerald M and Sugihara, George},
year = {2018},
date = {2018},
journal = {Fish and Fisheries},
pages = {769--781},
volume = {19},
number = {5},
doi = {10.1111/faf.12287},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12287},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/faf.12287},
langid = {en}
}
@article{sugihara2012,
title = {Detecting Causality in Complex Ecosystems},
author = {Sugihara, George and May, Robert and Ye, Hao and Hsieh, Chih-hao and Deyle, Ethan and Fogarty, Michael and Munch, Stephan},
year = {2012},
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url = {https://www.science.org/doi/10.1126/science.1227079},
note = {Publisher: American Association for the Advancement of Science}
}
@article{johnson2021,
title = {Leveraging spatial information to forecast nonlinear ecological dynamics},
author = {Johnson, Bethany and Gomez, Marcella and Munch, Stephan B.},
year = {2021},
date = {2021},
journal = {Methods in Ecology and Evolution},
pages = {266--279},
volume = {12},
number = {2},
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url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13511},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13511},
langid = {en}
}
@article{deyle2013,
title = {Predicting climate effects on Pacific sardine},
author = {Deyle, Ethan R. and Fogarty, Michael and Hsieh, Chih-hao and Kaufman, Les and MacCall, Alec D. and Munch, Stephan B. and Perretti, Charles T. and Ye, Hao and Sugihara, George},
year = {2013},
month = {04},
date = {2013-04-16},
journal = {Proceedings of the National Academy of Sciences},
pages = {6430--6435},
volume = {110},
number = {16},
doi = {10.1073/pnas.1215506110},
url = {https://www.pnas.org/doi/full/10.1073/pnas.1215506110},
note = {Publisher: Proceedings of the National Academy of Sciences}
}
@article{mcnamara2019,
title = {Insights into coral reef benthic dynamics from nonlinear spatial forecasting},
author = {McNamara, Dylan E. and Cortale, Nick and Edwards, Clinton and Eynaud, Yoan and Sandin, Stuart A.},
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date = {2019-04-10},
journal = {Journal of The Royal Society Interface},
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number = {153},
doi = {10.1098/rsif.2019.0047},
url = {https://royalsocietypublishing.org/doi/10.1098/rsif.2019.0047},
note = {Publisher: Royal Society}
}
@article{brito-millán2019,
title = {Influence of aggregation on benthic coral reef spatio-temporal dynamics},
author = {{Brito-Millán}, Marlene and Werner, B. T. and Sandin, Stuart A. and McNamara, Dylan E.},
year = {2019},
month = {02},
date = {2019-02-20},
journal = {Royal Society Open Science},
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number = {2},
doi = {10.1098/rsos.181703},
url = {https://royalsocietypublishing.org/doi/10.1098/rsos.181703},
note = {Publisher: Royal Society}
}
@article{overholtz2009,
title = {A simulation model to explore the response of the Gulf of Maine food web to large-scale environmental and ecological changes},
author = {Overholtz, William and Link, Jason},
year = {2009},
month = {10},
date = {2009-10-10},
journal = {Ecological Modelling},
pages = {2491--2502},
volume = {220},
number = {19},
doi = {10.1016/j.ecolmodel.2009.06.034},
url = {https://www.sciencedirect.com/science/article/pii/S0304380009004463},
langid = {en}
}
@article{link2009,
title = {Response of balanced network models to large-scale perturbation: Implications for evaluating the role of small pelagics in the Gulf of Maine},
author = {Link, Jason and Col, Laurel and Guida, Vincent and Dow, David and {O{\textquoteright}Reilly}, John and Green, Jack and Overholtz, William and Palka, Debra and Legault, Chris and Vitaliano, Joseph and Griswold, Carolyn and Fogarty, Michael and Friedland, Kevin},
year = {2009},
month = {02},
date = {2009-02-10},
journal = {Ecological Modelling},
pages = {351--369},
volume = {220},
number = {3},
doi = {10.1016/j.ecolmodel.2008.10.009},
url = {https://www.sciencedirect.com/science/article/pii/S0304380008004973},
langid = {en}
}
@article{tam2017,
title = {Towards ecosystem-based management: identifying operational food-web indicators for marine ecosystems},
author = {Tam, Jamie C. and Link, Jason S. and Rossberg, Axel G. and Rogers, Stuart I. and Levin, Philip S. and Rochet, {Marie-Joëlle} and Bundy, Alida and Belgrano, Andrea and Libralato, Simone and Tomczak, Maciej and van de Wolfshaar, Karen and Pranovi, Fabio and Gorokhova, Elena and Large, Scott I. and Niquil, Nathalie and Greenstreet, Simon P. R. and Druon, Jean-Noel and Lesutiene, Jurate and Johansen, Marie and Preciado, Izaskun and Patricio, Joana and Palialexis, Andreas and Tett, Paul and Johansen, Geir O. and Houle, Jennifer and Rindorf, Anna},
year = {2017},
month = {10},
date = {2017-10-01},
journal = {ICES Journal of Marine Science},
pages = {2040--2052},
volume = {74},
number = {7},
doi = {10.1093/icesjms/fsw230},
url = {https://doi.org/10.1093/icesjms/fsw230}
}
@article{ross2021,
title = {Projecting regions of North Atlantic right whale, Eubalaena glacialis, habitat suitability in the Gulf of Maine for the year 2050},
author = {Ross, Camille H. and Pendleton, Daniel E. and Tupper, Benjamin and Brickman, David and Zani, Monica A. and Mayo, Charles A. and Record, Nicholas R.},
year = {2021},
month = {04},
date = {2021-04-28},
journal = {Elementa: Science of the Anthropocene},
pages = {00058},
volume = {9},
number = {1},
doi = {10.1525/elementa.2020.20.00058},
url = {https://doi.org/10.1525/elementa.2020.20.00058}
}
@article{ye2015a,
title = {Distinguishing time-delayed causal interactions using convergent cross mapping},
author = {Ye, Hao and Deyle, Ethan R. and Gilarranz, Luis J. and Sugihara, George},
year = {2015},
month = {10},
date = {2015-10-05},
journal = {Scientific Reports},
volume = {5},
number = {1},
doi = {10.1038/srep14750},
url = {http://dx.doi.org/10.1038/srep14750},
langid = {en}
}
@article{mcgowan2017,
title = {Predicting coastal algal blooms in southern California},
author = {McGowan, John A. and Deyle, Ethan R. and Ye, Hao and Carter, Melissa L. and Perretti, Charles T. and Seger, Kerri D. and de Verneil, Alain and Sugihara, George},
year = {2017},
date = {2017},
journal = {Ecology},
pages = {1419--1433},
volume = {98},
number = {5},
doi = {10.1002/ecy.1804},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ecy.1804},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.1804},
langid = {en}
}
@article{clark2015,
title = {Spatial convergent cross mapping to detect causal relationships from short time series},
author = {Clark, Adam Thomas and Ye, Hao and Isbell, Forest and Deyle, Ethan R. and Cowles, Jane and Tilman, G. David and Sugihara, George},
year = {2015},
date = {2015},
journal = {Ecology},
pages = {1174--1181},
volume = {96},
number = {5},
doi = {10.1890/14-1479.1},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1890/14-1479.1},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1890/14-1479.1},
langid = {en}
}
@article{munch2023,
title = {Recent developments in empirical dynamic modelling},
author = {Munch, Stephan B. and Rogers, Tanya L. and Sugihara, George},
year = {2023},
date = {2023},
journal = {Methods in Ecology and Evolution},
pages = {732--745},
volume = {14},
number = {3},
doi = {10.1111/2041-210X.13983},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13983},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.13983},
langid = {en}
}
@article{li2021,
title = {Beyond linearity, stability, and equilibrium: The edm package for empirical dynamic modeling and convergent cross-mapping in Stata},
author = {Li, Jinjing and Zyphur, Michael J. and Sugihara, George and Laub, Patrick J.},
year = {2021},
month = {03},
date = {2021-03-01},
journal = {The Stata Journal},
pages = {220--258},
volume = {21},
number = {1},
doi = {10.1177/1536867X211000030},
url = {https://doi.org/10.1177/1536867X211000030},
note = {Publisher: SAGE Publications},
langid = {en}
}
@article{link2002,
title = {Does food web theory work for marine ecosystems?},
author = {Link, J},
year = {2002},
date = {2002},
journal = {Marine Ecology Progress Series},
pages = {1--9},
volume = {230},
doi = {10.3354/meps230001},
url = {http://www.int-res.com/abstracts/meps/v230/p1-9/},
langid = {en}
}
@article{truesdell2016,
title = {Effects of spatial heterogeneity in growth and fishing effort on yield-per-recruit models: an application to the US Atlantic sea scallop fishery},
author = {Truesdell, Samuel B. and Hart, Deborah R. and Chen, Yong},
year = {2016},
month = {03},
date = {2016-03-01},
journal = {ICES Journal of Marine Science},
pages = {1062--1073},
volume = {73},
number = {4},
doi = {10.1093/icesjms/fsv238},
url = {https://doi.org/10.1093/icesjms/fsv238}
}
@article{hart2003,
title = {Yield- and biomass-per-recruit analysis for rotational fisheries, with an application to the Atlantic sea scallop (Placopecten magellanicus)},
author = {Hart, Dvora},
year = {2003},
month = {01},
date = {2003-01-01},
journal = {Fishery Bulletin - National Oceanic and Atmospheric Administration},
pages = {44--57},
volume = {101},
url = {https://www.researchgate.net/publication/279700466_Yield-_and_biomass-per-recruit_analysis_for_rotational_fisheries_with_an_application_to_the_Atlantic_sea_scallop_Placopecten_magellanicus}
}
@article{glaser2011,
title = {Detecting and forecasting complex nonlinear dynamics in spatially structured catch-per-unit-effort time series for North Pacific albacore (Thunnus alalunga)},
author = {Glaser, Sarah M. and Ye, Hao and Maunder, Mark and MacCall, Alec and Fogarty, Michael and Sugihara, George},
year = {2011},
month = {03},
date = {2011-03},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
pages = {400--412},
volume = {68},
number = {3},
doi = {10.1139/F10-160},
url = {https://cdnsciencepub.com/doi/10.1139/F10-160},
note = {Publisher: NRC Research Press}
}
@article{dixon1999,
title = {Episodic Fluctuations in Larval Supply},
author = {Dixon, Paul A. and Milicich, Maria J. and Sugihara, George},
year = {1999},
month = {03},
date = {1999-03-05},
journal = {Science},
pages = {1528--1530},
volume = {283},
number = {5407},
doi = {10.1126/science.283.5407.1528},
url = {https://www.science.org/doi/10.1126/science.283.5407.1528},
note = {Publisher: American Association for the Advancement of Science}
}
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