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references.bib
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@article{Aguiar2019RevBia,
title = {Revealing Biases in the Sampling of Ecological Interaction Networks},
author = {de Aguiar, Marcus A. M. and Newman, Erica A. and Pires, Mathias M. and Yeakel, Justin D. and Boettiger, Carl and Burkle, Laura A. and Gravel, Dominique and Jr, Paulo R. Guimar{\~a}es and O'Donnell, James L. and Poisot, Timoth{\'e}e and Fortin, Marie-Jos{\'e}e and Hembry, David H.},
year = {2019},
journal = {PeerJ},
volume = {7},
pages = {e7566},
publisher = {{PeerJ Inc.}},
issn = {2167-8359},
doi = {10.7717/peerj.7566},
langid = {english}
}
@article{Albouy2019MarFis,
title = {The Marine Fish Food Web Is Globally Connected},
author = {Albouy, Camille and Archambault, Philippe and Appeltans, Ward and Ara{\'u}jo, Miguel B. and Beauchesne, David and Cazelles, Kevin and Cirtwill, Alyssa R. and Fortin, Marie-Jos{\'e}e and Galiana, Nuria and Leroux, Shawn J. and Pellissier, Lo{\"i}c and Poisot, Timoth{\'e}e and Stouffer, Daniel B. and Wood, Spencer A. and Gravel, Dominique},
year = {2019},
journal = {Nature Ecology \& Evolution},
volume = {3},
number = {8},
pages = {1153--1161},
issn = {2397-334X},
doi = {10.1038/s41559-019-0950-y},
langid = {english}
}
@article{Banville2021ManJl,
title = {Mangal.Jl and {{EcologicalNetworks}}.Jl: {{Two}} Complementary Packages for Analyzing Ecological Networks in {{Julia}}},
author = {Banville, Francis and Vissault, Steve and Poisot, Timoth{\'e}e},
year = {2021},
journal = {Journal of Open Source Software},
volume = {6},
number = {61},
pages = {2721},
issn = {2475-9066},
doi = {10.21105/joss.02721},
langid = {english}
}
@article{Bascompte2007PlaMut,
title = {Plant-{{Animal Mutualistic Networks}}: {{The Architecture}} of {{Biodiversity}}},
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langid = {english}
}
@misc{Becker2021OptPre,
title = {Optimizing Predictive Models to Prioritize Viral Discovery in Zoonotic Reservoirs},
author = {Becker, Daniel J. and Albery, Gregory F. and Sjodin, Anna R. and Poisot, Timoth{\'e}e and Bergner, Laura M. and Dallas, Tad A. and Eskew, Evan A. and Farrell, Maxwell J. and Guth, Sarah and Han, Barbara A. and Simmons, Nancy B. and Stock, Michiel and Teeling, Emma C. and Carlson, Colin J.},
year = {2021},
pages = {2020.05.22.111344},
publisher = {{bioRxiv}},
doi = {10.1101/2020.05.22.111344},
chapter = {New Results},
langid = {english}
}
@misc{Bezanson2015JulFre,
title = {Julia: {{A Fresh Approach}} to {{Numerical Computing}}},
author = {Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B.},
year = {2015},
number = {arXiv:1411.1607},
eprint = {1411.1607},
eprinttype = {arxiv},
primaryclass = {cs},
publisher = {{arXiv}},
doi = {10.48550/arXiv.1411.1607},
archiveprefix = {arXiv}
}
@article{Blanchet2020CooNot,
title = {Co-Occurrence Is Not Evidence of Ecological Interactions},
author = {Blanchet, F. Guillaume and Cazelles, Kevin and Gravel, Dominique},
year = {2020},
journal = {Ecology Letters},
volume = {23},
number = {7},
pages = {1050--1063},
issn = {1461-0248},
doi = {10.1111/ele.13525},
langid = {english}
}
@article{Blaom2020MljJul,
title = {{{MLJ}}: {{A Julia}} Package for Composable Machine Learning},
author = {Blaom, Anthony D. and Kiraly, Franz and Lienart, Thibaut and Simillides, Yiannis and Arenas, Diego and Vollmer, Sebastian J.},
year = {2020},
journal = {Journal of Open Source Software},
volume = {5},
number = {55},
pages = {2704},
issn = {2475-9066},
doi = {10.21105/joss.02704},
langid = {english}
}
@article{Boakes2015InfSpe,
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langid = {english}
}
@article{Canard2012EmeStr,
title = {Emergence of {{Structural Patterns}} in {{Neutral Trophic Networks}}},
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langid = {english}
}
@article{CaraDonna2017IntRew,
title = {Interaction Rewiring and the Rapid Turnover of Plant\textendash Pollinator Networks},
author = {CaraDonna, Paul J. and Petry, William K. and Brennan, Ross M. and Cunningham, James L. and Bronstein, Judith L. and Waser, Nickolas M. and Sanders, Nathan J.},
year = {2017},
journal = {Ecology Letters},
volume = {20},
number = {3},
pages = {385--394},
issn = {1461-0248},
doi = {10.1111/ele.12740},
langid = {english}
}
@misc{CaraDonna2018DatInt,
title = {Data from: {{Interaction}} Rewiring and the Rapid Turnover of Plant-Pollinator Networks},
author = {CaraDonna, Paul J. and Petry, William K. and Brennan, Ross M. and Cunningham, James L. and Bronstein, Judith L. and Waser, Nickolas M. and Sanders, Nathan J.},
year = {2018},
doi = {10.5061/dryad.s91p4}
}
@article{Carlson2020WhaWou,
title = {What Would It Take to Describe the Global Diversity of Parasites?},
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number = {1939},
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publisher = {{Royal Society}},
doi = {10.1098/rspb.2020.1841}
}
@article{Cazelles2016TheSpe,
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number = {1},
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issn = {1874-1746},
doi = {10.1007/s12080-015-0281-9},
langid = {english}
}
@article{Closs1994SpaTem,
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}
@article{Connor2017UsiNul,
title = {Using Null Models to Infer Microbial Co-Occurrence Networks},
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langid = {english}
}
@article{deAguiar2019RevBia,
title = {Revealing Biases in the Sampling of Ecological Interaction Networks},
author = {{de Aguiar}, Marcus A.M. and Newman, Erica A. and Pires, Mathias M. and Yeakel, Justin D. and Boettiger, Carl and Burkle, Laura A. and Gravel, Dominique and Guimar{\~a}es, Paulo R. and O'Donnell, James L. and Poisot, Timoth{\'e}e and Fortin, Marie-Jos{\'e}e and Hembry, David H.},
year = {2019},
journal = {PeerJ},
volume = {7},
pages = {e7566},
issn = {2167-8359},
doi = {10.7717/peerj.7566},
langid = {english}
}
@article{Gauzens2013FooAgg,
title = {Food-Web Aggregation, Methodological and Functional Issues},
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volume = {122},
number = {11},
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publisher = {{[Nordic Society Oikos, Wiley]}},
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}
@article{Giacomuzzo2021FooWeb,
title = {Food Web Aggregation: Effects on Key Positions},
author = {Giacomuzzo, Emanuele and Jord{\'a}n, Ferenc},
year = {2021},
journal = {Oikos},
volume = {130},
number = {12},
pages = {2170--2181},
issn = {1600-0706},
doi = {10.1111/oik.08541},
langid = {english}
}
@article{Griffiths1998SamEff,
title = {Sampling Effort, Regression Method, and the Shape and Slope of Size\textendash Abundance Relations},
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langid = {english}
}
@article{Gupta2023HowMan,
title = {How Many Predator Guts Are Required to Predict Trophic Interactions?},
author = {Gupta, Anubhav and Figueroa H., David and O'Gorman, Eoin and Jones, Iwan and Woodward, Guy and Petchey, Owen L.},
year = {2023},
journal = {Food Webs},
volume = {34},
pages = {e00269},
issn = {2352-2496},
doi = {10.1016/j.fooweb.2022.e00269},
langid = {english}
}
@article{Hadfield2014TalTwo,
title = {A {{Tale}} of {{Two Phylogenies}}: {{Comparative Analyses}} of {{Ecological Interactions}}.},
author = {Hadfield, Jarrod D. and Krasnov, Boris R. and Poulin, Robert and Nakagawa, Shinichi},
year = {2014},
journal = {The American Naturalist},
volume = {183},
number = {2},
pages = {174--187},
publisher = {{The University of Chicago Press}},
issn = {0003-0147},
doi = {10.1086/674445}
}
@article{Havens1992ScaStr,
title = {Scale and {{Structure}} in {{Natural Food Webs}}},
author = {Havens, Karl},
year = {1992},
journal = {Science},
volume = {257},
number = {5073},
pages = {1107--1109},
publisher = {{American Association for the Advancement of Science}},
doi = {10.1126/science.257.5073.1107}
}
@misc{IntRew,
title = {Interaction Rewiring and the Rapid Turnover of Plant\textendash Pollinator Networks - {{CaraDonna}} - 2017 - {{Ecology Letters}} - {{Wiley Online Library}}},
howpublished = {https://onlinelibrary.wiley.com/doi/full/10.1111/ele.12740}
}
@misc{IntRewa,
title = {Interaction Rewiring and the Rapid Turnover of Plant\textendash Pollinator Networks - {{CaraDonna}} - 2017 - {{Ecology Letters}} - {{Wiley Online Library}}},
howpublished = {https://onlinelibrary.wiley.com/doi/full/10.1111/ele.12740}
}
@misc{IntRewb,
title = {Interaction Rewiring and the Rapid Turnover of Plant\textendash Pollinator Networks - {{CaraDonna}} - 2017 - {{Ecology Letters}} - {{Wiley Online Library}}},
howpublished = {https://onlinelibrary.wiley.com/doi/full/10.1111/ele.12740}
}
@misc{Johnson2021BayEst,
title = {Bayesian Estimation of Population Size and Overlap from Random Subsamples},
author = {Johnson, Erik K. and Larremore, Daniel B.},
year = {2021},
pages = {2021.07.06.451319},
publisher = {{bioRxiv}},
doi = {10.1101/2021.07.06.451319},
chapter = {New Results},
langid = {english}
}
@article{Jordano2016ChaEco,
title = {Chasing {{Ecological Interactions}}},
author = {Jordano, Pedro},
year = {2016},
journal = {PLOS Biology},
volume = {14},
number = {9},
pages = {e1002559},
publisher = {{Public Library of Science}},
issn = {1545-7885},
doi = {10.1371/journal.pbio.1002559},
langid = {english}
}
@article{Jordano2016SamNet,
title = {Sampling Networks of Ecological Interactions},
author = {Jordano, Pedro},
year = {2016},
journal = {Functional Ecology},
volume = {30},
number = {12},
pages = {1883--1893},
issn = {1365-2435},
doi = {10.1111/1365-2435.12763},
langid = {english}
}
@article{Joseph2020NeuHie,
title = {Neural Hierarchical Models of Ecological Populations},
author = {Joseph, Maxwell B.},
year = {2020},
journal = {Ecology Letters},
volume = {23},
number = {4},
pages = {734--747},
issn = {1461-0248},
doi = {10.1111/ele.13462},
langid = {english}
}
@article{Kenall2014OpeFut,
title = {An Open Future for Ecological and Evolutionary Data?},
author = {Kenall, Amye and Harold, Simon and Foote, Christopher},
year = {2014},
journal = {BMC Evolutionary Biology},
volume = {14},
number = {1},
pages = {66},
issn = {1471-2148},
doi = {10.1186/1471-2148-14-66}
}
@misc{Khoshraftar2022SurGra,
title = {A {{Survey}} on {{Graph Representation Learning Methods}}},
author = {Khoshraftar, Shima and An, Aijun},
year = {2022},
number = {arXiv:2204.01855},
eprint = {2204.01855},
eprinttype = {arxiv},
primaryclass = {cs},
publisher = {{arXiv}},
doi = {10.48550/arXiv.2204.01855},
archiveprefix = {arXiv}
}
@article{Koleff2003MeaBet,
title = {Measuring Beta Diversity for Presence\textendash Absence Data},
author = {Koleff, Patricia and Gaston, Kevin J. and Lennon, Jack J.},
year = {2003},
journal = {Journal of Animal Ecology},
volume = {72},
number = {3},
pages = {367--382},
issn = {1365-2656},
doi = {10.1046/j.1365-2656.2003.00710.x},
langid = {english}
}
@article{Kopelke2017FooStr,
title = {Food-Web Structure of Willow-Galling Sawflies and Their Natural Enemies across {{Europe}}},
author = {Kopelke, Jens-Peter and Nyman, Tommi and Cazelles, K{\'e}vin and Gravel, Dominique and Vissault, Steve and Roslin, Tomas},
year = {2017},
journal = {Ecology},
volume = {98},
number = {6},
pages = {1730--1730},
issn = {1939-9170},
doi = {10.1002/ecy.1832},
langid = {english}
}
@article{Li2021PerCom,
title = {Percolation on Complex Networks: {{Theory}} and Application},
author = {Li, Ming and Liu, Run-Ran and L{\"u}, Linyuan and Hu, Mao-Bin and Xu, Shuqi and Zhang, Yi-Cheng},
year = {2021},
journal = {Physics Reports},
series = {Percolation on Complex Networks: {{Theory}} and Application},
volume = {907},
pages = {1--68},
issn = {0370-1573},
doi = {10.1016/j.physrep.2020.12.003},
langid = {english}
}
@article{Li2021PerComa,
title = {Percolation on Complex Networks: {{Theory}} and Application},
author = {Li, Ming and Liu, Run-Ran and L{\"u}, Linyuan and Hu, Mao-Bin and Xu, Shuqi and Zhang, Yi-Cheng},
year = {2021},
journal = {Physics Reports},
series = {Percolation on Complex Networks: {{Theory}} and Application},
volume = {907},
pages = {1--68},
issn = {0370-1573},
doi = {10.1016/j.physrep.2020.12.003},
langid = {english}
}
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