CaN.bib

  @Manual{RStatisticalSoftware,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2020},
    url = {https://www.R-project.org/},
  }
  
  @article{hall2004towards,
  title={Towards ecosystem-based fisheries management},
  author={Hall, Stephen J and Mainprize, B},
  journal={Fish and Fisheries},
  volume={5},
  number={1},
  pages={1--20},
  year={2004},
  publisher={Wiley Online Library}
}

@article{fulton2014integrated,
  title={An integrated approach is needed for ecosystem based fisheries management: insights from ecosystem-level management strategy evaluation},
  author={Fulton, Elizabeth A and Smith, Anthony DM and Smith, David C and Johnson, Penelope},
  journal={PloS one},
  volume={9},
  number={1},
  pages={e84242},
  year={2014},
  publisher={Public Library of Science}
}

@article{Heymans2016,
   author = {Heymans, Johanna Jacomina and Coll, Marta and Link, Jason S. and Mackinson, Steven and Steenbeek, Jeroen and Walters, Carl and Christensen, Villy},
   title = {Best practice in {E}copath with {E}cosim food-web models for ecosystem-based management},
   journal = {Ecological Modelling},
   volume = {331},
   pages = {173-184},
   ISSN = {0304-3800},
   DOI = {http://dx.doi.org/10.1016/j.ecolmodel.2015.12.007},
   url = {http://www.sciencedirect.com/science/article/pii/S030438001500575X},
   year = {2016},
   type = {Journal Article}
}

@article{Polovina1984,
   author = {Polovina, Jeffrey J.},
   title = {An overview of the {E}copath model},
   journal = {Fishbyte},
   volume = {2},
   pages = {5-7},
   year = {1984},
   type = {Journal Article}
}

@techreport{Plaganyi2007,
   author = {Plagányi, Éva E.},
   title = {Models for an ecosystem approach to fisheries.},
   institution = {Food and Agriculture Organisation of the United Nations},
   year = {2007},
   type = {Report}
}

@article{satman2014rcaller,
  title={R{C}aller: A software library for calling {R} from {J}ava},
  author={Satman, M Hakan},
  journal={Journal of Advances in Mathematics and Computer Science},
  pages={2188--2196},
  year={2014}
}

@article{WGIBAR2020,
   author = {ICES},
   title = {Working group on the integrated assessments of the Barents Sea ({WGIBAR})},
   journal = {ICES Scientific Reports},
   volume = {2},
   number = {30},
   pages = {212pp},
   url = {https://doi.org/10.17895/ices.pub.5998},
   year = {2020},
   type = {Journal Article}
}

@inproceedings{eriksen2019working,
  title={The Working Group on the Integrated Assessments of the Barents Sea (WGIBAR)},
  author={Eriksen, E and Filin, AA and Bag{\o}ien, E and Benzik, AN and Bogstad, B and Dalpadado, P and Chetyrkin, AA and Dolgov, AV and Gj{\o}s{\ae}ter, H and Ingvaldsen, R and others},
  year={2019},
  organization={ICES}
}

@article{planque2019modelling,
  title={Modelling chance and necessity in natural systems},
  author={Planque, Benjamin and Mullon, Christian},
  journal={ICES Journal of Marine Science},
  year={2019}
}

@book{brondsted2012introduction,
  title={An introduction to convex polytopes},
  author={Brondsted, Arne},
  volume={90},
  year={2012},
  publisher={Springer Science \& Business Media}
}

@article{sugihara1990nonlinear,
  title={Nonlinear forecasting as a way of distinguishing chaos from measurement error in time series},
  author={Sugihara, George and May, Robert M},
  journal={Nature},
  volume={344},
  number={6268},
  pages={734},
  year={1990},
  publisher={Nature Publishing Group}
}

@article{dickey2014complex,
  title={Why the complex nature of integrated ecosystem assessments requires a flexible and adaptive approach},
  author={Dickey-Collas, Mark},
  journal={ICES Journal of Marine Science},
  volume={71},
  number={5},
  pages={1174--1182},
  year={2014},
  publisher={Oxford University Press}
}

@article{rockmann2015interaction,
  title={The interaction triangle as a tool for understanding stakeholder interactions in marine ecosystem based management},
  author={R{\"o}ckmann, Christine and van Leeuwen, Judith and Goldsborough, David and Kraan, Marloes and Piet, Gerjan},
  journal={Marine Policy},
  volume={52},
  pages={155--162},
  year={2015},
  publisher={Elsevier}
}

@article{hamalainen2015behavioural,
  title={Behavioural issues in environmental modelling--The missing perspective},
  author={H{\"a}m{\"a}l{\"a}inen, Raimo P},
  journal={Environmental Modelling \& Software},
  volume={73},
  pages={244--253},
  year={2015},
  publisher={Elsevier}
}

@article{beddington2007current,
  title={Current problems in the management of marine fisheries},
  author={Beddington, John R and Agnew, David J and Clark, Colin W},
  journal={science},
  volume={316},
  number={5832},
  pages={1713--1716},
  year={2007},
  publisher={American Association for the Advancement of Science}
}

@book{wgibar2017,
	author = {ICES},
	 title ={Report of the {W}orking {G}roup on the {I}ntegrated {A}ssessments of the {B}arents {S}ea ({WGIBAR})},
year = {2017},
series = {ICES CM, 2017/SSGIEA:04: 191p}
}

@article{dalpadado2014productivity,
  title={Productivity in the Barents Sea-response to recent climate variability},
  author={Dalpadado, Padmini and Arrigo, Kevin R and Hj{\o}llo, Solfrid S and Rey, Francisco and Ingvaldsen, Randi B and Sperfeld, Erik and van Dijken, Gert L and Stige, Leif C and Olsen, Are and Ottersen, Geir},
  journal={PloS one},
  volume={9},
  number={5},
  pages={e95273},
  year={2014},
  publisher={Public Library of Science}
}

@article{degnbol2006painting,
  title={Painting the floor with a hammer: technical fixes in fisheries management},
  author={Degnbol, Poul and Gislason, Henrik and Hanna, Susan and Jentoft, Svein and Nielsen, Jesper Raakj{\ae}r and Sverdrup-Jensen, Sten and Wilson, Douglas Clyde},
  journal={Marine Policy},
  volume={30},
  number={5},
  pages={534--543},
  year={2006},
  publisher={Elsevier}
}

@book{monod1971chance,
  title={Chance and Necessity: an Essay on the Natural Philosophy of Modern Biology},
  author={Monod, Jacques},
  translator  = {Austryn Wainhouse},
  publisher = {Collins-Fontana Books},
  year={1971}
}

@article{planque2014non,
  title={Non-deterministic modelling of food-web dynamics},
  author={Planque, Benjamin and Lindstr{\o}m, Ulf and Subbey, Sam},
  journal={PloS one},
  volume={9},
  number={10},
  pages={e108243},
  year={2014},
  publisher={Public Library of Science}
}

@article{harwood2003coping,
  title={Coping with uncertainty in ecological advice: lessons from fisheries},
  author={Harwood, John and Stokes, Kevin},
  journal={Trends in Ecology \& Evolution},
  volume={18},
  number={12},
  pages={617--622},
  year={2003},
  publisher={Elsevier}
}

@article{planque2015projecting,
  title={Projecting the future state of marine ecosystems,“la grande illusion”?},
  author={Planque, Benjamin},
  journal={ICES Journal of Marine Science},
  volume={73},
  number={2},
  pages={204--208},
  year={2015},
  publisher={Oxford University Press}
}

@article{lindstrom2017multiple,
  title={Multiple Patterns of Food Web Dynamics Revealed by a Minimal Non-deterministic Model},
  author={Lindstr{\o}m, Ulf and Planque, Benjamin and Subbey, Sam},
  journal={Ecosystems},
  volume={20},
  number={1},
  pages={163--182},
  year={2017},
  publisher={Springer}
}

@article{stephenson2016integrating,
  title={Integrating fishers’ knowledge research in science and management},
  author={Stephenson, Robert L and Paul, Stacey and Pastoors, Martin A and Kraan, Marloes and Holm, Petter and Wiber, Melanie and Mackinson, Steven and Dankel, Dorothy J and Brooks, Kate and Benson, Ashleen},
  journal={ICES Journal of Marine Science},
  volume={73},
  number={6},
  pages={1459--1465},
  year={2016},
  publisher={Oxford University Press}
}


@article{lehuta2016,
  title = {Reconciling Complex System Models and Fisheries Advice: {{Practical}} Examples and Leads},
  shorttitle = {Reconciling Complex System Models and Fisheries Advice},
  author = {Lehuta, Sigrid and Girardin, Rapha{\"e}l and Mah{\'e}vas, St{\'e}phanie and {Travers-Trolet}, Morgane and Vermard, Youen},
  year = {2016},
  month = apr,
  volume = {29},
  pages = {208},
  issn = {0990-7440, 1765-2952},
  doi = {10.1051/alr/2016022},
  copyright = {\textcopyright{} EDP Sciences 2016},
  file = {/home/hilaire.drouineau/Documents/Bordeaux/pdf/Lehuta et al_2016_Reconciling complex system models and fisheries advice.pdf},
  journal = {Aquatic Living Resources},
  language = {en},
  number = {2}
}

@book{plummer2010,
  title = {Coda: {{Output}} Analysis and Diagnostics for {{MCMC}}},
  author = {Plummer, Martin and Best, Nicky and Cowles, Kate and Vines, Karen},
  year = {2010}
}

@Manual{ma2020,
    title = {{S}ym{E}ngine: Interface to the {S}ym{E}ngine Library},
    author = {Jialin Ma and Isuru Fernando and Xin Chen},
    year = {2020},
    note = {R package version 0.1.0},
    url = {https://github.com/symengine/symengine.R},
  }
  
@Manual{konis2020,
    title = {lpSolve{API}: R Interface to lp{S}olve},
    author = { Kjell Konis and Florian Schwendinger},
    year = {2020},
    note = {R package version 5.5.2.0-17.7},
    url = {https://CRAN.R-project.org/package=lpSolveAPI},
  }
  
@Article{eddelbuettel2017,
    title = {{Extending {R} with {C++}: A Brief Introduction to Rcpp}},
    author = {Dirk Eddelbuettel and James Joseph Balamuta},
    journal = {PeerJ Preprints},
    year = {2017},
    month = {aug},
    volume = {5},
    pages = {e3188v1},
    issn = {2167-9843},
    url = {https://doi.org/10.7287/peerj.preprints.3188v1},
    doi = {10.7287/peerj.preprints.3188v1},}

@Article{bates2013,
    title = {Fast and Elegant Numerical Linear Algebra Using the {RcppEigen} Package},
    author = {Douglas Bates and Dirk Eddelbuettel},
    journal = {Journal of Statistical Software},
    year = {2013},
    volume = {52},
    number = {5},
    pages = {1--24},
    url = {http://www.jstatsoft.org/v52/i05/},
},

@Manual{benham2020,
    title = {Uniform distribution over a convex polytope},
    author = {Tim Benham},
    year = {2020},
    note = { MATLAB Central File Exchange},
    url = {https://www.mathworks.com/matlabcentral/fileexchange/34208-uniform-distribution-over-a-convex-polytope},
}

@article{andersen2007,
  title = {Hit and {R}un as a Unifying Device},
  author = {Andersen, Hans C. and Diaconis, Persi},
  year = {2007},
  volume = {148},
  pages = {5--28},
  file = {/home/hilaire.drouineau/Documents/Bordeaux/pdf/Andersen_Diaconis_2007_Hit and run as a unifying device.pdf},
  journal = {Journal de la {S}oci\'et\'e {F}ran\c{c}aise de {S}tatistique},
  number = {4}
}

@article{laddha2020,
  title = {Convergence of {{Gibbs Sampling}}: {{Coordinate Hit}}-and-{{Run Mixes Fast}}},
  shorttitle = {Convergence of {{Gibbs Sampling}}},
  author = {Laddha, Aditi and Vempala, Santosh},
  year = {2020},
  month = sep,
  archivePrefix = {arXiv},
  eprint = {2009.11338},
  eprinttype = {arxiv},
  file = {/home/hilaire.drouineau/Documents/Bordeaux/pdf/Laddha_Vempala_2020_Convergence of Gibbs Sampling.pdf;/home/hilaire.drouineau/Documents/Bordeaux/zotero/storage/A2G377J7/Laddha et Vempala - 2020 - Convergence of Gibbs Sampling Coordinate Hit-and-.pdf},
  journal = {arXiv:2009.11338 [cs]},
  primaryClass = {cs}
}

@article{smith1984,
  title = {Efficient {{Monte Carlo Procedures}} for {{Generating Points Uniformly Distributed}} over {{Bounded Regions}}},
  author = {Smith, Robert L.},
  year = {1984},
  month = dec,
  volume = {32},
  pages = {1296--1308},
  publisher = {{INFORMS}},
  issn = {0030-364X},
  doi = {10.1287/opre.32.6.1296},
  file = {/home/hilaire.drouineau/Documents/Bordeaux/pdf/Smith_1984_Efficient Monte Carlo Procedures for Generating Points Uniformly Distributed.pdf},
  journal = {Operations Research},
  number = {6}
}



@article{saccenti2016a,
  title = {Approaches to {{Sample Size Determination}} for {{Multivariate Data}}: {{Applications}} to {{PCA}} and {{PLS}}-{{DA}} of {{Omics Data}}},
  shorttitle = {Approaches to {{Sample Size Determination}} for {{Multivariate Data}}},
  author = {Saccenti, Edoardo and Timmerman, Marieke E.},
  year = {2016},
  month = aug,
  volume = {15},
  pages = {2379--2393},
  publisher = {{American Chemical Society}},
  issn = {1535-3893},
  doi = {10.1021/acs.jproteome.5b01029},
  journal = {Journal of Proteome Research},
  number = {8}
}

 @Book{wickam2016,
    author = {Hadley Wickham},
    title = {ggplot2: {E}legant {G}raphics for {D}ata {A}nalysis},
    publisher = {Springer-Verlag New York},
    year = {2016},
    isbn = {978-3-319-24277-4},
    url = {https://ggplot2.tidyverse.org},
  }
@Article{glenn2012,
  title = {Trust in the Fisheries Scientific Community},
  author = {Helen Glenn and Diana Tingley and Sonia {S{\a'a}nchez Maro{\~n}o} and Dennis Holm and Laurence Kell and Gurpreet Padda and Ingi {Runar Edvardsson} and Johann Asmundsson and Alexis Conides and Kostas Kapiris and Mintewab Bezabih and Premachandra Wattage and Sakari Kuikka},
  date = {2012-01-01},
  journaltitle = {Marine Policy},
  shortjournal = {Marine Policy},
  volume = {36},
  pages = {54--72},
  issn = {0308-597X},
  doi = {10.1016/j.marpol.2011.03.008},
  file = {/home/hilaire.drouineau/Documents/Bordeaux/pdf/Glenn et al_2012_Trust in the fisheries scientific community.pdf},
  langid = {english},
  number = {1},
}
@Article{devos2011,
  title = {Trust Relationships between Fishers and Government: {{New}} Challenges for the Co-Management Arrangements in the {{Dutch}} Flatfish Industry},
  shorttitle = {Trust Relationships between Fishers and Government},
  author = {Birgit I. {de Vos} and Jan P. M. {van Tatenhove}},
  date = {2011-03-01},
  journaltitle = {Marine Policy},
  shortjournal = {Marine Policy},
  volume = {35},
  pages = {218--225},
  issn = {0308-597X},
  doi = {10.1016/j.marpol.2010.10.002},
  file = {/home/hilaire.drouineau/Documents/Bordeaux/pdf/de Vos_van Tatenhove_2011_Trust relationships between fishers and government.pdf},
  langid = {english},
  number = {2},
  options = {useprefix=true},
}
@Article{smith1990,
  title = {Chaos in Fisheries Management},
  author = {M. Estellie Smith},
  date = {1990},
  journaltitle = {Maritime Anthropological Studies},
  volume = {3},
  pages = {1--13},
  number = {2},
}

@techreport{BlanchardEcopath,
   author = {Blanchard, J.L. and Pinnegar, J.K. and Mackinson, S.},
   title = {Exploring marine mammal-fishery interactions using {E}copath with {E}cosim: modelling the Barents Sea Ecosystem},
   institution = {CEFAS},
   number = {117},
   year = {2002},
   type = {Report}
}


@article{thompson2012,
	title = {Food webs: reconciling the structure and function of biodiversity},
	volume = {27},
	issn = {0169-5347},
	shorttitle = {Food webs},
	url = {https://www.sciencedirect.com/science/article/pii/S0169534712002005},
	doi = {10.1016/j.tree.2012.08.005},
	language = {en},
	number = {12},
	urldate = {2021-05-04},
	journal = {Trends in Ecology \& Evolution},
	author = {Thompson, Ross M. and Brose, Ulrich and Dunne, Jennifer A. and Hall, Robert O. and Hladyz, Sally and Kitching, Roger L. and Martinez, Neo D. and Rantala, Heidi and Romanuk, Tamara N. and Stouffer, Daniel B. and Tylianakis, Jason M.},
	month = dec,
	year = {2012},
	pages = {689--697},
	file = {Thompson et al_2012_Food webs.pdf:/home/hilaire.drouineau/Documents/Bordeaux/pdf/Thompson et al_2012_Food webs.pdf:application/pdf}
}