%% This BibTeX bibliography file was created using BibDesk.
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@article{deBInfer,
    title = {{deBInfer}: Bayesian inference for dynamical models of biological systems},
    author = {Philipp H Boersch-Supan and Sadie J Ryan and Leah R Johnson},
    journal = {arXiv},
    year = {2016},
    volume = {1605.00021},
    url = {https://arxiv.org/abs/1605.00021},
  }

@article{rosenblum2010deadly,
    author = {Rosenblum, Erica Bree and Voyles, Jamie and Poorten, Thomas J and Stajich, Jason E},
    journal = {PLoS Pathogens},
    title = {The Deadly Chytrid Fungus: A Story of an Emerging Pathogen},
    year = {2010},
    month = {01},
    volume = {6},
    pages = {1-3},
    abstract = {},
    number = {1},
    doi = {10.1371/journal.ppat.1000550}
}

@Manual{devtools,
    title = {devtools: Tools to Make Developing R Packages Easier},
    author = {Hadley Wickham and Winston Chang},
    year = {2016},
    note = {R package version 1.10.0, http://CRAN.R-project.org/package=devtools},
    url = {},
  }

@Manual{filzbach,
    title = {Fit complex models to hetereogenous data: Bayesian and likelihood analysis made easy},
    author = {Drew Purves and Vassily Lyutsarev},
    year = {2016},
    note = {http://research.microsoft.com/en-us/um/cambridge/groups/science/tools/filzbach/filzbach.htm [accessed 06 September 2016]},
    url = {},
  }

@Manual{baseR,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2015},
    note = {http://www.R-project.org/},
  }

@manual{truncdist,
    title = {truncdist: Truncated Random Variables},
    author = {Frederick Novomestky and Saralees Nadarajah},
    year = {2012},
    note = {R package version 1.0-1, http://CRAN.R-project.org/package=truncdist},
    url = {},
  }

@article{stan,
    title = {Stan: A probabilistic programming language},
    author = {Bob Carpenter and Andrew Gelman and Matt Hoffman and Daniel Lee and Ben Goodrich and Michael Betancourt and Michael A. Brubaker and Jiqiang Guo and Peter Li and Allen Riddell},
    journal = {Journal of Statistical Software},
    year = {2016},
    volume = {in press},
  }

@article{coda,
    title = {CODA: Convergence Diagnosis and Output Analysis for {MCMC}},
    author = {Martyn Plummer and Nicky Best and Kate Cowles and Karen Vines},
    journal = {R News},
    year = {2006},
    volume = {6},
    number = {1},
    pages = {7--11},
    url = {http://CRAN.R-project.org/doc/Rnews/},
    pdf = {http://CRAN.R-project.org/doc/Rnews/Rnews_2006-1.pdf},
  }

@article{teixeira2014new,
	Author = {Teixeira, Carlos MGL and Sousa, T{\^a}nia and Marques, Gon{\c{c}}alo M and Domingos, Tiago and Kooijman, Sebastiaan ALM},
	Date-Added = {2015-12-18 21:26:16 +0000},
	Date-Modified = {2015-12-18 21:26:16 +0000},
	Journal = {Journal of Sea Research},
	Pages = {117--127},
	Publisher = {Elsevier},
	Title = {A new perspective on the growth pattern of the Wandering Albatross (Diomedea exulans) through DEB theory},
	Volume = {94},
	Year = {2014}}

@Manual{PBSddesolve,
  title = {PBSddesolve: Solver for Delay Differential Equations},
  author = {Alex Couture-Beil and Jon T. Schnute and Rowan Haigh and Nicholas Boers and Simon N. Wood and Ben J. Cairns},
  year = {2014},
  note = {R package version 1.11.29, http://CRAN.R-project.org/package=PBSddesolve},
  url = {http://CRAN.R-project.org/package=PBSddesolve},
  }

@book{brooks2011handbook,
	Author = {Brooks, Steve and Gelman, Andrew and Jones, Galin and Meng, Xiao-Li},
	Address = {Boca Raton, FL},
	Date-Added = {2015-12-17 20:38:54 +0000},
	Date-Modified = {2015-12-17 20:38:54 +0000},
	Publisher = {CRC Press},
	Title = {Handbook of Markov Chain Monte Carlo},
	Year = {2011}}

@article{lika2011covariation,
	Author = {Lika, Konstadia and Kearney, Michael R and Freitas, V{\^a}nia and van der Veer, Henk W and van der Meer, Jaap and Wijsman, Johannes WM and Pecquerie, Laure and Kooijman, Sebastiaan ALM},
	Date-Added = {2015-12-17 19:35:44 +0000},
	Date-Modified = {2015-12-17 19:35:44 +0000},
	Journal = {Journal of Sea Research},
	Number = {4},
	Pages = {270--277},
	Publisher = {Elsevier},
	Title = {The ``covariation method'' for estimating the parameters of the standard Dynamic Energy Budget model I: philosophy and approach},
	Volume = {66},
	Year = {2011}}

@book{clark2007models,
	Author = {Clark, James Samuel},
	Address = {Princeton, New Jersey, USA},
	Date-Added = {2015-12-16 23:05:00 +0000},
	Date-Modified = {2015-12-16 23:05:00 +0000},
	Publisher = {Princeton University Press},
	Title = {Models for Ecological Data: An Introduction},
	Year = {2007}}

@article{tarantola1982inverse,
	Author = {Tarantola, Albert and Valette, Bernard},
	Date-Added = {2015-12-16 22:11:52 +0000},
	Date-Modified = {2015-12-16 22:12:09 +0000},
	Journal = {Journal of Geophysics},
	Number = {3},
	Pages = {150--170},
	Title = {Inverse problems = quest for information},
	Volume = {50},
	Year = {1982}}

@book{kooijman2010dynamic,
	Author = {Kooijman, Sebastiaan Adriaan Louis Maria},
	Date-Added = {2015-12-14 20:22:51 +0000},
	Date-Modified = {2015-12-14 20:23:07 +0000},
	Publisher = {Cambridge University Press},
	Title = {Dynamic energy budget theory for metabolic organisation},
	Year = {2010}}

@book{aster2011parameter,
	Author = {Aster, Richard C and Borchers, Brian and Thurber, Clifford H},
	Address = {Amsterdam},
	Date-Added = {2015-12-14 20:11:47 +0000},
	Date-Modified = {2015-12-14 20:12:30 +0000},
	Edition = {2nd},
	Publisher = {Academic Press},
	Title = {Parameter Estimation and Inverse Problems},
	Year = {2011}}

@article{voyles2012temperature,
	Author = {Voyles, Jamie and Johnson, Leah R and Briggs, Cheryl J and Cashins, Scott D and Alford, Ross A and Berger, Lee and Skerratt, Lee F and Speare, Rick and Rosenblum, Erica Bree},
	Date-Added = {2015-12-14 19:34:21 +0000},
	Date-Modified = {2015-12-14 19:34:21 +0000},
	Journal = {Ecology and Evolution},
	Number = {9},
	Pages = {2241--2249},
	Publisher = {Wiley Online Library},
	Title = {Temperature alters reproductive life history patterns in \emph{Batrachochytrium dendrobatidis}, a lethal pathogen associated with the global loss of amphibians},
	Volume = {2},
	Year = {2012}}

@article{johnson2013bayesian,
	Author = {Johnson, Leah R and Pecquerie, Laure and Nisbet, Roger M},
	Date-Added = {2015-12-14 19:33:13 +0000},
	Date-Modified = {2015-12-14 19:33:13 +0000},
	Journal = {Ecology},
	Number = {4},
	Pages = {882--894},
	Title = {Bayesian inference for bioenergetic models},
	Volume = {94},
	Year = {2013}}

@article{smith2015inferred,
	Author = {Smith, Matthew J and Tittensor, Derek P and Lyutsarev, Vassily and Murphy, Eugene},
	Date-Added = {2015-12-14 19:27:27 +0000},
	Date-Modified = {2015-12-14 19:27:27 +0000},
	Journal = {Journal of Geophysical Research: Oceans},
	Number = {10},
	Pages = {7067--7090},
	Publisher = {Wiley Online Library},
	Title = {Inferred support for disturbance-recovery hypothesis of {North Atlantic} phytoplankton blooms},
	Volume = {120},
	Year = {2015}}

@article{poole2000inference,
	Author = {Poole, David and Raftery, Adrian E},
	Date-Added = {2015-12-14 19:26:04 +0000},
	Date-Modified = {2015-12-14 19:26:04 +0000},
	Journal = {Journal of the American Statistical Association},
	Number = {452},
	Pages = {1244--1255},
	Publisher = {Taylor \& Francis Group},
	Title = {Inference for deterministic simulation models: the {B}ayesian melding approach},
	Volume = {95},
	Year = {2000}}

@article{coelho2011bayesian,
	Author = {Coelho, Flavio Code{\c{c}}o and Code{\c{c}}o, Claudia Torres and Gomes, M Gabriela M},
	Date-Added = {2015-12-14 19:25:23 +0000},
	Date-Modified = {2015-12-14 19:25:23 +0000},
	Journal = {PloS one},
	Number = {5},
	Pages = {e19616},
	Publisher = {Public Library of Science},
	Title = {A {B}ayesian framework for parameter estimation in dynamical models},
	Volume = {6},
	Year = {2011}}

@article{lonergan2014data,
	Author = {Lonergan, Mike},
	Date-Added = {2015-12-08 17:09:44 +0000},
	Date-Modified = {2015-12-08 17:09:44 +0000},
	Journal = {Trends in Ecology \& Evolution},
	Pages = {301--302},
	Title = {Data availability constrains model complexity, generality, and utility: a response to Evans et al},
	Volume = {29},
	Year = {2014}}

@article{evans2013simple,
	Author = {Evans, Matthew R and Grimm, Volker and Johst, Karin and Knuuttila, Tarja and de Langhe, Rogier and Lessells, Catherine M and Merz, Martina and O'Malley, Maureen A and Orzack, Steve H and Weisberg, Michael and Wilkinson, Darren and Wolkenhauer, Olaf and Benton, Tim},
	Date-Added = {2015-12-08 17:08:31 +0000},
	Date-Modified = {2015-12-08 17:08:31 +0000},
	Journal = {Trends in Ecology \& Evolution},
	Number = {10},
	Pages = {578--583},
	Publisher = {Elsevier},
	Title = {Do simple models lead to generality in ecology?},
	Volume = {28},
	Year = {2013}}

@book{smith2011an,
	Address = {New York, NY},
	Author = {Smith, Hal},
	Date-Added = {2015-12-07 23:17:49 +0000},
	Date-Modified = {2015-12-07 23:17:49 +0000},
	Isbn = {978-1-4419-7645-1},
	Publisher = {Springer Verlag},
	Title = {An Introduction to Delay Differential Equations with Applications to the Life Sciences},
	Year = {2011}}

@book{jones2003differential,
	Address = {Boca Raton, FL},
	Author = {Jones, D. S.},
	Date-Added = {2015-12-07 23:15:23 +0000},
	Date-Modified = {2015-12-07 23:15:23 +0000},
	Isbn = {1584882964},
	Publisher = {Chapman \& Hall},
	Title = {Differential Equations and Mathematical Biology},
	Year = {2003}}

@article{marquet2014theory,
	Author = {Marquet, Pablo A and Allen, Andrew P and Brown, James H and Dunne, Jennifer A and Enquist, Brian J and Gillooly, James F and Gowaty, Patricia A and Green, Jessica L and Harte, John and Hubbell, Steve P and others},
	Date-Added = {2015-12-06 23:47:35 +0000},
	Date-Modified = {2015-12-06 23:47:35 +0000},
	Journal = {BioScience},
	Number = {8},
	Pages = {701--710},
	Publisher = {Oxford University Press},
	Title = {On theory in ecology},
	Volume = {64},
	Year = {2014}}

@article{soetaert2010solving,
	Author = {Soetaert, KER and Petzoldt, Thomas and Setzer, R Woodrow},
	Date-Added = {2015-12-06 23:29:36 +0000},
	Date-Modified = {2015-12-06 23:30:27 +0000},
	Journal = {Journal of Statistical Software},
	Number = {9},
	Pages = {1--25},
	Title = {Solving differential equations in {R}: package {deSolve}},
	Volume = {33},
	Year = {2010}}
	
@manual{soetaert2009r,
  title={R package desolve, writing code in compiled languages},
  author={Soetaert, Karline and Petzoldt, Thomas and Setzer, R Woodrow},
  note={R package vignette, URL http://CRAN. R-project. org/package= deSolve},
  year={2009}
}

@article{brewer2008fitting,
	Author = {Brewer, Daniel and Barenco, Martino and Callard, Robin and Hubank, Michael and Stark, Jaroslav},
	Journal = {Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences},
	Number = {1865},
	Pages = {519--544},
	Title = {Fitting ordinary differential equations to short time course data},
	Volume = {366},
	Year = {2008}}

@article{kermack1927contribution,
	Author = {Kermack, William O and McKendrick, Anderson G},
	Journal = {Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences},
	Number = {772},
	Pages = {700--721},
	Title = {A contribution to the mathematical theory of epidemics},
	Volume = {115},
	Year = {1927}}

@article{volterra1926fluctuations,
	Author = {Volterra, Vito},
	Journal = {Nature},
	Pages = {558--560},
	Title = {Fluctuations in the abundance of a species considered mathematically},
	Volume = {118},
	Year = {1926}}
	
@article{he2009plug,
  title={Plug-and-play inference for disease dynamics: measles in large and small populations as a case study},
  author={He, Daihai and Ionides, Edward L and King, Aaron A},
  journal={Journal of the Royal Society Interface},
  year={2009},
  publisher={The Royal Society}
}

@article{chkrebtii2013bayesian,
  title={Bayesian Solution Uncertainty Quantification for Differential Equations},
  author={Chkrebtii, Oksana A and Campbell, David A and Calderhead, Ben and Girolami, Mark A},
  journal={arXiv preprint arXiv:1306.2365},
  year={2015}
}

@article{king2016pomp,
  title={pomp: Statistical inference for partially observed Markov processes (R package)},
  author={King, AA and Ionides, EL and Bret{\'o}, CM and Ellner, S and Kendall, B and Wearing, H and Ferrari, MJ and Lavine, M and Reuman, DC},
  journal={Journal of Statistical Software},
  year={in press}
}

@article{horbelt2002parameter,
  title={Parameter estimation in nonlinear delayed feedback systems from noisy data},
  author={Horbelt, Werner and Timmer, Jens and Voss, HU},
  journal={Physics Letters A},
  volume={299},
  number={5},
  pages={513--521},
  year={2002}
}
@article{baker2005computational,
  title={Computational approaches to parameter estimation and model selection in immunology},
  author={Baker, Christopher TH and Bocharov, GA and Ford, Judith M and Lumb, Patricia M and Norton, Stewart J and Paul, CAH and Junt, Tobias and Krebs, Philippe and Ludewig, Burkhard},
  journal={Journal of Ccomputational and Applied mathematics},
  volume={184},
  number={1},
  pages={50--76},
  year={2005}
}
@article{toni2009approximate,
  title={Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems},
  author={Toni, Tina and Welch, David and Strelkowa, Natalja and Ipsen, Andreas and Stumpf, Michael PH},
  journal={Journal of the Royal Society Interface},
  volume={6},
  number={31},
  pages={187--202},
  year={2009},
  publisher={The Royal Society}
}
@incollection{liu2001combined,
  title={Combined parameter and state estimation in simulation-based filtering},
  author={Liu, Jane and West, Mike},
  booktitle={Sequential Monte Carlo methods in practice},
  pages={197--223},
  year={2001},
  publisher={Springer}
}
@article{andrieu2010particle,
  title={Particle markov chain monte carlo methods},
  author={Andrieu, Christophe and Doucet, Arnaud and Holenstein, Roman},
  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume={72},
  number={3},
  pages={269--342},
  year={2010},
  publisher={Wiley Online Library}
}