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simecol.bib
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@Manual{Rcore2006,
Title = {\proglang{R}: A Language and Environment for Statistical
Computing},
Address = {Vienna, Austria},
Author = {{\proglang{R} Development Core Team}},
Note = {{ISBN} 3-900051-07-0},
Organization = {R Foundation for Statistical Computing},
Year = {2006},
Url = {http://www.R-project.org}
}
@Manual{Rexts2006,
Title = {Writing \proglang{R} Extensions},
Address = {Vienna, Austria},
Author = {{\proglang{R} Development Core Team}},
Note = {{ISBN} 3-900051-11-9},
Organization = {R Foundation for Statistical Computing},
Year = {2006},
Url = {http://www.R-project.org}
}
@Manual{minqa,
Title = {{minqa}: {D}erivative-free optimization algorithms by quadratic
approximation},
Author = {Douglas Bates and Katharine M. Mullen and John C. Nash and Ravi Varadhan},
Note = {{R} package version 1.2.4},
Year = {2014},
Url = {http://CRAN.R-project.org/package=minqa}
}
@InProceedings{Bengtsson2003,
Title = {The \pkg{R.oo} Package -- Object-Oriented Programming with
References Using Standard \proglang{R} Code},
Author = {Bengtsson, Henrik},
Booktitle = {Proceedings of the 3rd International Workshop on
Distributed Statistical Computing {(DSC} 2003)},
Year = {2003},
Address = {Vienna, Austria},
Editor = {Kurt Hornik and Friedrich Leisch and Achim Zeileis},
Note = {ISSN 1609-395X},
Pages = {1--18},
Language = {english},
Url = {http://www.maths.lth.se/help/R/R.oo/}
}
@Article{Benz2001a,
Title = {{ECOBAS} - Modelling and Documentation},
Author = {J. Benz and R. Hoch and T. Legovic},
Journal = {Ecological Modelling},
Year = {2001},
Pages = {3--15},
Volume = {138}
}
@Article{Blasius1999,
Title = {Complex Dynamics and Phase Synchronization in Spatially
Extended Ecological Systems},
Author = {Blasius, Bernd and Huppert, Amit and Stone, Lewi},
Journal = {Nature},
Year = {1999},
Pages = {354--359},
Volume = {399},
Abstract = {chaos UPCA model Lotka Volterra grid},
Language = {english}
}
@Book{Bolker2007,
Title = {Ecological Models and Data in \proglang{R}},
Author = {Bolker, Ben},
Publisher = {Princeton University Press},
Year = {in prep.},
Address = {Princeton}
}
@Article{Bossel1992,
Title = {Real-structure Process Description as the Basis of
Understanding Ecosystems and Their Development},
Author = {Bossel, Hartmut},
Journal = {Ecological Modelling},
Year = {1992},
Month = sep,
Number = {1-4},
Pages = {261--276},
Volume = {63}
}
@Article{Bottrell1976,
Title = {A Review of Some Problems in Zooplankton Production Studies},
Author = {Bottrell, H. H. and Duncan, A. and Gliwicz, Z. M. and
Grygierek, E. and Herzig, A. and
Hillbricht-Ilkowska, A. and Kurasawa, H. and
Larsson, P. and Weglenska, T.},
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Year = {1976},
Pages = {419--456},
Volume = {24},
Abstract = {dependence of egg development time (D) from temperature, IBP data},
Language = {english}
}
@Unpublished{Chambers2001,
Title = {Classes and Methods in the \proglang{S} Language},
Author = {Chambers, John M.},
Note = {Bell Laboratories, Lucent Technologies August 9, 2001},
Year = {2001},
Language = {english},
Url = {http://www.omegahat.net/RSMethods/Intro.pdf}
}
@Article{Chambers2000,
Title = {Users, Programmers, and Statistical Software},
Author = {Chambers, John M.},
Journal = {Journal of Computational and Graphical Statistics},
Year = {2000},
Number = {3},
Pages = {404--422},
Volume = {9}
}
@Article{Cribari-Neto1999,
Title = {\proglang{R}: Yet Another Econometric Programming
Environment},
Author = {Francisco Cribari-Neto and Spyros G. Zarkos},
Journal = {Journal of Applied Econometrics},
Year = {1999},
Number = {3},
Pages = {319--329},
Volume = {14}
}
@Article{Dunning1995,
Title = {Spatially Explicit Population Models: Current Forms and Uses},
Author = {Dunning, J. B. Jr. and D. J. Stewart and B. J. Danielson
and B. R. Noon and T. L. Root and R. H. Lamberson
and E. E. Stevens},
Journal = {Ecological Applications},
Year = {1995},
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Volume = {5}
}
@Book{Fowler1997,
Title = {{UML} Distilled. Applying the Standard Object Modelling
Language},
Author = {Fowler, Martin and Scott, Kendall},
Publisher = {Addison Wesley},
Year = {1997},
Language = {english},
Pages = {1--208}
}
@Article{Fussmann2003,
Title = {Evolution as a Critical Component of Plankton Dynamics},
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Year = {2003},
Pages = {1015--1022},
Volume = {270}
}
@Article{Gardner1970,
Title = {The Fantastic Combinations of {John Conway's} New Solitaire Game 'Life'},
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Volume = {223}
}
@Article{Gentleman2000,
Title = {Lexical Scope and Statistical Computing},
Author = {Gentleman, Robert and Ihaka, Ross},
Journal = {Journal of Computational and Graphical Statistics},
Year = {2000},
Number = {3},
Pages = {491--508},
Volume = {9},
Abstract = {Programming environments such as S and Lisp-Stat have languages for performing computations, data storage mechanisms, and a graphical interface. These languages provide an interactive interface to data analysis that is invaluable. To take full advantage of these programming environments, statisticians must understand the differences between them. Ihaka and Gentleman introduced R, a version of S which uses a different scoping regimen. In some ways this makes R behave more like Lisp-Stat. This article discusses the concept of scoping rules and shows how lexical scope can enhance the functionality of a language. [ABSTRACT FROM AUTHOR]},
Language = {english}
}
@Article{Grimm1999,
Title = {Ten Years of Individual-Based Modelling in Ecology: What Have We Learned and What Could We Learn in Future?},
Author = {Grimm, Volker},
Journal = {Ecological Modelling},
Year = {1999},
Pages = {129--148},
Volume = {115},
Language = {english}
}
@Article{Grimm2006,
Title = {A Standard Protocol for Describing Individual-Based and
Agent-Based Models},
Author = {Volker Grimm and Uta Berger and Finn Bastiansen and
Sigrunn Eliassen and Vincent Ginot and Jarl Giske
and John Goss-Custard and Tamara Grand and Simone
K. Heinz and Geir Huse and Andreas Huth and Jane
U. Jepsen and Christian Jørgensen and Wolf M. Mooij
and Birgit Müller and Guy {Péer} and Cyril Piou and
Steven F. Railsback and Andrew M. Robbins and Martha
M. Robbins and Eva Rossmanith and Nadja Rüger and
Espen Strand and Sami Souissi and Richard
A. Stillman and Rune Vabø and Ute Visser and Donald
L. DeAngelis},
Journal = {Ecological Modelling},
Year = {2006},
Pages = {115--126},
Volume = {198}
}
@Book{Grimm2005,
Title = {Individual-based Modeling and Ecology},
Author = {V. Grimm and S. F. Railsback},
Publisher = {Princeton University Press},
Year = {2005},
Address = {Princeton N.J.},
Pages = {1--428}
}
@Article{Grimm2005a,
Title = {Pattern-Oriented Modeling of Agent-Based Complex Systems:
Lessons from Ecology},
Author = {Volker Grimm and Eloy Revilla and Uta Berger and Florian
Jeltsch and Wolf M. Mooij and Steven F. Railsback
and Hans-Hermann Thulke and Jacob Weiner and
Thorsten Wiegand and Donald L. DeAngelis},
Journal = {Science},
Year = {2005},
Pages = {987--991},
Volume = {310}
}
@Book{Gurney1998,
Title = {Ecological Dynamics},
Author = {Gurney, W. S. C. and Nisbet, R. M.},
Publisher = {Oxford University Press},
Year = {1998},
Address = {New York, Oxford},
Language = {english},
Pages = {1--335}
}
@Article{Hartley2006,
Title = {Hyperinfectivity: A Critical Element in the Ability of
\textit{V. cholerae} to Cause Epidemics?},
Author = {Hartley, D. M. and Morris J. G. {Jr} and Smith, D. L.},
Journal = {PLoS Medicine},
Year = {2006},
Number = {1},
Pages = {63--69},
Volume = {3},
Abstract = {ODE model solved by odesolve/lsoda of R},
Doi = {10.1371/journal.pmed.0030007},
Language = {english}
}
@Article{Huelsmann2002,
Title = {Life History of \textit{Daphnia galeata} in a Hypertrophic
Reservoir and Consequences of Non-consumptive
Mortality for the Initiation of a Midsummer Decline},
Author = {Hülsmann, S. and Voigt, H.},
Journal = {Freshwater Biology},
Year = {2002},
Pages = {2313--2324},
Volume = {47}
}
@Article{Ihaka1996,
Title = {\proglang{R}: A Language for Data Analysis and Graphics},
Author = {Ross Ihaka and Robert Gentleman},
Journal = {Journal of Computational and Graphical Statistics},
Year = {1996},
Number = {3},
Pages = {299--314},
Volume = {5},
Language = {english}
}
@Article{Jachner2007,
Title = {Statistical Methods for the Qualitative Assessment of Dynamic Models with Time Delay (\proglang{R} Package \pkg{qualV})},
Author = {Jachner, S. and van den Boogaart, G. and Petzoldt, T.},
Journal = {Journal of Statistical Software},
Year = {this volume}
}
@Article{Jensen2006,
Title = {Modeling the Role of Bacteriophage in the Control of Cholera Outbreaks},
Author = {Mark A. Jensen and Shah M. Faruque and John J. Mekalanos and Bruce R. Levin},
Journal = {PNAS},
Year = {2006},
Pages = {4652--4657},
Volume = {103}
}
@Manual{Kates2005,
Title = {The \proglang{R} \pkg{proto} Package},
Author = {Kates, Louis and Petzoldt, Thomas},
Note = {Package vignette of the CRAN \pkg{proto} package},
Year = {2005},
Pages = {1--17},
Url = {http://cran.r-project.org/doc/vignettes/proto/proto.pdf}
}
@Article{Levey2005,
Title = {Effects of Landscape Corridors on Seed Dispersal by
Birds},
Author = {Douglas J. Levey and Benjamin M. Bolker and Joshua
J. Tewksbury and Sarah Sargent and Nick M. Haddad},
Journal = {Science},
Year = {2005},
Pages = {146--148},
Volume = {309}
}
@Book{Ludyk1995,
Title = {{Theoretische Regelungstechnik 1: Grundlagen, Synthese
linearer Regelungssysteme}},
Author = {Ludyk, Günther},
Publisher = {Springer},
Year = {1995},
Address = {Berlin}
}
@Article{Maas2006,
Title = {A Dynamical Model of General Intelligence: The Positive Manifold of Intelligence by Mutualism},
Author = {Han L. J. van der Maas and Conor V. Dolan and Raoul P. P. P. Grasman and Jelte M. Wicherts and Hilde M. Huizenga and Maartje E. J. Raijmakers},
Journal = {Psychological Review},
Year = {2006},
Number = {4},
Pages = {842--861},
Volume = {113}
}
@Unpublished{Maechler2004,
Title = {Good Programming Practice},
Author = {Mächler, Martin},
Note = {Keynote lecture at the useR!-2004 conference},
Year = {2004},
Url = {http://www.ci.tuwien.ac.at/Conferences/useR-2004/Keynotes/Maechler.pdf}
}
@Article{Mehner1998,
Title = {Is the Midsummer Decline of \textit{Daphnia} Really Induced
by Age-0 Fish Predation? Comparison of Fish
Consumption and \textit{Daphnia} Mortality and Life
History Parameters in a Biomanipulated Reservoir},
Author = {Mehner, T. and Hülsmann, S. and Worischka, S. and Plewa,
M. and Benndorf, J.},
Journal = {Journal of Plankton Research},
Year = {1998},
Pages = {1797-1811},
Volume = {20}
}
@Article{Mooij1996,
Title = {An Object Oriented Simulation Framework for
Individual-Based Simulations ({OSIRIS}):
\textit{Daphnia} Population Dynamics as an Example},
Author = {Mooij, Wolf M. and Boersma, Maarten},
Journal = {Ecological Modelling},
Year = {1996},
Pages = {139--153},
Volume = {93},
Language = {english}
}
@Article{Mooij1997,
Title = {The effect of size-selective predation on the population
growth rate, the production to biomass ratio and the
population structure of Daphnia galeata: a modelling
approach.},
Author = {Mooij, W. M. and Boersma, M. and Vijverberg, J.},
Journal = {Archiv für Hydrobiologie Special Issue Advances in Limnology},
Year = {1997},
Pages = {87-97},
Volume = {49}
}
@Article{Mooij2003,
Title = {Modeling \textit{Daphnia} Population Dynamics and
Demography Under Natural Conditions},
Author = {W. M. Mooij and S. Hülsmann and J. Vijverberg and A. Veen
and E. H. R. R. Lammens},
Journal = {Hydrobiologia},
Year = {2003},
Pages = {19--34},
Volume = {491}
}
@Book{Nash1990,
Title = {Compact numerical methods for computers: linear algebra and function minimisation},
Author = {Nash, John C},
Publisher = {CRC Press},
Year = {1990},
__markedentry = {[thpe:]},
Owner = {thpe},
Timestamp = {2015.08.01}
}
@Article{Petzold1983,
Title = {Automatic Selection of Methods for Solving Stiff and
Nonstiff Systems of Ordinary Differential Equations},
Author = {Petzold, Linda R.},
Journal = {{SIAM} Journal on Scientific and Statistical Computing},
Year = {1983},
Pages = {136--148},
Volume = {4}
}
@Article{Petzoldt2003a,
Title = {\proglang{R} as a Simulation Platform in Ecological Modelling},
Author = {Petzoldt, Thomas},
Journal = {R News},
Year = {2003},
Number = {3},
Pages = {8--16},
Volume = {3}
}
@Article{Petzoldt2007,
Title = {\pkg{simecol}: An Object-Oriented Framework for Ecological
Modeling in \proglang{R}},
Author = {Thomas Petzoldt and Karsten Rinke},
Journal = {Journal of Statistical Software},
Year = {2007},
Number = {9},
Pages = {1--31},
Volume = {22},
Coden = {JSSOBK},
ISSN = {1548-7660},
Url = {http://www.jstatsoft.org/v22/i09}
}
@TechReport{Powell2009,
Title = {The {BOBYQA} algorithm for bound constrained optimization without derivatives (Technical Report No. {DAMTP 2009/NA06})},
Author = {Powell, M. J. D.},
Institution = {{Cambridge: University of Cambridge, Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences}},
Year = {2009}
}
@Manual{RCore2015,
Title = {R: A Language and Environment for Statistical Computing},
Address = {Vienna, Austria},
Author = {{R Core Team}},
Organization = {R Foundation for Statistical Computing},
Year = {2015},
Url = {http://www.R-project.org/}
}
@Article{Radivoyevitch2004,
Title = {A Two-Way Interface between Limited Systems Biology Markup
Language and \proglang{R}},
Author = {Tomas Radivoyevitch},
Journal = {BMC Bioinformatics},
Year = {2004},
Volume = {5}
}
@Article{Reichert1994,
Title = {{AQUASIM} - {A} Tool for Simulation and Data Analysis of
Aquatic Systems},
Author = {Reichert, P.},
Journal = {Water Science and Technology},
Year = {1994},
Number = {2},
Pages = {21--30},
Volume = {30}
}
@Article{Reichert2001,
Title = {River Water Quality Model No. 1 {(RWQM1)}: {II}. Biochemical Process Equations},
Author = {Reichert, P. and Borchardt, D. and Henze, M. and Rauch, W. and Shanahan, P. and Somly{\'o}dy, L. and Vanrolleghem, P.},
Journal = {Water Science and Technology},
Year = {2001},
Pages = {11--30},
Volume = {43},
Language = {english}
}
@Article{Rinke2003,
Title = {Modelling the Effects of Temperature and Food on Individual Growth and Reproduction of \textit{Daphnia} and Their Consequences on the Population Level},
Author = {Rinke, Karsten and Petzoldt, Thomas},
Journal = {Limnologica},
Year = {2003},
Number = {4},
Pages = {293--304},
Volume = {33},
Language = {english}
}
@Article{Rinke2005,
Title = {A Model Approach to Evaluate the Effect of Temperature and Food Concentration an Individual Life-History and Population Dynamics of \textit{Daphnia}},
Author = {Rinke, Karsten and Vijverberg, Jacobus},
Journal = {Ecological Modelling},
Year = {2005},
Pages = {326--344},
Volume = {186},
Language = {english}
}
@Article{Rinke2005a,
Title = {Individual and Population Level Dynamics of \textit{Daphnia} at Varying Conditions of Food, Temperature and Fish Predation: A Model Approach},
Author = {Karsten Rinke and Jacobus Vijverberg and Thomas Petzoldt and Jürgen Benndorf},
Journal = {{Verhandlungen der Internationalen Vereinigung für Limnologie}},
Year = {2005},
Pages = {310--314},
Volume = {29}
}
@Article{Rolinski2005,
Title = {{Das physikalisch-ökologisch gekoppelte Talsperrenmodell}},
Author = {Rolinski, S. and Petzoldt, T. and Baumert, H. Z. and
Bigalke, K and Horn, H. and Benndorf, J.},
Journal = {Wasserwirtschaft},
Year = {2005},
Pages = {34--38},
Volume = {95}
}
@Book{Soetaert2009,
Title = {A Practical Guide to Ecological Modelling Using R as a
Simulation Platform},
Author = {Soetaert, Karline and Herman, Peter M. J.},
Publisher = {Springer},
Year = {2009},
Pages = {1--372.},
Url = {http://www.springer.com/life+sci/ecology/book/978-1-4020-8623-6}
}
@Article{Soetaert2010,
Title = {Inverse Modelling, Sensitivity and Monte Carlo Analysis in
\proglang{R} Using Package \pkg{FME}},
Author = {Soetaert, Karline and Petzoldt, Thomas},
Journal = {Journal of Statistical Software},
Year = {2010},
Number = {3},
Pages = {1--28},
Volume = {33},
Url = {http://www.jstatsoft.org/v33/i03/}
}
@Article{deSolve_jss,
Title = {Solving Differential Equations in \proglang{R}: Package
\proglang{deSolve}},
Author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow
Setzer},
Journal = {Journal of Statistical Software},
Year = {2010},
Number = {9},
Pages = {1--25},
Volume = {33},
Url = {http://www.jstatsoft.org/v33/i09}
}
@Manual{deSolve2009,
Title = {\pkg{deSolve}: General Solvers for Ordinary Differential
Equations (ODE) and for Differential Algebraic
Equations (DAE)},
Author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
Note = {R package version 1.2-3},
Year = {2009}
}
@Article{Torno2004a,
Title = {Non-Linear Mixed-Effects Pharmacokinetic/Pharmacodynamic
Modelling in NLME Using Differential Equations},
Author = {Torn\o{}, Christoffer W. and Agers\o{}, Henrik and
Jonsson, E. Niclas and Madsen, Henrik and Nielsen,
Henrik A.},
Journal = {Computer Methods and Programs in Biomedicine},
Year = {2004},
Number = {1},
Pages = {31--40},
Volume = {76}
}
@Article{Bertalanffy1957,
Title = {Quantitative Laws in Metabolism and Growth},
Author = {{von Bertalanffy}, L.},
Journal = {Quartely Review of Biology},
Year = {1957},
Pages = {217--231},
Volume = {32}
}
@Article{Wolkenhauer2005,
Title = {The Dynamic Systems Approach to Control and Regulation of
Intracellular Networks},
Author = {Olaf Wolkenhauer and Mukhtar Ullah and Peter Wellstead and
Kwang-Hyun Cho},
Journal = {FEBS Letters},
Year = {2005},
Pages = {1846--1853},
Volume = {579}
}
@Article{Zeileis2005,
Title = {Monitoring structural change in dynamic econometric models},
Author = {Zeileis, Achim and Leisch, Friedrich and Kleiber,
Christian and Hornik, Kurt},
Journal = {Journal of Applied Econometrics},
Year = {2005},
Number = {1},
Pages = {99--121},
Volume = {20},
Url = {http://dx.doi.org/10.1002/jae.776}
}
@Proceedings{DeAngelis1992a,
Title = {Individual-Based Models and Approaches in Ecology:
Populations, Communities, and Ecosystems.},
Year = {1992},
Address = {Knoxwille, Tennessee},
Editor = {DeAngelis, Donald L. and Gross, Louis J.},
Month = {May 16--19},
Note = {Proceedings of a Symposium/Workshop},
Publisher = {Chapmann and Hall},
Language = {english}
}
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