Encoding: Cp1252

@INPROCEEDINGS{Bengtsson2003,
  author = {Bengtsson, Henrik},
  title = {The \pkg{R.oo} Package -- Object-Oriented Programming with References
	Using Standard \proglang{R} Code},
  booktitle = {Proceedings of the 3rd International Workshop on Distributed Statistical
	Computing {(DSC} 2003)},
  year = {2003},
  editor = {Kurt Hornik and Friedrich Leisch and Achim Zeileis},
  pages = {1--18},
  address = {Vienna, Austria},
  note = {ISSN 1609-395X},
  url = {http://www.maths.lth.se/help/R/R.oo/},
  language = {english}
}

@ARTICLE{Benz2001a,
  author = {J. Benz and R. Hoch and T. Legovic},
  title = {{ECOBAS} - Modelling and Documentation},
  journal = {Ecological Modelling},
  year = {2001},
  volume = {138},
  pages = {3--15}
}

@ARTICLE{Blasius1999,
  author = {Blasius, Bernd and Huppert, Amit and Stone, Lewi},
  title = {Complex Dynamics and Phase Synchronization in Spatially Extended
	Ecological Systems},
  journal = {Nature},
  year = {1999},
  volume = {399},
  pages = {354--359},
  abstract = {chaos UPCA model Lotka Volterra grid},
  language = {english}
}

@BOOK{Bolker2007,
  title = {Ecological Models and Data in \proglang{R}},
  publisher = {Princeton University Press},
  year = {in prep.},
  author = {Bolker, Ben},
  address = {Princeton}
}

@ARTICLE{Bottrell1976,
  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.},
  title = {A Review of Some Problems in Zooplankton Production Studies},
  journal = {Norvegian Journal of Zoology},
  year = {1976},
  volume = {24},
  pages = {419--456},
  abstract = {dependence of egg development time (D) from temperature, IBP data},
  language = {english}
}

@UNPUBLISHED{Chambers2001,
  author = {Chambers, John M.},
  title = {Classes and Methods in the \proglang{S} Language},
  year = {2001},
  abstract = {This document introduces formally designed classes and methods for the
	S language. It is adapted from a small part of the related material
	in the bookProgramming with Data, [Cha98]. The adapted version describes
	compatible implementations of classes and methods for S-Plus and
	R.},
  language = {english},
  owner = {thpe},
  timestamp = {2007.01.20},
  url = {http://www.omegahat.org/RSMethods/Intro.pdf}
}

@ARTICLE{Chambers2000,
  author = {Chambers, John M.},
  title = {Users, Programmers, and Statistical Software},
  journal = {Journal of Computational and Graphical Statistics},
  year = {2000},
  volume = {9},
  pages = {404--422},
  number = {3},
  owner = {thpe},
  timestamp = {2007.01.20}
}

@ARTICLE{Fussmann2003,
  author = {Gregor F. Fussmann and Stephen P. Ellner and Hairston, Nelson G.
	{Jr.}},
  title = {Evolution as a Critical Component of Plankton Dynamics},
  journal = {Proceedings of the Royal Society of London Series B},
  year = {2003},
  volume = {270},
  pages = {1015--1022},
  owner = {thpe},
  timestamp = {2007.01.29}
}

@ARTICLE{Gardner1970,
  author = {Gardner, Martin},
  title = {The Fantastic Combinations of {John Conway's} New Solitaire Game
	'Life'},
  journal = {Scientific American},
  year = {1970},
  volume = {223},
  pages = {120--123}
}

@ARTICLE{Gentleman2000,
  author = {Gentleman, Robert and Ihaka, Ross},
  title = {Lexical Scope and Statistical Computing},
  journal = {Journal of Computational and Graphical Statistics},
  year = {2000},
  volume = {9},
  pages = {491--508},
  number = {3},
  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,
  author = {Grimm, Volker},
  title = {Ten Years of Individual-Based Modelling in Ecology: What Have We
	Learned and What Could We Learn in Future?},
  journal = {Ecological Modelling},
  year = {1999},
  volume = {115},
  pages = {129--148},
  language = {english}
}

@ARTICLE{Grimm2006,
  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},
  title = {A Standard Protocol for Describing Individual-Based and Agent-Based
	Models},
  journal = {Ecological Modelling},
  year = {2006},
  volume = {198},
  pages = {115--126}
}

@BOOK{Grimm2005,
  title = {Individual-based Modeling and Ecology},
  publisher = {Princeton University Press},
  year = {2005},
  author = {V. Grimm and S. F. Railsback},
  pages = {1--428},
  address = {Princeton N.J.}
}

@ARTICLE{Grimm2005a,
  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},
  title = {Pattern-Oriented Modeling of Agent-Based Complex Systems: Lessons
	from Ecology},
  journal = {Science},
  year = {2005},
  volume = {310},
  pages = {987--991},
  owner = {thpe},
  timestamp = {2007.02.04}
}

@ARTICLE{Ihaka1996,
  author = {Ross Ihaka and Robert Gentleman},
  title = {\proglang{R}: A Language for Data Analysis and Graphics},
  journal = {Journal of Computational and Graphical Statistics},
  year = {1996},
  volume = {5},
  pages = {299--314},
  number = {3},
  language = {english}
}

@ARTICLE{Jachner2007,
  author = {Jachner, S. and van den Boogaart, G. and Petzoldt, T.},
  title = {Statistical Methods for the Qualitative Assessment of Dynamic Models
	with Time Delay (\proglang{R} Package \pkg{qualV})},
  journal = {Journal of Statistical Software},
  year = {this volume}
}

@ARTICLE{Jensen2006,
  author = {Mark A. Jensen and Shah M. Faruque and John J. Mekalanos and Bruce
	R. Levin},
  title = {Modeling the Role of Bacteriophage in the Control of Cholera Outbreaks},
  journal = {PNAS},
  year = {2006},
  volume = {103},
  pages = {4652--4657}
}

@MANUAL{Kates2005,
  title = {The \proglang{R} \pkg{proto} Package},
  author = {Kates, Louis and Petzoldt, Thomas},
  year = {2005},
  note = {Package vignette of the CRAN \pkg{proto} package},
  pages = {1--17},
  url = {http://cran.r-project.org/doc/vignettes/proto/proto.pdf}
}

@ARTICLE{Maas2006,
  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},
  title = {A Dynamical Model of General Intelligence: The Positive Manifold
	of Intelligence by Mutualism},
  journal = {Psychological Review},
  year = {2006},
  volume = {113},
  pages = {842--861},
  number = {4}
}

@UNPUBLISHED{Maechler2004,
  author = {Mächler, Martin},
  title = {Good Programming Practice},
  note = {Keynote lecture at the useR!-2004 conference},
  year = {2004},
  url = {http://www.ci.tuwien.ac.at/Conferences/useR-2004/Keynotes/Maechler.pdf}
}

@ARTICLE{Petzold1983,
  author = {Petzold, Linda R.},
  title = {Automatic Selection of Methods for Solving Stiff and Nonstiff Systems
	of Ordinary Differential Equations},
  journal = {{SIAM} Journal on Scientific and Statistical Computing},
  year = {1983},
  volume = {4},
  pages = {136--148}
}

@ARTICLE{Petzoldt2003a,
  author = {Petzoldt, Thomas},
  title = {\proglang{R} as a Simulation Platform in Ecological Modelling},
  journal = {R News},
  year = {2003},
  volume = {3},
  pages = {8--16},
  number = {3}
}

@MANUAL{Rcore2006,
  title = {\proglang{R}: A Language and Environment for Statistical Computing},
  author = {{\proglang{R} Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2006},
  note = {{ISBN} 3-900051-07-0},
  url = {http://www.R-project.org}
}

@ARTICLE{Radivoyevitch2004,
  author = {Tomas Radivoyevitch},
  title = {A Two-Way Interface between Limited Systems Biology Markup Language
	and \proglang{R}},
  journal = {BMC Bioinformatics},
  year = {2004},
  volume = {5}
}

@ARTICLE{Reichert1994,
  author = {Reichert, P.},
  title = {{AQUASIM} - {A} Tool for Simulation and Data Analysis of Aquatic
	Systems},
  journal = {Water Science and Technology},
  year = {1994},
  volume = {30},
  pages = {21--30},
  number = {2}
}

@ARTICLE{Reichert2001,
  author = {Reichert, P. and Borchardt, D. and Henze, M. and Rauch, W. and Shanahan,
	P. and Somly{\'o}dy, L. and Vanrolleghem, P.},
  title = {River Water Quality Model No. 1 {(RWQM1)}: {II}. Biochemical Process
	Equations},
  journal = {Water Science and Technology},
  year = {2001},
  volume = {43},
  pages = {11--30},
  language = {english}
}

@ARTICLE{Rinke2003,
  author = {Rinke, Karsten and Petzoldt, Thomas},
  title = {Modelling the Effects of Temperature and Food on Individual Growth
	and Reproduction of \textit{Daphnia} and Their Consequences on the
	Population Level},
  journal = {Limnologica},
  year = {2003},
  volume = {33},
  pages = {293--304},
  number = {4},
  language = {english}
}

@ARTICLE{Rinke2005,
  author = {Rinke, Karsten and Vijverberg, Jacobus},
  title = {A Model Approach to Evaluate the Effect of Temperature and Food Concentration
	an Individual Life-History and Population Dynamics of \textit{Daphnia}},
  journal = {Ecological Modelling},
  year = {2005},
  volume = {186},
  pages = {326--344},
  language = {english}
}

@ARTICLE{Rinke2005a,
  author = {Karsten Rinke and Jacobus Vijverberg and Thomas Petzoldt and Jürgen
	Benndorf},
  title = {Individual and Population Level Dynamics of \textit{Daphnia} at Varying
	Conditions of Food, Temperature and Fish Predation: A Model Approach},
  journal = {{Verhandlungen der Internationalen Vereinigung für Limnologie}},
  year = {2005},
  volume = {29},
  pages = {310--314}
}

@ARTICLE{Rolinski2005,
  author = {Rolinski, S. and Petzoldt, T. and Baumert, H. Z. and Bigalke, K and
	Horn, H. and Benndorf, J.},
  title = {{Das physikalisch-ökologisch gekoppelte Talsperrenmodell}},
  journal = {Wasserwirtschaft},
  year = {2005},
  volume = {95},
  pages = {34--38}
}

@ARTICLE{Torno2004a,
  author = {Torn\o{}, Christoffer W. and Agers\o{}, Henrik and Jonsson, E. Niclas
	and Madsen, Henrik and Nielsen, Henrik A.},
  title = {Non-Linear Mixed-Effects Pharmacokinetic/Pharmacodynamic Modelling
	in NLME Using Differential Equations},
  journal = {Computer Methods and Programs in Biomedicine},
  year = {2004},
  volume = {76},
  pages = {31--40},
  number = {1},
  abstract = {The standard software for non-linear mixed-effect analysis of pharma-cokinetic/phar-macodynamic
	(PK/PD) data is NONMEM while the non-linear mixed-effects package
	NLME is an alternative as long as the models are fairly simple.
	We present the nlmeODE package which combines the ordinary differential
	equation (ODE) solver package odesolve and the non-linear mixed
	effects package NLME thereby enabling the analysis of complicated
	systems of ODEs by non-linear mixed-effects modelling. The pharmacokinetics
	of the anti-asthmatic drug theophylline is used to illustrate the
	applicability of the nlmeODE package for population PK/PD analysis
	using the available data analysis tools in R for model inspection
	and validation. The nlmeODE package is numerically stable and provides
	accurate parameter estimates which are consistent with NONMEM estimates.},
  timestamp = {2007.01.30}
}


@ARTICLE{Mooij1996,
  author = {Mooij, Wolf M. and Boersma, Maarten},
  title = {An Object Oriented Simulation Framework for Individual-Based Simulations
	({OSIRIS}): \textit{Daphnia} Population Dynamics as an Example},
  journal =  {Ecological Modelling},
  year = {1996},
  volume = {93},
  pages = {139--153},
  language = {english}
}

@BOOK{Gurney1998,
  title = {Ecological Dynamics},
  publisher = {Oxford University Press},
  year = {1998},
  author = {Gurney, W. S. C. and Nisbet, R. M.},
  pages = {1--335},
  address = {New York, Oxford},
  language = {english}
}

@ARTICLE{Hartley2006,
  author = {Hartley, D. M. and Morris J. G. {Jr} and Smith, D. L.},
  title = {Hyperinfectivity: A Critical Element in the Ability of \textit{V.
	cholerae} to Cause Epidemics?},
  journal = {PLoS Medicine},
  year = {2006},
  volume = {3},
  pages = {63--69},
  number = {1},
  abstract = {ODE model solved by odesolve/lsoda of R},
  doi = {10.1371/journal.pmed.0030007},
  language = {english},
  owner = {thpe},
  pdf = {Hartley2006.pdf},
  timestamp = {2007.05.28}
}


@ARTICLE{Cribari-Neto1999,
  author = {Francisco Cribari-Neto and Spyros G. Zarkos},
  title = {\proglang{R}: Yet Another Econometric Programming Environment},
  journal = {Journal of Applied Econometrics},
  year = {1999},
  volume = {14},
  pages = {319--329},
  number = {3},
  owner = {thpe},
  timestamp = {2007.05.28}
}

@BOOK{Fowler1997,
  title = {{UML} Distilled. Applying the Standard Object Modelling Language},
  publisher = {Addison Wesley},
  year = {1997},
  author = {Fowler, Martin and Scott, Kendall},
  pages = {1--208},
  language = {english}
}


@ARTICLE{Mooij2003,
  author = {W. M. Mooij and S. Hülsmann and J. Vijverberg and A. Veen and E.
	H. R. R. Lammens},
  title = {Modeling \textit{Daphnia} Population Dynamics and Demography Under
	Natural Conditions},
  journal = {Hydrobiologia},
  year = {2003},
  volume = {491},
  pages = {19--34}
}


@ARTICLE{Zeileis2005,
  author = {Zeileis, Achim and Leisch, Friedrich and Kleiber, Christian and Hornik,
	Kurt},
  title = {Monitoring structural change in dynamic econometric models},
  journal = {Journal of Applied Econometrics},
  year = {2005},
  volume = {20},
  pages = {99--121},
  number = {1},
  abstract = {The classical approach to testing for structural change employs retrospective
	tests using a historical data set of a given length. Here we consider
	a wide array of fluctuation-type tests in a monitoring situation - given
	a history period for which a regression relationship is known to
	be stable, we test whether incoming data are consistent with the
	previously established relationship. Procedures based on estimates
	of the regression coefficients are extended in three directions:
	we introduce (a) procedures based on OLS residuals, (b) rescaled
	statistics and (c) alternative asymptotic boundaries. Compared to
	the existing tests our extensions offer ease of computation, improved
	size in finite samples for dynamic models and better power against
	certain alternatives, respectively. We apply our methods to three
	data sets, German M1 money demand, US labour productivity and S&P
	500 stock returns. Copyright © 2005 John Wiley & Sons, Ltd.},
  owner = {thpe},
  pdf = {Zeileis2005.pdf},
  timestamp = {2007.05.28},
  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},
  editor = {DeAngelis, Donald L. and Gross, Louis J.},
  address = {Knoxwille, Tennessee},
  publisher = {Chapmann and Hall},
  note = {Proceedings of a Symposium/Workshop},
  month = {May 16--19},
  language = {english}
}


@ARTICLE{Mehner1998,
  author = {Mehner, T. and Hülsmann, S. and Worischka, S. and Plewa, M. and Benndorf,
	J.},
  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},
  journal = {Journal of Plankton Research},
  year = {1998},
  volume = {20},
  pages = {1797-1811},
  owner = {thpe},
  timestamp = {2007.05.25}
}

@ARTICLE{Huelsmann2002,
  author = {Hülsmann, S. and Voigt, H.},
  title = {Life History of \textit{Daphnia galeata} in a Hypertrophic Reservoir and Consequences
	of Non-consumptive Mortality for the Initiation of a Midsummer Decline},
  journal = {Freshwater Biology},
  year = {2002},
  volume = {47},
  pages = {2313--2324}
}

@ARTICLE{Bertalanffy1957,
  author = {{von Bertalanffy}, L.},
  title = {Quantitative Laws in Metabolism and Growth},
  journal = {Quartely Review of Biology},
  year = {1957},
  volume = {32},
  pages = {217--231}
}

@ARTICLE{Mooij1997,
  author = {Mooij, W. M. and Boersma, M. and Vijverberg, J.},
  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.},
  journal = {Archiv für Hydrobiologie Special Issue Advances in Limnology},
  year = {1997},
  volume = {49},
  pages = {87-97}
}

@BOOK{Ludyk1995,
  title = {{Theoretische Regelungstechnik 1: Grundlagen, Synthese linearer Regelungssysteme}},
  publisher = {Springer},
  year = {1995},
  author = {Ludyk, Günther},
  address = {Berlin}
}

@ARTICLE{Bossel1992,
  author = {Bossel, Hartmut},
  title = {Real-structure Process Description as the Basis of Understanding
	Ecosystems and Their Development},
  journal = {Ecological Modelling},
  year = {1992},
  volume = {63},
  pages = {261--276},
  number = {1-4},
  month = sep
}

@ARTICLE{Wolkenhauer2005,
  author = {Olaf Wolkenhauer and Mukhtar Ullah and Peter Wellstead and Kwang-Hyun
	Cho},
  title = {The Dynamic Systems Approach to Control and Regulation of Intracellular
	Networks},
  journal = {FEBS Letters},
  year = {2005},
  volume = {579},
  pages = {1846--1853}
}

@Article{Levey2005,
	author = {Douglas J. Levey and Benjamin M. Bolker and
		Joshua J. Tewksbury and Sarah Sargent and Nick M.
			Haddad},
	title={Effects of Landscape Corridors on Seed Dispersal by Birds},
	journal = {Science},
	year = {2005},
	pages = {146--148},
	volume = {309}
}

@ARTICLE{Dunning1995,
  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},
  year = {1995},
  title={Spatially Explicit Population Models: Current Forms and Uses},
  journal ={Ecological Applications},
  volume = {5},
  pages = {3--11}
}

@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},
  volume = {22},
  number = {9},
  pages = {1--31},
  year = {2007},
  coden = {JSSOBK},
  issn = {1548-7660},
  url = {http://www.jstatsoft.org/v22/i09},
  keywords = {ecological modeling, individual-based model,
             object-oriented programming (OOP),
             code-sharing, R.},
}

@MANUAL{Rexts2006,
  title = {Writing \proglang{R} Extensions},
  author = {{\proglang{R} Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2006},
  note = {{ISBN} 3-900051-11-9},
  url = {http://www.R-project.org}
}

@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},
  year = {2009},
  note = {R package version 1.2-3},
}

@BOOK{Soetaert2009,
  title = {A Practical Guide to Ecological Modelling Using R as a Simulation
	Platform},
  publisher = {Springer},
  year = {2009},
  author = {Soetaert, Karline and Herman, Peter M. J.},
  pages = {1--372.},
  url = {http://www.springer.com/life+sci/ecology/book/978-1-4020-8623-6}
}

