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@ARTICLE{Bogacki1989,
  author = {Bogacki, P and Shampine, L F},
  title = {A 3(2) Pair of Runge-Kutta Formulas},
  journal = {Applied Mathematics Letters},
  year = {1989},
  volume = {2},
  pages = {1--9}
}

@BOOK{Brenan96,
  title = {Numerical Solution of Initial-Value Problems in Differential-Algebraic
	Equations},
  publisher = {SIAM Classics in Applied Mathematics},
  year = {1996},
  author = {Brenan, K E and Campbell, S L and Petzold, L R}
}


@ARTICLE{Brown89,
  author = {Brown, P N and Byrne, G D and Hindmarsh, A C},
  title = {\pkg{VODE}, A Variable-Coefficient ODE Solver},
  journal = {SIAM Journal on Scientific and Statistical Computing},
  year = {1989},
  volume = {10},
  pages = {1038--1051}
}

@BOOK{Butcher1987,
  title = {The Numerical Analysis of Ordinary Differential Equations, Runge-Kutta
	and General Linear Methods},
  publisher = {John Wiley \& Sons},
  year = {1987},
  author = {Butcher, J C},
  volume = {2},
  pages = {1--9},
  address = {Chichester and New York.}
}
@MANUAL{bvpSolve,
  title = {\pkg{bvpSolve}: Solvers for Boundary Value Problems of Ordinary Differential
  	Equations},
  author = {Karline Soetaert and Jeff R. Cash and Francesca Mazzia},
  year = {2010},
  note = {\proglang{R} package version 1.2},
  url = {http://CRAN.R-project.org/package=bvpSolve}
}

@ARTICLE{Cash1990,
  author = {Cash, J R and Karp, A H},
  title = {A Variable Order Runge-Kutta Method for Initial Value Problems With
	Rapidly Varying Right-Hand Sides},
  journal = {ACM Transactions on Mathematical Software},
  year = {1990},
  volume = {16},
  pages = {201--222}
}

@MANUAL{compiledCode,
  title = {\proglang{R} package \pkg{deSolve}: Writing Code in Compiled Languages},
  author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
  year = {2008},
  note = {\pkg{deSolve} vignette - \proglang{R} package version 1.8}
}

@MANUAL{deSolve,
  title = {deSolve: General solvers for initial value problems of ordinary differential
	equations (ODE), partial differential equations (PDE), differential
	algebraic equations (DAE) and delay differential equations (DDE)},
  author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
  year = {2010},
  note = {R package version 1.8}
}

@ARTICLE{deSolve_jss,
  author = {Soetaert, K and Petzoldt, T and Setzer, RW},
  title = {Solving Differential Equations in \proglang{R}: Package \pkg{deSolve}},
  journal = {Journal of Statistical Software},
  year = {2010},
  volume = {33},
  pages = {1--25},
  number = {9},
  coden = {JSSOBK},
  issn = {1548-7660},
  url = {http://www.jstatsoft.org/v33/i09}
}

@ARTICLE{Dormand1980,
  author = {Dormand, J R and Prince, P J},
  title = {A family of embedded Runge-Kutta formulae},
  journal = {Journal of Computational and Applied Mathematics},
  year = {1980},
  volume = {6},
  pages = {19--26},
  issue = {1}
}

@ARTICLE{Dormand1981,
  author = {Dormand, J R and Prince, P J},
  title = {High Order Embedded Runge-Kutta Formulae},
  journal = {Journal of Computational and Applied Mathematics},
  year = {1981},
  volume = {7},
  pages = {67--75},
  issue = {1}
}

@ARTICLE{Fehlberg1967,
  author = {Fehlberg, E},
  title = {Klassische Runge-Kutta-Formeln fuenfter and siebenter Ordnung mit
	Schrittweiten-Kontrolle},
  journal = {Computing (Arch. Elektron. Rechnen)},
  year = {1967},
  volume = {4},
  pages = {93--106}
}

@BOOK{Hairer1,
  title = {Solving Ordinary Differential Equations I: Nonstiff Problems. Second
	Revised Edition},
  publisher = {Springer-Verlag},
  year = {2009},
  author = {Hairer, E and Norsett, S. P. and Wanner, G},
  address = {Heidelberg}
}

@BOOK{Hairer2,
  title = {Solving Ordinary Differential Equations II: Stiff and Differential-Algebraic
	Problems. Second Revised Edition},
  publisher = {Springer-Verlag},
  year = {2010},
  author = {Hairer, E and Wanner, G},
  address = {Heidelberg}
}

@INCOLLECTION{Hindmarsh83,
  author = {Hindmarsh, A. C.},
  title = {\pkg{ODEPACK}, a Systematized Collection of {ODE} Solvers},
  booktitle = {Scientific Computing, Vol. 1 of IMACS Transactions on Scientific
	Computation},
  publisher = {IMACS / North-Holland},
  year = {1983},
  editor = {Stepleman, R.},
  pages = {55-64},
  address = {Amsterdam}
}

@ARTICLE{Petzold1983,
  author = {Linda R. Petzold},
  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}
}

@Conference{Petzoldt-Rennes,
  author =    {Petzoldt, Thomas},
  title =     {Dynamic simulation models - is R powerful enough?},
  booktitle = {UseR!2009, July 8-10, Rennes, France},
  year =      {2009}
}

@Conference{Petzoldt-UCLA,
  author =    {Petzoldt, Thomas},
  title =     {Swimming in clear lakes: How model coupling with R helps to improve water quality},
  booktitle = {user!2014},
  year =      {2014}
}

@Conference{Petzoldt-Warwick,
  author =    {Petzoldt, T. and Soetaert, K.},
  title =     {Using R for Systems Understanding - A Dynamic Approach},
  booktitle = {UseR!2011, August 16-18, University of Warwick, Coventry, UK},
  year =      {2011}
}

@BOOK{Press92,
  title = {Numerical Recipes in FORTRAN. The Art of Scientific Computing},
  publisher = {Cambridge University Press},
  year = {1992},
  author = {Press, W H and Teukolsky, S A and Vetterling, W T and Flannery, B
	P},
  edition = {2nd}
}

@MANUAL{Rcore,
  title = {\proglang{R}: A Language and Environment for Statistical Computing},
  author = {{\proglang{R} Development Core Team}},
  organization = {\proglang{R} Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2008},
  note = {{ISBN} 3-900051-07-0},
  url = {http://www.R-project.org}
}

@Manual{ReacTran,
    title = {ReacTran: Reactive transport modelling in 1D, 2D and 3D},
    author = {Karline Soetaert and Filip Meysman},
    year = {2010},
    note = {R package version 1.3},
  }@MANUAL{Rexts2009,
  title = {Writing \proglang{R} Extensions},
  author = {{\proglang{R} Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2009},
  note = {{ISBN} 3-900051-11-9},
  url = {http://www.R-project.org}
}

@MANUAL{Setzer01,
  title = {The \pkg{odesolve} Package: Solvers for Ordinary Differential Equations},
  author = {R. Woodrow Setzer},
  year = {2001},
  note = {R package version 0.1-1}
}

@BOOK{Soetaert08,
  title = {A Practical Guide to Ecological Modelling. Using \proglang{R} as
	a Simulation Platform},
  publisher = {Springer},
  year = {2009},
  author = {Soetaert, K and Herman, P M J},
  pages = {372},
  note = {ISBN 978-1-4020-8623-6}
}

@Conference{Soetaert-ICNAAM,
  author =    {Soetaert, K., Meysman, F. and Petzoldt, T.},
  title =     {Solving Differential Equations in R},
  booktitle = {ICNAAM 2010: International Conference of Numerical Analysis and Applied Mathematics, September 19-25, Rhodos, Greece},
  year =      {2010},
  doi =       {doi:10.1063/1.3498463}
}

@Conference{Soetaert-Rennes,
  author =    {Soetaert, Karline},
  title =     {Mathematical modelling of the environment - are there enough data?},
  booktitle = {UseR!2009, July 8-10, Rennes, France},
  year =      {2009}
}

@Manual{ST2000,
  author = {Shampine, L.F and Thompson, S.},
  year = {2000},
  title = {Solving Delay Differential Equations with dde23},
  url = {http://www.runet.edu/~thompson/webddes/tutorial.pdf}
}

@MANUAL{testset,
  title = {Test Set for Initial Value Problem Solvers, release 2.4},
  author = {Francesca Mazzia and Cecilia Magherini},
  note = {Report 4/2008},
  address = {Department of Mathematics, University of Bari, Italy},
  year = {2008},
  url = {http://pitagora.dm.uniba.it/~testset}
}

@Conference{Tutorial-UCLA,
  author =    {Soetaert, Karline and Petzoldt, Thomas},
  title =     {Simulating differential equation models in R},
  booktitle = {Pre-conference tutorial at the useR!2014 conference, UCLA, Los Angeles, June 30 - July 3 2014},
  year =      {2014},
  url =       {http://user2014.stat.ucla.edu/}
}

@Conference{,
  author =    {Soetaert, Karline},
  title =     {Solving differential equations in R (plenary talk)},
  booktitle = {useR!2014 conference, UCLA, Los Angeles, June 30 - July 3 2014},
  year =      {2014}
}
