% Encoding: UTF-8
@Article{Bogacki1989,
author = {Bogacki, P and Shampine, L F},
title = {A 3(2) Pair of {R}unge-{K}utta Formulas},
journal = {Applied Mathematics Letters},
year = {1989},
volume = {2},
pages = {1--9}
}
@Book{Brenan1996,
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{Brown1989,
author = {Brown, P N and Byrne, G D and Hindmarsh, A C},
title = {{VOD}E, A Variable-Coefficient ODE Solver},
journal = {{SIAM} J. Sci. Stat. Comput.},
year = {1989},
volume = {10},
pages = {1038--1051}
}
@Article{Brown1994,
author = {Peter N. Brown and Alan C. Hindmarsh and Linda R. Petzold},
title = {Using {K}rylov Methods in the Solution of Large-Scale Differential-Algebraic Systems},
journal = {{SIAM} J. Sci. Comput.},
year = {1994},
volume = {15},
number = {6},
pages = {1467--1488},
address = {Philadelphia, PA, USA},
doi = {10.1137/0915088},
issn = {1064-8275},
publisher = {Society for Industrial and Applied Mathematics}
}
@Article{BrownHindmarsh1989,
author = {Brown, Peter N and Hindmarsh, Alan C},
title = {Reduced storage matrix methods in stiff ODE systems},
journal = {Applied Mathematics and Computation},
year = {1989},
volume = {31},
pages = {40--91},
publisher = {Elsevier}
}
@Article{BrownHindmarshPetzold1998,
author = {Brown, Peter N and Hindmarsh, Alan C and Petzold, Linda R},
title = {Consistent initial condition calculation for differential-algebraic systems},
journal = {SIAM Journal on Scientific Computing},
year = {1998},
volume = {19},
number = {5},
pages = {1495--1512},
publisher = {SIAM}
}
@Book{Butcher1987,
title = {The Numerical Analysis of Ordinary Differential Equations, {R}unge-{K}utta and General Linear Methods},
publisher = {John Wiley \& Sons},
year = {1987},
author = {Butcher, J C},
volume = {2},
address = {Chichester and New York.},
pages = {1--9}
}
@Article{Cash1990,
author = {Cash, J R and Karp, A H},
title = {A Variable Order {R}unge-{K}utta 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 = {{R} package {deSolve}: Writing Code in Compiled Languages},
author = {Karline Soetart and Thomas Petzoldt and R. Woodrow Setzer},
year = {2016},
note = {{deSolve} vignette - {R} package version 1.13},
url = {http://cran.r-project.org/web/packages/deSolve/vignettes/compiledCode.pdf}
}
@Manual{deSolve-introduction,
title = {{R} package {deSolve}: Solving Initial Value Differential Equations in R},
author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
year = {2016},
note = {{deSolve} vignette - {R} package version 1.13},
url = {http://cran.r-project.org/web/packages/deSolve/vignettes/deSolve.pdf}
}
@Manual{deSolve-Manual,
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 = {2016},
note = {R package version 1.13},
url = {http://cran.r-project.org/web/packages/deSolve/deSolve.pdf}
}
@Article{Dormand1980,
author = {Dormand, J R and Prince, P J},
title = {A family of embedded {R}unge-{K}utta formulae},
journal = {Journal of Computational and Applied Mathematics},
year = {1980},
volume = {6},
pages = {19--26},
issue = {1}
}
@Book{Ellner2006,
title = {Dynamic Models in Biology},
publisher = {Princeton University Press},
year = {2006},
author = {Stephen P. Ellner and John Guckenheimer},
file = {Ellner2006-Book_Chap1.pdf:Ellner2006-Book_Chap1.pdf:PDF;Ellner2006-Book_Chap9.pdf:Ellner2006-Book_Chap9.pdf:PDF;Ellner2006-Book_Chap7.pdf:Ellner2006-Book_Chap7.pdf:PDF},
pages = {1--329},
url = {http://www.cam.cornell.edu/~dmb/DMBsupplements.html}
}
@Book{EngelnMuellges1996,
title = {Numerik Algorithmen: Entscheidungshilfe zur Auswahl und Nutzung},
publisher = {VDI Verlag},
year = {1996},
author = {Engeln-Muellges, G and Reutter, F},
address = {Duesseldorf}
}
@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{Hairer2009,
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{Hairer2010,
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{Hindmarsh1983,
author = {Hindmarsh, A. C.},
title = {ODEPACK, A Systematized Collection of {ODE} Solvers},
booktitle = {Scientific Computing. Applications of Mathematics and Computing to the Physical Sciences},
publisher = {IMACS / North-Holland},
year = {1983},
editor = {Stepleman, R.},
pages = {55--64},
address = {Amsterdam}
}
@Article{Kutta1901,
author = {Kutta, Wilhelm},
title = {{Beitrag zur n{\"a}herungweisen Integration totaler Differentialgleichungen}},
journal = {Z. Math. Phys.},
year = {1901},
volume = {46},
pages = {435--453}
}
@Article{Mazzia2014-bvpSolve,
author = {Francesca Mazzia and Jeff R. Cash and Karline Soetaert},
title = {Solving boundary value problems in the open source software R: Package {bvpSolve}},
journal = {Opuscula mathematica},
year = {2014},
volume = {34},
number = {2},
pages = {387--403},
doi = {10.7494/OpMath.2014.34.2.387}
}
@InCollection{Petzold1983,
author = {Petzold, Linda R},
title = {A description of {DASSL}: A differential/algebraic system solver},
booktitle = {Scientific Computing. Applications of Mathematics and Computing to the Physical Sciences},
publisher = {IMACS / North-Holland},
year = {1983},
editor = {Stepleman, R. A.},
pages = {65--68},
address = {Amsterdam}
}
@Article{Petzold1983a,
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, UCLA, Los Angeles, June 30 - July 3 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},
url = {slides/petz_soet2011.pdf}
}
@Book{Press2007,
title = {Numerical Recipes in {C}},
publisher = {Cambridge University Press},
year = {2007},
author = {Press, W H and Teukolsky, S A and Vetterling, W T and Flannery, B P},
edition = {3\textsuperscript{rd}}
}
@Article{Prince1981,
author = {Prince, P J and Dormand, J R},
title = {High Order Embedded {R}unge-{K}utta Formulae},
journal = {Journal of Computational and Applied Mathematics},
year = {1981},
volume = {7},
pages = {67--75},
issue = {1}
}
@Manual{RCore,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2016},
url = {https://www.R-project.org/}
}
@Manual{Setzer2001,
title = {The {odesolve} Package: Solvers for Ordinary Differential Equations},
author = {R. Woodrow Setzer},
year = {2001},
note = {R package version 0.1-1}
}
@Book{Soetaert2009-Book,
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}
}
@InProceedings{Soetaert2010-AIP,
author = {Karline Soetaert and Filip Meysman and Thomas Petzoldt},
title = {Solving Differential Equations in R},
booktitle = {AIP Conference Proceedings},
year = {2010},
editor = {Theodore E. Simos and George Psihoyios and Ch. Tsitouras},
volume = {1281},
number = {1},
pages = {31-34},
publisher = {AIP},
doi = {10.1063/1.3498463},
keywords = {partial differential equations; differential equations; matrix algebra; programming languages},
url = {http://link.aip.org/link/?APC/1281/31/1}
}
@Article{Soetaert2010-bvpSolve,
author = {Soetaert, Karline and Cash, JR and Mazzia, Francesca},
title = {bvpSolve: solvers for boundary value problems of ordinary differential equations},
journal = {R package version},
year = {2010}
}
@Article{Soetaert2010-JSS-deSolve,
author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
title = {Solving Differential Equations in R: Package {deSolve}},
journal = {Journal of Statistical Software},
year = {2010},
volume = {33},
number = {9},
pages = {1--25},
coden = {JSSOBK},
doi = {10.18637/jss.v033.i09},
issn = {1548-7660},
keywords = {ordinary differential equations, partial differential equations, differential algebraic equations, initial value problems, R, FORTRAN, C},
url = {http://www.jstatsoft.org/v33/i09}
}
@Article{Soetaert2010-JSS-FME,
author = {Karline Soetaert and Thomas Petzoldt},
title = {Inverse Modelling, Sensitivity and {M}onte {C}arlo Analysis in {R} Using Package {FME}},
journal = {Journal of Statistical Software},
year = {2010},
volume = {33},
number = {3},
pages = {1--28},
month = {2},
day = {2},
doi = {10.18637/jss.v033.i03},
url = {http://www.jstatsoft.org/v33/i03}
}
@Manual{Soetaert2010-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}
}
@Article{Soetaert2010-RJournal,
author = {Karline Soetaert and Thomas Petzoldt and R. Woodrow Setzer},
title = {Solving Differential Equations in {R}},
journal = {The R Journal},
year = {2010},
volume = {2},
number = {2},
pages = {5--15},
month = {December},
url = {http://journal.r-project.org/archive/2010-2/RJournal_2010-2_Soetaert~et~al.pdf}
}
@Article{Soetaert2012,
author = {Soetaert, Karline and Meysman, Filip},
title = {Reactive transport in aquatic ecosystems: Rapid model prototyping in the open source software {R}},
journal = {Environmental Modelling and Software},
year = {2012},
volume = {32},
number = {0},
pages = {49--60},
month = jun,
doi = {10.1016/j.envsoft.2011.08.011},
issn = {1364-8152},
keywords = {Reactive transport, Model, Open source, Software, R},
url = {http://www.sciencedirect.com/science/article/pii/S1364815211001940}
}
@Book{Soetaert2012-Book,
title = {Solving Differential Equations in R},
publisher = {Springer},
year = {2012},
author = {Soetaert, Karline and Cash, Jeff and Mazzia, Francesca},
url = {http://www.springer.com/statistics/computational+statistics/book/978-3-642-28069-6}
}
@Conference{Soetaert2014,
author = {Soetaert, Karline},
title = {Solving differential equations in R (plenary talk)},
booktitle = {UseR!2014, UCLA, Los Angeles, June 30 - July 3 2014},
year = {2014}
}
@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 = {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}
}
@Conference{Soetaert-Tutorial-Warwick,
author = {Soetaert, Karline and Petzoldt, Thomas},
title = {Simulating differential equation models in R -- Pre-conference tutorial},
booktitle = {UseR!2011, August 16-18, University of Warwick, Coventry, UK},
year = {2011},
url = {slides/tutorial.pdf}
}
@Book{Stevens2009,
title = {A Primer of Ecology with R},
publisher = {Springer},
year = {2009},
author = {Stevens, Martin Henry},
pages = {1--401},
url = {http://www.springer.com/us/book/9780387898810}
}
@Conference{Tutorial-UCLA,
author = {Soetaert, Karline and Petzoldt, Thomas},
title = {Simulating differential equation models in R -- Pre-conference tutorial},
booktitle = {UseR!2014, UCLA, Los Angeles, June 30 - July 3 2014},
year = {2014},
url = {user2014/tutorial.pdf}
}