% 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.2014342.387} } @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年08月01日1}, 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} } @Comment{jabref-meta: databaseType:bibtex;}

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