Simecol: An object-oriented framework for ecological modeling in R

Journal of Statistical Software

Volumn 22, Issue 9, 2007, Pages 1-31

  Petzoldt, Thomas ^a   Rinke, Karsten ^b  

^a DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

Code sharing; Ecological modeling; Individual based model; Object oriented programming (OOP); R

Indexed keywords

EID: 37649014308     PISSN: 15487660     EISSN: 15487660     Source Type: Journal    
DOI: 10.18637/jss.v022.i09     Document Type: Article

References (45)

1. Bengtsson H (2003). "The R.oo Package - Object-Oriented Programming with References Using Standard R Code." In K Hornik, F Leisch, A Zeileis (eds.), "Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003)," pp. 1-18. Vienna, Austria. ISSN 1609-395X, URL http://www.ci.tuwien.ac.at/Conferences/ DSC-2003/ Proceedings/.
2. Benz J, Hoch R, Legovic T (2001). "ECOBAS - Modelling and Documentation." Ecological Modelling, 138, 3-15.
3. Blasius B, Huppert A, Stone L (1999). "Complex Dynamics and Phase Synchronization in Spatially Extended Ecological Systems." Nature, 399, 354-359.
4. Bossel H (1992). "Real-structure Process Description as the Basis of Understanding Ecosystems and Their Development." Ecological Modelling, 63(1-4), 261-276.
5. Bottrell HH, Duncan A, Gliwicz ZM, Grygierek E, Herzig A, Hillbricht-Ilkowska A, Kurasawa H, Larsson P, Weglenska T (1976). "A Review of Some Problems in Zooplankton Production Studies." Norvegian Journal of Zoology, 24, 419-456.
6. Chambers JM (2000). "Users, Programmers, and Statistical Software." Journal of Computational and Graphical Statistics, 9(3), 404-422.
7. Chambers JM (2001). "Classes and Methods in the S Language." URL http://www. omegahat.org/RSMethodos/Intro.pdf.
8. Cribari-Neto F, Zarkos SG (1999). "R: Yet Another Econometric Programming Environment." Journal of Applied Econometrics, 14(3), 319-329.
9. DeAngelis DL, Gross LJ (eds.) (1992). Individual-Based Models and Approaches in Ecology: Populations, Communities, and Ecosystems. Chapmann and Hall, Knoxwille, Tennessee. Proceedings of a Symposium/Workshop.
10. Dunning JBJ, Stewart DJ, Danielson BJ, Noon BR, Root TL, Lamberson RH, Stevens EE (1995). "Spatially Explicit Population Models: Current Forms and Uses." Ecological Applications, 5, 3-11.
11. Fowler M, Scott K (1997). UML Distilled. Applying the Standard Object Modelling Language. Addison Wesley.
12. Fussmann GF, Ellner SP, Hairston NGJ (2003). "Evolution as a Critical Component of Plankton Dynamics." Proceedings of the Royal Society of London Series B, 270, 1015-1022.
13. Gentleman R, Ihaka R (2000). "Lexical Scope and Statistical Computing." Journal of Computational and Graphical Statistics, 9(3), 491-508.
14. Grimm V (1999). "Ten Years of Individual-Based Modelling in Ecology: What Have We Learned and What Could We Learn in Future?" Ecological Modelling, 115, 129-148.
15. Grimm V, Berger U, Bastiansen F, Eliassen S, Ginot V, Giske J, Goss-Custard J, Grand T, Heinz SK, Huse G, Huth A, Jepsen JU, Jørgensen C, Mooij WM, Müller B, Péer G, Piou C, Railsback SF, Robbins AM, Robbins MM, Rossmanith E, Rüger N, Strand E, Souissi S, Stillman RA, Vabø R, Visser U, DeAngelis DL (2006). "A Standard Protocol for Describing Individual-Based and Agent-Based Models." Ecological Modelling, 198, 115-126.
16. Grimm V, Railsback SF (2005). Individual-based Modeling and Ecology. Princeton University Press, Princeton N.J.
17. Gurney WSC, Nisbet RM (1998). Ecological Dynamics. Oxford University Press, New York, Oxford.
18. Hartley DM, Jr MJG, Smith DL (2006). "Hyperinfectivity: A Critical Element in the Ability of V. cholerae to Cause Epidemics?" PLoS Medicine, 3(1), 63-69. doi:10.1371/journal.pmed.0030007.
19. Hülsmann S, Voigt H (2002). "Life History of Daphnia galeota in a Hypertrophic Reservoir and Consequences of Non-consumptive Mortality for the Initiation of a Midsummer Decline." Freshwater Biology, 47, 2313-2324.
20. Ihaka R, Gentleman R (1996). "R: A Language for Data Analysis and Graphics." Journal of Computational and Graphical Statistics, 5(3), 299-314.
21. Jachner S, van den Boogaart G, Petzoldt T (2007). "Statistical Methods for the Qualitative Assessment of Dynamic Models with Time Delay (R Package qualV)." Journal of Statistical Software, 22(8). URL http://www.jstatsoft.org/v22/108/.
22. Jensen MA, Faruque SM, Mekalanos JJ, Levin BR (2006). "Modeling the Role of Bacteriophage in the Control of Cholera Outbreaks." PNAS, 103, 4652-4657.
23. Kates L, Petzoldt T (2005). The R proto Package. Package vignette of the CRAN proto package, URL http://CRAN.R~project. org/.
24. Levey DJ, Bolker BM, Tewksbury JJ, Sargent S, Haddad NM (2005). "Effects of Landscape Corridors on Seed Dispersal by Birds." Science, 309, 146-148.
25. Ludyk G (1995). Theoretische Regelungstechnik 1: Grundlagen, Synthese linearer Regelungssysteme. Springer, Berlin.
26. Mächler M (2004). "Good Programming Practice." Keynote lecture at the useR! 2004 conference, URL http://www.ci.tuwien.ac.at/ Conferences/useR-2004/.
27. Mehner T, Hülsmann S, Worischka S, Plewa M, Benndorf J (1998). "Is the Midsummer Decline of Daphnia Really Induced by Age-0 Fish Predation? Comparison of Fish Consumption and Daphnia Mortality and Life History Parameters in a Biomanipulated Reservoir." Journal of Plankton Research, 20, 1797-1811.
28. Mooij WM, Boersma M (1996). "An Object Oriented Simulation Framework for IndividualBased Simulations (OSIRIS): Daphnia Population Dynamics as an Example." Ecological Modelling, 93, 139-153.
29. Mooij WM, Boersma M, Vijverberg J (1997). "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." Archiv für Hydrobiologie Special Issue Advances in Limnology, 49, 87-97.
30. Mooij WM, Hülsmann S, Vijverberg J, Veen A, Lammens EHRR (2003). "Modeling Daphnia Population Dynamics and Demography Under Natural Conditions." Hydrobiologia, 491, 19-34.
31. Petzoldt T (2003). "R as a Simulation Platform in Ecological Modelling." R News, 3(3), 8-16.
32. Radivoyevitch T (2004). "A Two-Way Interface between Limited Systems Biology Markup Language and R." BMC Bioinformatics, 5.
33. R Development Core Team (2007). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http: //www.R-project.org/.
34. Reichert P (1994). "AQUASIM - A Tool for Simulation and Data Analysis of Aquatic Systems." Water Science and Technology, 30(2), 21-30.
35. Reichert P, Borchardt D, Henze M, Rauch W, Shanahan P, Somlyódy L, Vanrolleghem P (2001). "River Water Quality Model No. 1 (RWQM1): II. Biochemical Process Equations." Water Science and Technology, 43, 11-30.
36. Rinke K, Petzoldt T (2003). "Modelling the Effects of Temperature and Food on Individual Growth and Reproduction of Daphnia and Their Consequences on the Population Level." Limnologica, 33(4), 293-304.
37. Rinke K, Vijverberg J (2005). "A Model Approach to Evaluate the Effect of Temperature and Food Concentration an Individual Life-History and Population Dynamics of Daphnia." Ecological Modelling, 186, 326-344.
38. Rinke K, Vijverberg J, Petzoldt T, Benndorf J (2005). "Individual and Population Level Dynamics of Daphnia at Varying Conditions of Food, Temperature and Fish Predation: A Model Approach." Verhandlungen der Internationalen Vereinigung für Limnologie, 29, 310-314.
39. Rolinski S, Petzoldt T, Baumert HZ, Bigalke K, Horn H, Benndorf J (2005). "Das physikalischökologisch gekoppelte Talsperrenmodell." Wasserwirtschaft, 95, 34-38.
40. The MathWorks, Ine (2007). MATLAB - The Language of Technical Computing, Version 7.5. The MathWorks, Inc., Natick, Massachusetts. URL http://www.MathWorks. com/products/matlab/.
41. Tornø CW, Agersø H, Jonsson EN, Madsen H, Nielsen HA (2004). "Non-Linear Mixed-Effects Pharmacokinetic/Pharmacodynamic Modelling in NLME Using Differential Equations." Computer Methods and Programs in Biomedicine, 76(1), 31-40.
42. van der Maas HLJ, Dolan CV, Grasman RPPP, Wicherts JM, Huizenga HM, Raijmakers MEJ (2006). "A Dynamical Model of General Intelligence: The Positive Manifold of Intelligence by Mutualism." Psychological Review, 113(4), 842-861.
43. von Bertalanffy L (1957). "Quantitative Laws in Metabolism and Growth." Quartely Review of Biology, 32, 217-231.
44. Wolkenhauer O, Ullah M, Wellstead P, Cho KH (2005). "The Dynamic Systems Approach to Control and Regulation of Intracellular Networks." FEBS Letters, 579, 1846-1853.
45. Zeileis A, Leisch F, Kleiber C, Hornik K (2005). "Monitoring Structural Change in Dynamic Econometric Models." Journal of Applied Econometrics, 20(1), 99-121. doi:10.1002/jae.776.