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simecol: An Object-Oriented Framework for Ecological Modeling in R

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  • Petzoldt, Thomas
  • Rinke, Karsten

Abstract

The simecol package provides an open structure to implement, simulate and share ecological models. A generalized object-oriented architecture improves readability and potential code re-use of models and makes simecol-models freely extendable and simple to use. The simecol package was implemented in the S4 class system of the programming language R. Reference applications, e.g. predator-prey models or grid models are provided which can be used as a starting point for own developments. Compact example applications and the complete code of an individual-based model of the water flea Daphnia document the efficient usage of simecol for various purposes in ecological modeling, e.g. scenario analysis, stochastic simulations and individual based population dynamics. Ecologists are encouraged to exploit the abilities of simecol to structure their work and to use R and object-oriented programming as a suitable medium for the distribution and share of ecological modeling code.

Suggested Citation

  • Petzoldt, Thomas & Rinke, Karsten, 2007. "simecol: An Object-Oriented Framework for Ecological Modeling in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i09).
    • Handle: RePEc:jss:jstsof:v:022:i09
    DOI: http://hdl.handle.net/10.18637/jss.v022.i09
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    References listed on IDEAS

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    1. Jachner, Stefanie & Gerald van den Boogaart, K. & Petzoldt, Thomas, 2007. "Statistical Methods for the Qualitative Assessment of Dynamic Models with Time Delay (R Package qualV)," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i08).
    2. Cribari-Neto, Francisco & Zarkos, Spyros G, 1999. "R: Yet Another Econometric Programming Environment," Journal of Applied Econometrics, John Wiley & Sons, Ltd., vol. 14(3), pages 319-329, May-June.
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    1. James W Rudge & Piya Hanvoravongchai & Ralf Krumkamp & Irwin Chavez & Wiku Adisasmito & Pham Ngoc Chau & Bounlay Phommasak & Weerasak Putthasri & Chin-Shui Shih & Mart Stein & Aura Timen & Sok Touch &, 2012. "Health System Resource Gaps and Associated Mortality from Pandemic Influenza across Six Asian Territories," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-10, February.
    2. Petzoldt, Thomas & Rudolf, Lars & Rinke, Karsten & Benndorf, Jürgen, 2009. "Effects of zooplankton diel vertical migration on a phytoplankton community: A scenario analysis of the underlying mechanisms," Ecological Modelling, Elsevier, vol. 220(9), pages 1358-1368.
    3. Soetaert, Karline & Petzoldt, Thomas & Setzer, R. Woodrow, 2010. "Solving Differential Equations in R: Package deSolve," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i09).
    4. Carus, Jana & Heuner, Maike & Paul, Maike & Schröder, Boris, 2017. "Which factors and processes drive the spatio-temporal dynamics of brackish marshes?—Insights from development and parameterisation of a mechanistic vegetation model," Ecological Modelling, Elsevier, vol. 363(C), pages 122-136.
    5. Martínez-López, Javier & Martínez-Fernández, Julia & Naimi, Babak & Carreño, María F. & Esteve, Miguel A., 2015. "An open-source spatio-dynamic wetland model of plant community responses to hydrological pressures," Ecological Modelling, Elsevier, vol. 306(C), pages 326-333.
    6. Tancredi Caruso & Jeff R Powell & Matthias C Rillig, 2012. "Compositional Divergence and Convergence in Local Communities and Spatially Structured Landscapes," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-10, April.
    7. repec:jss:jstsof:33:i03 is not listed on IDEAS
    8. Eline M. Krijkamp & Fernando Alarid-Escudero & Eva A. Enns & Hawre J. Jalal & M. G. Myriam Hunink & Petros Pechlivanoglou, 2018. "Microsimulation Modeling for Health Decision Sciences Using R: A Tutorial," Medical Decision Making, , vol. 38(3), pages 400-422, April.
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    11. Kneib, Thomas & Petzoldt, Thomas, 2007. "Introduction to the Special Volume on "Ecology and Ecological Modeling in R"," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i01).
    12. Soetaert, Karline & Petzoldt, Thomas, 2010. "Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i03).
    13. Langston, Amy K. & Kaplan, David A., 2020. "Modelling the effects of climate, predation, and dispersal on the poleward range expansion of black mangrove (Avicennia germinans)," Ecological Modelling, Elsevier, vol. 434(C).
    14. Krug, Rainer M. & Richardson, David M., 2014. "Modelling the effect of two biocontrol agents on the invasive alien tree Acacia cyclops—Flowering, seed production and agent survival," Ecological Modelling, Elsevier, vol. 278(C), pages 100-113.

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