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

• Main Authors: Thomas Petzoldt, Karsten Rinke
• Format: Article
• Language: English
• Published: Foundation for Open Access Statistics 2007-06-01
• Series: Journal of Statistical Software
• Subjects: ecological modeling; individual-based model; object-oriented programming (OOP); code-sharing; R
• Online Access: http://www.jstatsoft.org/v22/i09/paper

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.