[R-sig-dyn-mod] Individual-based modelling
Hi Sibylle, a non-spatial individual based model can be found in the following JSS paper (**): https://www.jstatsoft.org/article/view/v022i09 ... that is also a package vignette of simecol. The class "indbasedModel" is now built-in. Instead of the empirical equations found in "main" of the model above, you may consider to replace (or amend) this with an ODE model that describes the live cycle of an **individual**, e.g. a bioenergetic model. This means that the ODE part of the model does NOT describe the population size, because this is done by the IBM part counting the population. The population size is a so-called "emergent property" of the model. Package simeolModels (https://r-forge.r-project.org/scm/viewvc.php/pkg/simecolModels/?root=simecol) contains an ODE empowered IBM. You can install it via: install.packages("simecolModels", repos="http://R-Forge.R-project.org") and then have a look at ?daphnia_deb_ibm Note that all these are just examples, and that many other approaches are possible (e.g. with spatial coordinates), depending on your needs. Implementing individual-based model in R can be much fun for an experienced R person, because it is very flexible. Compared to pure ODEs it requires a little bit more programming skills, so it would be a good idea to do it in a team or on supervision of an experienced person. Even more important is a clear idea what to do and of course enough creativity to think around the corners. I don't yet understand your goals in detail, but would suggest to start with a simple non-spatial IBM along the lines of the JSS paper. Here the population is represented as a data frame and its columns are the traits of the individuals. When this works, start to refine the model. Hope it helps, Thomas (**) Another implementation of a Daphnia IBM without the "simecol" framework was already published in R News 03(2003) http://cran.r-project.org/doc/Rnews/Rnews_2003-3.pdf
Dr. Thomas Petzoldt Technische Universitaet Dresden Faculty of Environmental Sciences Institute of Hydrobiology 01062 Dresden, Germany E-Mail: thomas.petzoldt at tu-dresden.de http://tu-dresden.de/Members/thomas.petzoldt -- limnology and ecological modelling --