Limnological systems laboratory in R

During the last years, plenty of ecological models have been developed in the field of aquatic ecology, e.g. for rivers and lakes. However, it occurred that tunnel-vision and re-inventing the wheel became main hurdles for further progress (Mooij et al., 2010), but also the Babylon of software systems and proprietary codes.

The aim of this project is to provide an experimental platform for integrating existing model source codes, for further development at the process level and for model comparisons between different groups. We are currently working on an open source version of our own lake model SALMO in form of an R package and released under the GPL.

The ecological lake model SALMO

The “Ecological Lake Model SALMO” (Simulation by means of an Analytical MOdel) is a dynamic model, originally developed at TU Dresden, Institute of Hydrobiology. It describes essential parts of the aquatic foodweb of lakes and reservoirs.

The system of ordinary differential equations originates from the habilitation thesis of Benndorf (1979) who modelled annual time-dependend development of phytoplankton (two groups), zooplankton, oxygen, nutrients (N and P) and external detritus of the water body, based on eld observations and laboratory experiments. First implementations in Fortran and HPL (Hewlett Packard Language) have been developed by Recknagel (Recknagel, 1980; Recknagel and Benndorf, 1982) and were used for numerous theoretical and practical studies (e.g., Benndorf and Recknagel, 1979b,a, 1982; Benndorf et al., 1985; Petzoldt and Recknagel, 1991). Since then, several versions, implementations and spin-offs followed.

R package rSALMO

This R package aims to make an “almost original version” of the foodweb-part of the model publicly available under the GPL 2 and to foster further development. Its source code is derived from an independent implementation of the system of equations of model version SALMO II (Benndorf, 1988). The JAVA version of Dietze and Planke (Willmitzer et al., 1998) was then followed by the C version SALMO-1D of Rolinski (Petzoldt and Siemens, 2002; Rolinski et al., 2005; Petzoldt et al., 2005; Petzoldt and Uhlmann, 2006), that allowed coupling to hydrophysical models such as LAKE (Baumert et al., 1989, 2005b,a) or GOTM (Umlauf et al., 2007). During this time, the system equations underwent fundamental generalisation (same equation for all seasons) and slow but steady evolution.

Recently, Sachse et al. (2014) coupled SALMO-1D to a macrophyte module based on the model PCLake (Janse and van Liere, 1995; Janse et al., 1998) to simulate growth of and interaction effects with submersed water plants. The code is now maintained by Thomas Petzoldt at TU Dresden, Institute of Hydrobiology as a starting point for further developments.

Note that all this is recent work in progress, so please contact me before trying to run applications or investing your valuable work.

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Funding

The recent developments where funded by the German Federal Ministry of Education and Research (BMBF) with grants FKZ:02WT0233 (Getas), FKZ:02WT0720 (IntegTA), FKZ:033L041E (NITROLIMIT) and by Deutsche Forschungsgemeinschaft within the AQUASHIFT priority program (DFG Pa 1202/1-2,3).


2015-04-02, ThPe