NUMmodel
Reference implementation of the Nutrient-Unicellular-Multicellular modelling framework. The model is described in:
- Unicellular plankton: Andersen and Visser: From cell size and first principles to structure and function of unicellular plankton communities
- Copepods: Serra-Pompei et al (2020): A general size- and trait-based model of plankton communities.
- Application to biological pump: Serra-Pompei et al (2022) Progress in Oceanography (189) 102473: Zooplankton trophic dynamics drive carbon export efficiency.
- An introduction to the modelling principles given by Camila Serra-Pompei.
The core library is written in Fortran2008 and is interfaced from matlab and with a minimal frontend in R (see http://oceanlife.dtuaqua.dk/Plankton/R).
The figure above shows a setup with only unicellular generalists run with the MIT ECCO transport matrices. The inset shows a high latitude water column at 60N, 15E, with the lower panel illustrating the trophic strategies: blue for DOC uptake (osmotrophy/bacteria), green for phototrophy, and red for phagotrophy.
Papers using the NUM model:
- Application to the biological carbon pump: C. Serra-Pompei, B.A Ward, J. Pinti, A.W Visser, T. Kiørboe, K.H Andersen (2022): Linking plankton size spectra and community composition to carbon export and its efficiency. Global Biogeochemical Cycles 36(5), e2021GB007275.
- Grigoratou, Maria, Camila Serra-Pompei, Adam Kemberling, and Andrew J. Pershing. Hot and hungry: A mechanistic approach to the direct and indirect effects of marine heatwaves on plankton communities. (2024).
Installation
The library requires a recent version of matlab (2021 or later). Installation and compilation instructions are given in the wiki.
Basic structure
There are three levels of routines: top-level, medium-level and low-level. There are two model systems: an upper ocean represented as a chemostat and a global simulation with transport matrices.
Top-level matlab routines
These routines run a simulation and returns the results in a sim structure:
baserunChemostat(). Runs a chemostat version of the model and plots the output.baserunWatercolumn. Runs a watercolumn extracted from a transport matrix at a specific location.baserunGlobal(). Runs a global simulation with only unicellular generalists.
All units are in micro gC/l (or micro gN/l for nutrient concentration). Units of light are micro mol photons per m2 per second.
Medium-level matlab routines
The routines operates with two basic structures: a parameter structure and a simulation structure. The parameter structure contains all parameters needed for a simulation. The simulation structure contains all the output, which can be used for analysis or for plotting. See more details on the wiki page.
Parameters are set with two calls: one to setup the size spectra to simulate and one to add the parameters for the simulation (chemostat or global). The size spectra are setup with a call to setupXX where XX represent the setup, e.g., setupNUMmodel or setupGeneralistsOnly or (the latter onlu includes unicellular generalists). Parameters for the simulation are subsequently set with a call to parametersChemostat, parametersWatercolumn, or parametersGlobal. For example: p = parametersChemostat( setupGeneralistsOnly() ); (see the wiki for a description of the parameter structure).
Simulations are performed with calls to a simulation routine: sim = simulationChemostat(p), sim = simulationWatercolumn(p, latitude, longitude), or sim = simulationGlobal(p), where p is the parameter structure (see the wiki for a description of the simulation structure).
Plots are made with calls to the plot routines. plotSimulation(sim) makes a series of basic plots of a simulation.