EcoSISTEM.jl

EcoSISTEM is a Julia package that provides functionality for simulating species undergoing dynamic biological processes such as birth, death, competition and dispersal, as well as environmental changes in climate and habitat.

The package was primarily developed for global scale simulations of plant biodiversity. The underlying model for this is described in the arXiv paper arXiv:1911.12257 (q-bio.QM) Dynamic virtual ecosystems as a tool for detecting large-scale responses of biodiversity to environmental and land-use change. The paper is the reference for the model; How the model works is the reference for what the package currently implements.

Species are regulated by competition for a shared pool of resources: in each cell the demands of everything present are summed against what the cell supplies, so births fall and deaths rise as that total approaches the supply. Carrying capacity is not a parameter anywhere in the package - it is what those two pressures leave behind. Conditions such as temperature decide where a species can persist; resources decide how many.

A simulation is assembled from three things - an environment, a list of species, and the fit between them - on a grid decided in advance. The basics walks through a first run and How the model works explains the population model underneath; Layers, conditions and resources covers what an environmental layer means and where climate data comes from; Time in EcoSISTEM covers the simulation clock and environments that change as a run proceeds; Interventions covers changing the ecosystem itself part way through a run; Integration with Diversity.jl covers what to measure once it has run; and Running at scale covers sizing a large run and spreading one across MPI ranks. Examples is the shortest route to something running.

This package is in beta now, so please raise an issue if you find any problems. For more information on how to contribute, please read our contributing guidelines.