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Scripts to accompany the paper "A working guide to spatial mechanistic modelling in Julia" by Rafael Schouten, James Maino, Virgile Baudrot and Paul Umina.

These scripts should be reproducible on all systems, including all the binaries used by various packages.

Setup

Download and add Julia to your system.

Julia v1.6 is required.

Then, download or clone this code repository locally. To install exact versions of all packages, start a julia REPL in the downloaded project folder, and in package mode (with ]) activate and instantiate the project:

] 
activate .
instantiate

Or from a command line, in the repository directory:

julia -e 'using Pkg; Pkg.activate("."); Pkg.instantiate()'

Use

To e.g. build all the plots from the command line, in the repository directory you can run:

julia --project=. src/plots.jl

Scripts can also be stepped through in an editor like VSCode, with the julia-vscode plugin. This may be a better way to explore and analyse the code, and to run the simulations in outputs.jl.

Be sure to start Julia in the project folder. The project directory should be activated automatically in VSCode, if not, or in other editors, in the REPL type:

] 
activate .
instantiate

This will ensure that you have the exact versions of all dependencies, which means these scripts will continue to work into the future.

Included scripts

To run directly:

  • plots.jl: creates most plots seen in paper from rules.jl/data.jl.
  • benchmarks.jl: runs simulation bechmarks and creates benchmark plot.
  • outputs.jl: provides some interface visualisations of the simulations.
  • growthmaps.jl: builds the growth-rate data used to drive growth models.

Called by the other scripts:

  • rules.jl: defines the rules used in the simulations.
  • data.jl: prepares simulation data.