Computer code for: Evolutionary-developmental (evo-devo) dynamics of hominin brain size

  • Mauricio González-Forero (University of St Andrews) (Creator)

Dataset

Description

This software contains the computer code of "Evolutionary-developmental (evo-devo) dynamics of hominin brain size" by Mauricio González-Forero. Below I describe and explain the files to run the brain model and make the figures and video in the main text and supplementary information. These files were prepared to run in Julia 1.7.2 using the editor Visual Studio Code 1.81.1. Julia and Visual Studio Code can be installed as indicated in https://www.julia-vscode.org/docs/dev/gettingstarted/. The following Julia packages are needed: Plots, Dates, CSV, DataFrames, LinearAlgebra, Distributions, LazySets, and Polyhedra. There are two sets of files: Set 1 lists the files that produce the figures: run each file to obtain the figure indicated by the file name; restart Julia before running each file, then open the desired file with Visual Code Studio and press the Execute button. Fig1.jl must be run first, before most other files. Set 2 contains the underlying code for the model or figures. Each file is described below. Set 1 Fig1.jl: Generates Fig. 1. It takes about 30 min to run. This file must be run first, before most of the other files. Fig2a,S12.jl: Generates Figs. 2a and S12. It takes about 1 hour and 25GB of RAM to run. If less time or RAM are desired, reduce sampleSize. Fig2b.jl: Generates Fig. 2b. It takes about 1 min to run. Fig3.jl: Generates Fig. 3. It takes about 1 min to run. Fig4.jl: Generates Fig. 4. It takes about 55 min to run. Fig6.jl: Generates Fig. 6. It takes about 1 min to run. EDFig2.jl: Generates Extended Data Fig. 2. It takes about 1 min to run. EDFig3.jl: Generates Extended Data Fig. 3. It takes about 1 min to run. EDFig4.jl: Generates Extended Data Fig. 4. It takes about 2 min to run. FigS1.jl: Generates Fig. S1. It takes about 5 min to run. FigS2.jl: Generates Fig. S2. It takes about 5 min to run. FigS3.jl: Generates Fig. S3. It takes about 5 min to run. FigS4.jl: Generates Fig. S4. It takes about 1 min to run. FigS5.jl: Generates Fig. S5. It takes about 1 min to run. FigS6.jl: Generates Fig. S6. It takes about 40 min to run. FigS7.jl: Generates Fig. S7. It takes about 1 min to run. FigS8.jl: Generates Fig. S8. It takes about 55 min to run. FigS9.jl: Generates Fig. S9. It takes about 3 min to run. FigS10.jl: Generates Fig. S10. It takes about 3 min to run. FigS11.jl: Generates Fig. S11. It takes about 2 min to run. SVideoTop.jl: Generates a gif file for the top panel of the Supplementary Video. SVideoBottom.jl: Generates gif files for the bottom panels of the Supplementary Video. Set 2 RunBrain.jl: This file runs the brain model and is called by Fig1.jl. BrainParameters.jl: This file specifies the parameter values. BrainInitialConditions.jl: This file specifies the initial conditions. BrainFunctions.jl: This file defines the functions used to run the brain model, except for the functions used in the socio-devo dynamics phase. BrainFunctionsSDS.jl: This file defines the functions used in the socio-devo dynamics phase. BrainPlotFunctions.jl: This file defines the functions used to make the figures. PrimateData.jl: This file contains the primate data used in the figures.
Date made available27 Mar 2024
PublisherZenodo

Software

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