There are scripts in C, Mathematica and R. You can download all the scripts as a zipped file here: click to download.

C

Stochastic simulations:

Folders

• Scripts/ will store the combined scripts;
• Results/ will store the outputs of the simulations.

C files

They are combined to form a single file, depending on the life-cycle

• htg-island_base.c (click here to download)
• htg-island_onestepBD.c (click here to download)
• htg-island_onestepDB.c (click here to download)
• htg-island_onestepWF.c (click here to download)

Submission file

The simulations were run on the Migale cluster, which has a qsub type queuing system.

To execute the scripts:

• Upload the entire C/ folder to the cluster,
• Update the value of THEPATH in the submit_*.sh file, so that the path matches the path to the scripts in your system. Type

  ./submit_all.sh
  

  to submit all the jobs for all simulations to the cluster. The submit_all.sh file is available (here)

The results (.txt files) are stored in a Results/ folder.

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Mathematica

Analytical part:

• .pdf output of the Mathematica notebook (click here to download)
• .nb source file (same content as pdf version, but editable) (click here to download)

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R

To plot the figures, using simulation data and outputs from Mathematica.

• AllFigs.R is a script to plot all Figures at once (click here to download),
• globalGraphParms.R contains graphical parameters (e.g. colors) (click here to download),
• loadData.R is a script to… load the simulation data (click here to download),
• Rplots.R plots the panels of Figure 1 (click here to download),
• EXplots.R plots the panels of Figure 2, and supplementary Figures S1-S4 (click here to download).
• explainDB.R plots the panels of Figure 3 (click here to download),
• Qplots.R plots the panels of Figure S5 (click here to download),

You also need a Pics/ folder, that will contain the pdf of the generated figures.

NB: There are commands to open the newly created figures (system("xdg-open...")). This only works with Unix. With a Mac, you need to replace xdg-open by open. On Windows… I don’t know! But it does not matter, you can always open the files manually!