Scripts:

• ./generate_system.R (kryptotype dimension) (input dimension) (output dimension)

• ./do_plots.R (name of directory with params.R in) (number of extra dimensions) (system sigma) (number of replicates) Plots:

  • mutations
  • deletions
  • kryptotypes
  • eigenvalues

• ./evolve_population.R (name of system directory) (population_size) (max_generation) (p_mut) (sigma_mut) (p_del) (p_new)

• ./evolve_sexual.R (name of system directory) (population_size) (max_generation) (p_mut) (sigma_mut)

Applies to output of evolution experiments:

• ./plot_fitness_traces.R (simulation directory 1) (simulation directory 2) [number of systems per step]
• ./plot_population.R (Rdata fossil file)