Defining Initial Clone Fitness

The fitness of an initial clone is defined using the fitness_array.

If fitness_array is defined, it must contain a fitness value for each unique initial clone.
If no fitness_array is provided, all initial clones will be given a fitness value of 1.

The fitness of mutations that are generated during a simulation is more complex, and described in other tutorial guides.

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With no fitness defined, all of the clones are given a fitness of 1

from clone_competition_simulation import Parameters, TimeParameters, PopulationParameters
import numpy as np
p = Parameters(
    algorithm='Moran',
    times=TimeParameters(max_time=10, division_rate=1), 
    population=PopulationParameters(initial_size_array=np.ones(16))
)
s = p.get_simulator()
s.run_sim()
print(s.view_clone_info())

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Give each initial clone a random fitness value between 0.5 and 1.5

from clone_competition_simulation import FitnessParameters

p = Parameters(
    algorithm='Moran', 
    times=TimeParameters(max_time=10, division_rate=1), 
    population=PopulationParameters(initial_size_array=np.ones(16)),
    fitness=FitnessParameters(fitness_array=np.random.uniform(0.5, 1.5, size=16))
)
s = p.get_simulator()
s.run_sim()
print(s.view_clone_info())

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The same principle works for clones defined using a grid

p = Parameters(
    algorithm='Moran2D',
    times=TimeParameters(max_time=10, division_rate=1), 
    population=PopulationParameters(initial_grid=np.arange(16).reshape(4, 4), cell_in_own_neighbourhood=False),
    fitness=FitnessParameters(fitness_array=np.random.uniform(0.5, 1.5, size=16))
)
s = p.get_simulator()
s.run_sim()
print(s.view_clone_info())