def input_models(mate_encounter: float, mate_radius: float):
"""
Create all the input models
Args:
mate_encounter: mate encounter constant
mate_radius: mate radius
Returns:
input models
"""
return [
growth.max_gut(),
growth.growth(param.alpha_ss, param.alpha_rr, param.beta_ss,
param.beta_rr, dominance),
init_bio.init_num(param.lam_0_egg),
init_bio.init_mass(param.mu_0_egg_ss, param.mu_0_egg_rr,
param.sig_0_egg_ss, param.sig_0_egg_rr,
dominance),
init_bio.init_juvenile(param.mu_0_larva_ss, param.mu_0_larva_rr,
param.sig_0_larva_ss, param.sig_0_larva_rr,
dominance),
init_bio.init_mature(param.mu_0_mature_ss, param.mu_0_mature_rr,
param.sig_0_mature_ss, param.sig_0_mature_rr,
dominance),
init_bio.init_plant(param.mu_leaf, param.sig_leaf),
move.adult(param.adult_scale, param.adult_shape),
repro.mating(mate_encounter),
repro.radius(mate_radius),
repro.fecundity(param.fecundity_maximum, param.fecundity_decay),
repro.density(param.eta, param.gamma),
repro.init_sex(param.female_prob)
]
class Fecundity(object):
"""
Class to setup and run a simulation of the female fecundity
Variables:
fecundity: the fecundity model
"""
init_num = init_bio.init_num(param.lam_0_egg)
fecundity = repro.fecundity(param.fecundity_maximum, param.fecundity_decay)
def run(self, ages: list) -> list:
"""
Run the model for each age
Args:
ages: list of ages
Returns:
list of number of eggs
"""
numbers = []
for age in ages:
number_egg_mass = self.fecundity(age, 0, 'none')
number_eggs = self.init_num('none')
numbers.append(number_egg_mass * number_eggs)
return numbers
@classmethod
def run_sim(cls, ages: list) -> list:
"""
Setup and rum the sim
Args:
ages: ages to simulate
Returns:
number of eggs produced
"""
new = cls()
return new.run(ages)
dominance),
develop.pupa_dev(param.mu_pupa_dev,
param.sig_pupa_dev),
forage.adlibitum(param.forage_steps),
forage.egg(param.egg_factor),
forage.larva(param.larva_factor),
forage.fight(param.fight_slope),
forage.encounter(cannib),
forage.radius(param.cannibalism_radius),
move.larva(param.larva_scale,
param.larva_shape),
move.adult(param.adult_scale,
param.adult_shape),
repro.mating(param.mate_encounter),
repro.radius(param.mate_radius),
repro.fecundity(param.fecundity_maximum,
param.fecundity_decay),
repro.density(param.eta,
param.gamma),
repro.init_sex(param.female_prob),
survive.egg_sur(param.egg_prob),
survive.pupa_sur(param.pupa_prob),
survive.adult_sur(param.adult_prob),
survive.larva_sur(param.larva_prob_non_bt_rr,
param.larva_prob_non_bt_ss,
param.larva_prob_bt_rr,
sur,
dominance)
]
base_dir = sys.argv[0].split('.')[0]
base_save = base_dir.split('/')[-1]
class Simulator(object):
"""
Class to setup and run a simulation of only biomass growth:
Variables:
nums: initial population numbers
bt_prop: bt proportion
"""
grid = [graph.graph(field_grid), (keyword.hexagon, 1, 1, True)]
attrs = {0: tracking.genotype_attrs}
data = (np.inf, )
steps = [({
keyword.female: [keyword.move, keyword.reproduce],
keyword.male: [keyword.move]
}, param.forage_steps),
({
keyword.female: [keyword.advance_age, keyword.reset],
keyword.male: [keyword.advance_age, keyword.reset]
}, )]
emigration = []
immigration = []
input_models = [
growth.max_gut(),
growth.growth(param.alpha_ss, param.alpha_rr, param.beta_ss,
param.beta_rr, dominance),
init_bio.init_num(param.lam_0_egg),
init_bio.init_mass(param.mu_0_egg_ss, param.mu_0_egg_rr,
param.sig_0_egg_ss, param.sig_0_egg_rr, dominance),
init_bio.init_juvenile(param.mu_0_larva_ss, param.mu_0_larva_rr,
param.sig_0_larva_ss, param.sig_0_larva_rr,
dominance),
init_bio.init_mature(param.mu_0_mature_ss, param.mu_0_mature_rr,
param.sig_0_mature_ss, param.sig_0_mature_rr,
dominance),
init_bio.init_plant(param.mu_leaf, param.sig_leaf),
move.adult(param.adult_scale, param.adult_shape),
repro.mating(param.mate_encounter),
repro.radius(param.mate_radius),
repro.fecundity(param.fecundity_maximum, param.fecundity_decay),
repro.density(param.eta, param.gamma),
repro.init_sex(param.female_prob)
]
input_variables = param.repro_values
nums: hint.init_pops
bt_prop: float
simulation: hint.simulation = None
def __post_init__(self):
self.simulation = main_simulation.Simulation. \
setup(self.nums,
self.grid,
self.attrs,
self.data,
self.bt_prop,
self.steps,
self.emigration,
self.immigration,
*self.input_models,
**self.input_variables)
def collect(self) -> int:
"""
Collect the number of egg_masses
Returns:
number of egg_masses
"""
egg_masses = self.simulation.agents.agents(keyword.egg_mass)
return len(egg_masses)
def run(self, times: list) -> tuple:
"""
Run the simulation for each time
Args:
times: the times for the simulation
Returns:
num egg_mass, densities
"""
#
# females = self.simulation.agents[(0,)]['female'].agents
# for agent in females:
# print('Agent: {}, Num_eggs: {}'.format(agent.unique_id,
# agent.num_eggs))
data = [self.collect()]
for time in times[1:]:
print(' {} Running step: {}'.format(datetime.datetime.now(),
time))
self.simulation.step()
data.append(self.collect())
# females = self.simulation.agents[(0,)]['female'].agents
# for agent in females:
# print('Agent: {}, Num_eggs: {}'.format(agent.unique_id,
# agent.num_eggs))
density = []
for number in data:
density.append(number / (field_grid**2))
return data, density
