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)
]
develop.larva_dev(param.mu_larva_dev_ss,
param.mu_larva_dev_rr,
param.sig_larva_dev_ss,
param.sig_larva_dev_rr,
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)
class Simulator(object):
"""
Class to setup and run a simulation of only biomass growth:
Variables:
nums: initial population numbers
forage: the plant forage model
"""
attrs = {1: tracking.genotype_attrs,
2: tracking.genotype_attrs}
data = (np.inf,)
steps = [({keyword.larva: [keyword.move],
keyword.female: [keyword.move]},)]
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),
sex_model,
move.larva(param.larva_scale,
param.larva_shape),
move.adult(param.adult_scale,
param.adult_shape)]
input_variables = param.repro_values
nums: hint.init_pops
grid: hint.grid_generators
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) -> tuple:
"""
Collect a list of locations
Returns:
tuple of locations
"""
larvae = self.simulation.agents.agents(keyword.larva)
adults = self.simulation.agents.agents(keyword.female)
larvae_values = []
for agent in larvae:
larvae_values.append(agent.location.copy())
adult_values = []
for agent in adults:
adult_values.append(agent.location.copy())
return larvae_values, adult_values
def run(self, times: list) -> tuple:
"""
Run the simulation for each time
Args:
times: the times for the simulation
Returns:
biomass data
"""
larva, adult = self.collect()
larvae = [larva]
adults = [adult]
for time in times[1:]:
print(' {} Running step: {}'.
format(datetime.datetime.now(), time))
self.simulation.step()
new_larva, new_adult = self.collect()
larvae.append(new_larva)
adults.append(new_adult)
return larvae, adults
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.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) -> tuple:
"""
Collect the number of egg_masses
Returns:
number of egg_masses
"""
females = self.simulation.agents.agents(keyword.female)
mated = []
for female in females:
if female.mate is not None:
mated.append(female)
return len(females), len(mated)
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, mated = self.collect()
data_females = [females]
data_mated = [mated]
data_prop = [mated / females]
for time in times[1:]:
print(' {} Running step: {}'.format(datetime.datetime.now(),
time))
self.simulation.step()
females, mated = self.collect()
data_females.append(females)
data_mated.append(mated)
data_prop.append(mated / females)
return data_females, data_mated, data_prop
