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]
try:
work_path = os.environ['WORK']
path_save = '{}/{}/{}'.format(work_path,
'FallArmyworm_Thesis',
class Simulator(object):
"""
Class to setup and run a simulation of only biomass growth:
Variables:
nums: initial population numbers
forage: the plant forage model
"""
grid = [(keyword.hexagon, 1, 1, True), (keyword.hexagon, 1, 1, True)]
attrs = {1: tracking.genotype_attrs}
data = (np.inf, )
steps = [({
keyword.larva: [keyword.survive],
keyword.egg: [keyword.survive],
keyword.pupa: [keyword.survive],
keyword.female: [keyword.survive]
}, )]
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,
sur.egg_sur(param.egg_prob),
sur.pupa_sur(param.pupa_prob),
sur.adult_sur(param.adult_prob)
]
input_variables = param.repro_values
# input_survive.larva_survival,
nums: hint.init_pops
bt_prop: float
ss_bt_sur: float = param.larva_prob_bt_low_ss
simulation: hint.simulation = None
def __post_init__(self):
larva_survive = sur.larva_sur(param.larva_prob_non_bt_rr,
param.larva_prob_non_bt_ss,
param.larva_prob_bt_rr, self.ss_bt_sur,
dominance)
input_models = self.input_models.copy()
input_models.append(larva_survive)
self.simulation = main_simulation.Simulation. \
setup(self.nums,
self.grid,
self.attrs,
self.data,
self.bt_prop,
self.steps,
self.emigration,
self.immigration,
*input_models,
**self.input_variables)
def run(self, times: list) -> None:
"""
Run the simulation for each time
Args:
times: the times for the simulation
Returns:
biomass data
"""
for _ in times[1:]:
self.simulation.step()
