def run(self):
'''run simulation'''
i = 0
while i < self.Config.simulation_steps:
try:
self.tstep()
except KeyboardInterrupt:
print('\nCTRL-C caught, exiting')
sys.exit(1)
#check whether to end if no infecious persons remain.
#check if self.frame is above some threshold to prevent early breaking when simulation
#starts initially with no infections.
if self.Config.endif_no_infections and self.frame >= 500:
if len(self.population[(self.population[:,6] == 1) |
(self.population[:,6] == 4)]) == 0:
i = self.Config.simulation_steps
if self.Config.save_data:
save_data(self.population, self.pop_tracker)
#report outcomes
print('\n-----stopping-----\n')
print('total timesteps taken: %i' %self.frame)
print('total dead: %i' %len(self.population[self.population[:,6] == 3]))
print('total recovered: %i' %len(self.population[self.population[:,6] == 2]))
print('total infected: %i' %len(self.population[self.population[:,6] == 1]))
print('total infectious: %i' %len(self.population[(self.population[:,6] == 1) |
(self.population[:,6] == 4)]))
print('total unaffected: %i' %len(self.population[self.population[:,6] == 0]))
def run(self):
'''run simulation'''
if self.Config.visualise:
self.fig, self.spec, self.ax1, self.ax2, self.tight_bbox = build_fig(
self.Config)
i = 0
while i < self.Config.simulation_steps:
try:
self.tstep()
except KeyboardInterrupt:
print('\nCTRL-C caught, exiting')
sys.exit(1)
#check whether to end if no infectious persons remain.
#check if self.frame is above some threshold to prevent early breaking when simulation
#starts initially with no infections.
if self.Config.endif_no_infections and self.frame >= 300:
if len(self.population[(self.population[:, 6] == 1) |
(self.population[:, 6] == 4)]) == 0:
i = self.Config.simulation_steps
else:
i += 1
if self.Config.plot_last_tstep:
self.fig_sir, self.spec_sir, self.ax1_sir = build_fig_SIRonly(
self.Config)
draw_SIRonly(self.Config, self.population, self.pop_tracker,
self.frame, self.fig_sir, self.spec_sir, self.ax1_sir)
if self.Config.save_data:
save_data(self.population, self.pop_tracker)
#report outcomes
if self.Config.verbose:
print('\n-----stopping-----\n')
print('total timesteps taken: %i' % self.frame)
print('total dead: %i' %
len(self.population[self.population[:, 6] == 3]))
print('total recovered: %i' %
len(self.population[self.population[:, 6] == 2]))
print('total infected: %i' %
len(self.population[self.population[:, 6] == 1]))
print('total infectious: %i' %
len(self.population[(self.population[:, 6] == 1) |
(self.population[:, 6] == 4)]))
print('total unaffected: %i' %
len(self.population[self.population[:, 6] == 0]))
print('mean distance travelled: %f' %
np.mean(self.pop_tracker.distance_travelled))
infection_chance, speed, recovery_duration, mortality_chance,
xbounds, ybounds, x_plot, y_plot, wander_range, risk_age,
critical_age, critical_mortality_chance, risk_increase,
no_treatment_factor, treatment_factor, healthcare_capacity,
age_dependent_risk, treatment_dependent_risk, visualise,
verbose, self_isolate, self_isolate_proportion,
isolation_bounds, traveling_infects, lockdown,
lockdown_percentage, lockdown_vector, plot_style)
if len(population[population[:, 6] == 1]) == 0 and i > 100:
print('\n-----stopping-----\n')
print('total dead: %i' %
len(population[population[:, 6] == 3]))
print('total immune: %i' %
len(population[population[:, 6] == 2]))
if save_population:
save_data(population, infected_plot, fatalities_plot)
i = simulation_steps + 1
sys.stdout.write('\r')
sys.stdout.write(
'%i: healthy: %i, infected: %i, immune: %i, in treatment: %i, \
dead: %i, of total: %i' % (i, len(population[population[:, 6] == 0]),
len(population[population[:, 6] == 1]),
len(population[population[:, 6] == 2]),
len(population[population[:, 10] == 1]),
len(population[population[:, 6] == 3]), pop_size))
i += 1
print('\n-----stopping after all sick recovered or died-----\n')
print('total dead: %i' % len(population[population[:, 6] == 3]))