B_opt_country = get_B_policy(
file_B_opt,
country,
'Uncontained',
)
Ng = B_opt_country.shape[0]
assert len(
age_groups
) == 9, 'Check the defined age-groups. Something is wrong there.'
ref_obj = epid_sim(
model_type=model_type,
B=B_opt_country,
Gamma=Gamma,
Sigma=Sigma,
dir_save_plots_main=dir_save_plots,
country='Iran',
policy_list=['Uncontained'],
policy_switch_times=[0],
x0=x0_vec,
t_end=t_end,
str_policy='Uncontained',
group_labels=age_groups,
)
# %% current estimate
t_s = 60
list_t_switch = [0] + list(np.arange(t_s, t_s + 30 * 7, 30))
str_ts = '_start_' + str(t_s) + 'D'
all_containment_list = [
'Uncontained',
1.5,
1.2,
B_opt_country = get_B_policy(
file_B_opt,
country,
'Uncontained',
)
Ng = B_opt_country.shape[0]
assert len(
age_groups
) == 9, 'Check the defined age-groups. Something is wrong there.'
ref_obj = epid_sim(
model_type=model_type,
B=B_opt_country,
Gamma=Gamma,
Sigma=Sigma,
dir_save_plots_main=dir_save_plots_main,
country=country,
policy_list=my_policy,
policy_switch_times=[0],
x0=x0_vec,
t_end=t_end,
str_policy=str_policy,
group_labels=age_groups,
)
list_sol_I = []
list_sol_R = []
# pc1 = 45.
pc2 = pc1 + 10
x0R_array = list(np.arange(0., pc1, 5.0)/100) +\
list(np.arange(pc1, pc2, 1.0)/100)
for x0R in x0R_array:
print('x0R --------------> ', x0R)
file_B_opt,
country,
'Uncontained',
)
Ng = B_opt_country.shape[0]
assert len(
age_groups
) == 9, 'Check the defined age-groups. Something is wrong there.'
dir_save = Path(dir_save_plots, 'T_I_variable', str(T_I))
epid_obj = epid_sim(
model_type=model_type,
B=B_opt_country,
Gamma=Gamma,
Sigma=Sigma,
dir_save_plots_main=dir_save,
country=country,
policy_list=all_containment_list,
policy_switch_times=list_t_switch,
x0=x0_vec,
t_end=t_end,
str_policy=policy_name,
group_labels=age_groups,
)
sol_agg_I = epid_obj.sol_agg_dict['I']
sol_agg_R = epid_obj.sol_agg_dict['R']
list_sol_I.append(sol_agg_I)
list_sol_R.append(sol_agg_R)
# dir_save_plots.mkdir(exist_ok=True, parents=True)
filesave_I = Path(dir_save_plots,
model_type + '_' + country + '_I_AGG_ALL_T_I.png')
filesave_R = Path(dir_save_plots,
#
Sigma = Gamma *10
model_type = 'SIR'
#%% reference policy: uncontained
policy_name = 'Uncontained'
list_t_switch = [0,]
all_containment_list = ['Uncontained',]
ref_obj = epid_sim(model_type=model_type,
B=B_opt_SIR,
Gamma=Gamma,
Sigma=Sigma,
dir_save_plots_main=dir_save_plots_main,
country='Germany',
policy_list=all_containment_list,
policy_switch_times=list_t_switch,
x0=x0_vec,
t_end=t_end,
str_policy=policy_name,
group_labels=age_groups,)
ref_obj.plot_agg()
ref_obj.plot_strat()
ref_obj.plot_strat_multiax()
print('*************************************************************')
#%% Uncontained_then_switching_R0
list_t_switch = [0, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360, ]
all_containment_list = ['Uncontained',
'R0_is_1',
'Uncontained',
'R0_is_1',
print(country)
B_opt_country = get_B_policy(file_B_opt, country, 'Uncontained', )
Gamma = load_mat(file_B_opt, 'Gamma')
Ng = B_opt_country.shape[0]
assert len(age_groups) == 9, 'Check the defined age-groups. Something is wrong there.'
if model_type == 'SEIR':
Sigma = load_mat(file_B_opt, 'Sigma')
else:
Sigma = np.zeros((Ng, Ng))
epid_obj = epid_sim(model_type=model_type,
B=B_opt_country,
Gamma=Gamma,
Sigma=Sigma,
dir_save_plots_main=dir_save_plots,
country=country,
policy_list=all_policies,
policy_switch_times=list_t_switch,
x0=x0_vec,
t_end=t_end,
str_policy='00_OVERALL',
group_labels=age_groups,)
sol_agg_I = epid_obj.sol_agg_dict['I']
sol_agg_R = epid_obj.sol_agg_dict['R']
list_sol_I.append(sol_agg_I)
list_sol_R.append(sol_agg_R)
# dir_save_plots.mkdir(exist_ok=True, parents=True)
filesave_I = Path(dir_save_plots, model_type + '_I_AGG_ALL_countries.png')
filesave_R = Path(dir_save_plots, model_type + '_R_AGG_ALL_countries.png')
# plot aggregate plots to compare all policies.