Fix scenarios extra argument parsing + tweak variant scenario (10)

README.md

@@ -11,9 +11,10 @@
 ```bash
 pip install pandemic-simulation  # Last stable version
 # or
+apt-get install python3-venv gcc python3-dev
 python3 -m venv ./venv
 source ./venv/bin/activate
-pip install --upgrade -r requirements.txt
+pip install -r requirements.txt
 
 
 ### To plot new daily cases

scenario/example/sc10_variant.py

@@ -17,10 +17,13 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
     random.seed(specific_seed)
     np.random.seed(specific_seed)
 
-    if len(params[additional_scenario_params_key]) < 1:
+    if len(params[additional_scenario_params_key]) < 3:
         raise AssertionError("Need more additional_scenario parameter")
     else:
+        assert(params[additional_scenario_params_key][2] in ["False", "True"])
         rate_daily_vaccinated = int(params[additional_scenario_params_key][0])
+        variant_kind = params[additional_scenario_params_key][1]
+        restrict_genetic_cost = params[additional_scenario_params_key][2] == "True"
 
     if rate_daily_vaccinated < 0:
         # Morrocan daily rate of vaccination
@@ -36,14 +39,23 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
     variant_immunization = 1
     variant_mortality = 1  # tradeoff parameter
     variant_hospital = 1  # tradeoff parameter
-    restrict_genetic_cost = False
+
     death_stat = []
 
     for param_variant_iter in range(params[nvariant_key]):
-        run_stats = get_zero_run_stats(params)
         # Update parameters
-        # Range [0.5, 1.5] with a 1/param stem (+/- 50%)
-        variant_hospital = 0.5 + param_variant_iter/params[nvariant_key]
+        # Range [0.25, 1.75] with a 1/param step (+/- 75%)
+        if variant_kind == "C":
+            variant_contagiosity = 0.25 + 1.5 * param_variant_iter / params[nvariant_key]
+        if variant_kind == "I":
+            variant_immunization = 1 + 2 * param_variant_iter / params[nvariant_key]
+        if variant_kind == "M":
+            variant_mortality = 0.25 + 1.5 * param_variant_iter / params[nvariant_key]
+        if variant_kind == "H":
+            variant_hospital = 0.25 + 1.5 * param_variant_iter / params[nvariant_key]
+        if variant_kind == "MH" or variant_kind == "HM":
+            variant_mortality = 0.25 + 1.5 * param_variant_iter / params[nvariant_key]
+            variant_hospital = 1.75 - 1.5 * param_variant_iter / params[nvariant_key]
 
         if restrict_genetic_cost:
             variant_total_cost = variant_contagiosity + variant_immunization + variant_mortality + variant_hospital
@@ -56,16 +68,22 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
         params[work_infection_key] = 0.05 * variant_contagiosity
         params[store_infection_key] = 0.02 * variant_contagiosity
         params[transport_infection_key] = 0.01 * variant_contagiosity
+
         params[variant_mortality_k] = variant_mortality
+        params[death_bounds_key] = (8 / variant_mortality, 31 / variant_mortality)
+
         params[variant_hospitalization_k] = variant_hospital
-        params[immunity_bounds_key] = (270, 450) * variant_immunization  # assuming about a year of immunity (~flu)
+        params[hospitalization_bounds_key] = (8 / variant_hospital, 16 / variant_hospital)
+
+        # assuming about a year of immunity (~flu)
+        params[immunity_bounds_key] = (int(270/variant_immunization), int(450/variant_immunization))
         virus_dic = get_virus_simulation_t0(params)
 
         for day in range(params[nday_key]):
             pba.update.remote(1)
             old_healthy = [(k, env_dic[IAG_K][k]) for k, v in virus_dic[STA_K].items() if v == HEALTHY_V]
             nb_indiv_vaccinated = max(0, int(params[nindividual_key] * rate_daily_vaccinated * (1-day/100)))
-            if len(old_healthy) > nb_indiv_vaccinated:
+            if len(old_healthy) > nb_indiv_vaccinated and day <= 100:
                 old_sorted = sorted(old_healthy, key=lambda kv: -kv[1])
                 old_lucky = [o[0] for o in old_sorted[:nb_indiv_vaccinated]]
                 virus_dic[STA_K].update((o, IMMUNE_V) for o in old_lucky)

scenario/example/sc1_simple_lockdown_removal.py

@@ -32,7 +32,7 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
     if len(params[additional_scenario_params_key]) < 1:
         raise AssertionError("Need an additional_scenario parameter")
 
-    days_to_lockdown_loosening = params[additional_scenario_params_key][0]
+    days_to_lockdown_loosening = float(params[additional_scenario_params_key][0])
     days_with_no_cases = 0
     first_day_lockdown_loosening = -1
     virus_dic = get_virus_simulation_t0(params)

scenario/example/sc2_yoyo_lockdown_removal.py

@@ -32,9 +32,9 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
 
     if len(params[additional_scenario_params_key]) < 3:
         raise AssertionError("Need more additional_scenario parameter")
-    days_to_lockdown_loosening = params[additional_scenario_params_key][0]
-    factor_bed = params[additional_scenario_params_key][1]
-    max_lockdown = params[additional_scenario_params_key][2]
+    days_to_lockdown_loosening = float(params[additional_scenario_params_key][0])
+    factor_bed = float(params[additional_scenario_params_key][1])
+    max_lockdown = float(params[additional_scenario_params_key][2])
 
     days_with_no_cases = 0
     days_to_lockdown_change = 0

scenario/example/sc3_loose_lockdown.py

@@ -23,7 +23,7 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
     if len(params[additional_scenario_params_key]) < 1:
         raise AssertionError("Need more additional_scenario parameter")
 
-    percent_increase = params[additional_scenario_params_key][0]
+    percent_increase = float(params[additional_scenario_params_key][0])
 
     params[store_preference_key] = 0.3
     params[remote_work_key] = 0.58

scenario/example/sc4_rogue_citizen.py

@@ -26,7 +26,7 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
         raise AssertionError("Need more additional_scenario parameter")
 
     nb_rogue = int(params[additional_scenario_params_key][0])
-    rogue_factor = params[additional_scenario_params_key][1]
+    rogue_factor = float(params[additional_scenario_params_key][1])
 
     params[store_preference_key] = 0.95
     params[remote_work_key] = 0.98

scenario/example/sc5_rogue_neighborhood.py

@@ -26,7 +26,7 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
         raise AssertionError("Need more additional_scenario parameter")
 
     nb_bloc = int(params[additional_scenario_params_key][0])
-    rogue_factor = params[additional_scenario_params_key][1]
+    rogue_factor = float(params[additional_scenario_params_key][1])
 
     rogues_blocks_x = np.random.choice(range(params[nb_1d_block_key]), nb_bloc)
     rogues_blocks_y = np.random.choice(range(params[nb_1d_block_key]), nb_bloc)

scenario/example/sc9_vaccination.py

@@ -45,7 +45,7 @@ def do_parallel_run(env_dic, params, run_id, specific_seed, pba: ActorHandle):
         pba.update.remote(1)
         old_healthy = [(k, env_dic[IAG_K][k]) for k, v in virus_dic[STA_K].items() if v == HEALTHY_V]
         nb_indiv_vaccinated = max(0, int(params[nindividual_key] * rate_daily_vaccinated * (1-day/100)))
-        if len(old_healthy) > nb_indiv_vaccinated:
+        if len(old_healthy) > nb_indiv_vaccinated and day <= 100:
             old_sorted = sorted(old_healthy, key=lambda kv: -kv[1])
             old_lucky = [o[0] for o in old_sorted[:nb_indiv_vaccinated]]
             virus_dic[STA_K].update((o, IMMUNE_V) for o in old_lucky)

simulator/helper/parser.py

@@ -51,7 +51,7 @@ def get_parser():
                         action='store_true')
 
     # Scenarios related
-    parser.add_argument('--extra-scenario-params', type=float, nargs="*", help='Additional scenario parameters',
+    parser.add_argument('--extra-scenario-params', type=str, nargs="*", help='Additional scenario parameters',
                         dest=additional_scenario_params_key)
 
     return parser

simulator/helper/plot.py

@@ -50,6 +50,7 @@ def draw_new_daily_cases(stats_arg, show_plot, x_tick=10):
 def draw_meta_simulation(death_stat_arg, show_plot):
     fig, ax = plt.subplots(figsize=(15, 10))
     set_ax_meta_simulation(ax, death_stat_arg)
+    print("ok")
     if show_plot:
         plt.show()
     else:
@@ -325,12 +326,16 @@ def set_ax_meta_simulation(ax, death_stat_arg):
 
     p1 = ax.bar(indices, death_serie, width, yerr=err, align='center', alpha=0.5, ecolor="#808080", color="#44A1A0")
 
+    bottom_y = int(min(death_serie) * 0.8)
+    top_y = int(1+max(death_serie) * 1.2)
+
+    ax.set_ylim(bottom=bottom_y, top=top_y)
     ax.set_ylabel('Total death')
     ax.set_xlabel('Variant parameter')
     ax.set_title('Total death / covid-19 variant type')
     ax.set_xticks(np.arange(0, n_variant_arg, 1))
-    ax.set_xticklabels(tuple([str(i-n_variant_arg/2) for i in range(n_variant_arg)]))
-    ax.set_yticks(np.arange(0, int(1+max(death_serie) * 1.1), int(1+max(death_serie) / 10)))
+    ax.set_xticklabels([round(s, 2) for s in np.arange(0.25, 1.75, 1.5 / n_variant_arg)])
+    ax.set_yticks(np.arange(bottom_y, top_y, int(1+max(death_serie) / 10)))
     ax.legend((p1[0],), ('Death',))
 
 

simulator/helper/simulation.py

@@ -55,8 +55,8 @@ def get_infection_params():
         DEA_INIT_K: copy.deepcopy(time_to_death),
         IMM_INIT_K: copy.deepcopy(time_to_end_immunity),
 
-        variant_mortality_k: 1,
-        variant_hospitalization_k: 1,
+        variant_mortality_k: params_arg[variant_mortality_k] if variant_mortality_k in params_arg else 1,
+        variant_hospitalization_k: params_arg[variant_hospitalization_k] if variant_hospitalization_k in params_arg else 1,
 
         STA_K: life_state,
         NC_K: 0