removed proportion_asymptomatic (this is no longer used in the opencl…

… model)
Urban-Analytics · Nov 11, 2020 · 8cc167e · 8cc167e
1 parent 59cb127
commit 8cc167e
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Showing 2 changed files with 7 additions and 15 deletions.
diff --git a/experiments/opencl_runner.py b/experiments/opencl_runner.py
@@ -86,7 +86,6 @@ def get_mean_total_counts(summaries, disease_status: int):
     @staticmethod
     def create_parameters(parameters_file: str = None,
                           current_risk_beta: float = None,
-                          proportion_asymptomatic: float = None,
                           infection_log_scale: float = None,
                           infection_mode: float = None,
                           presymptomatic: float = None,
@@ -131,13 +130,11 @@ def create_parameters(parameters_file: str = None,
         )
 
         # Some parameters are set in the default.yml file and can be overridden
-        if proportion_asymptomatic is None:
-            proportion_asymptomatic = disease_params["asymp_rate"]
+        pass  # None here yet
 
         p = Params(
             location_hazard_multipliers=location_hazard_multipliers,
             individual_hazard_multipliers=individual_hazard_multipliers,
-            proportion_asymptomatic=proportion_asymptomatic
         )
 
         # Remaining parameters are defined within the Params class and have to be manually overridden
@@ -251,17 +248,15 @@ def run_model_with_params(cls, input_params: List, return_full_details=False):
                             "Call the OpenCLRunner.init() function")
 
         current_risk_beta = input_params[0]
-        proportion_asymptomatic = input_params[1]
-        infection_log_scale = input_params[2]
-        infection_mode = input_params[3]
-        presymptomatic = input_params[4]
-        asymptomatic = input_params[5]
-        symptomatic = input_params[6]
+        infection_log_scale = input_params[1]
+        infection_mode = input_params[2]
+        presymptomatic = input_params[3]
+        asymptomatic = input_params[4]
+        symptomatic = input_params[5]
 
         params = OpenCLRunner.create_parameters(
             parameters_file=cls.PARAMETERS_FILE,
             current_risk_beta=current_risk_beta,
-            proportion_asymptomatic=proportion_asymptomatic,
             infection_log_scale=infection_log_scale,
             infection_mode=infection_mode,
             presymptomatic=presymptomatic,

diff --git a/tests/experiments/opencl_runner_tests.py b/tests/experiments/opencl_runner_tests.py
@@ -65,11 +65,10 @@ def test_run_model_with_params():
 
     (fitness, sim, obs, out_params, summaries) = OpenCLRunner.run_model_with_params(np.array([
         0.005,  # current_risk_beta
-        0.123,  # proportion_asymptomatic
         0.75,  # infection_log_scale
         7.123,  # infection_mode
         1.0,  # presymptomatic
-        0.75, # asymptomatic
+        0.75,  # asymptomatic
         0.5  #symptomatic
     ]), return_full_details=True)
 
@@ -78,8 +77,6 @@ def test_run_model_with_params():
     assert len(sim) == len(obs)  # Returned observations should be same length as the simulated number of iterations
 
     # Check the returned parameters are correct (should be different to the default)
-    assert OpenCLRunner.create_parameters().proportion_asymptomatic != out_params.proportion_asymptomatic
-    assert out_params.proportion_asymptomatic == 0.123
     assert out_params.infection_mode == 7.123
 
     # Individual hazard multipliers should be correct (I'm not sure why I can't access them with their