Merge pull request #327 from nanglo123/add_control_variables

Add control variables to the mapping of parameters for a MIRA template model ingested from a Vensim model

mira/sources/system_dynamics/pysd.py

@@ -26,15 +26,6 @@
 
 logger = logging.getLogger(__name__)
 
-CONTROL_VARIABLE_NAMES = {
- "FINALTIME",
- "INITIALTIME",
- "SAVEPER",
- "TIMESTEP",
- "FINAL TIME",
- "INITIAL TIME",
- "TIME STEP",
-}
 UNITS_MAPPING = {
  sympy.Symbol("Person"): sympy.Symbol("person"),
  sympy.Symbol("Persons"): sympy.Symbol("person"),
@@ -274,6 +265,8 @@ def template_model_from_pysd_model(
  param_unit.expression = param_unit.expression.subs(
  old_unit_symbol, new_unit_symbol
  )
+
+
  # construct transitions mapping that determine inputs and outputs states to a rate-law
  transition_map = {}
 

mira/sources/system_dynamics/vensim.py

@@ -33,8 +33,6 @@
 )
 UTF_ENCODING = "{UTF-8} "
 
-CONTROL_VARIABLES = {"SAVEPER", "FINAL TIME", "INITIAL TIME", "TIME STEP"}
-
 
 def template_model_from_mdl_file(
  fname, *, grounding_map=None, initials=None, initials_from_integ: bool = False
@@ -203,11 +201,6 @@ def extract_vensim_variable_expressions(
  # also, the initial value might be an expression that needs normalizing
  initial_values[_norm(old_var_name)] = initial and _norm(initial)
 
- # remove any control variables listed past the control section that were added to the
- # expression map
- for control_var in CONTROL_VARIABLES:
- expression_map.pop(control_var)
-
  return expression_map, initial_values
 
 

notebooks/evaluation_2024.03/epi_scenario4/scenario4_petrinet.json

@@ -259,6 +259,15 @@
  "expression_mathml": "<ci>people</ci>"
  }
  },
+ {
+ "id": "time_step",
+ "description": "The time step for the simulation.",
+ "value": 0.125,
+ "units": {
+ "expression": "day",
+ "expression_mathml": "<ci>day</ci>"
+ }
+ },
  {
  "id": "behavior_reaction_time",
  "description": "Time from first infection for behavioral risk reductions to be fully implemented.",
@@ -356,6 +365,24 @@
  "expression": "people",
  "expression_mathml": "<ci>people</ci>"
  }
+ },
+ {
+ "id": "final_time",
+ "description": "The final time for the simulation.",
+ "value": 300.0,
+ "units": {
+ "expression": "day",
+ "expression_mathml": "<ci>day</ci>"
+ }
+ },
+ {
+ "id": "initial_time",
+ "description": "The initial time for the simulation.",
+ "value": 0.0,
+ "units": {
+ "expression": "day",
+ "expression_mathml": "<ci>day</ci>"
+ }
  }
  ],
  "observables": [],

notebooks/evaluation_2024.03/epi_scenario4/scenario4_stockflow.json

@@ -167,6 +167,12 @@
  "expression": "n_imported_infections",
  "expression_mathml": "<ci>n_imported_infections</ci>"
  },
+ {
+ "id": "time_step",
+ "name": "time_step",
+ "expression": "time_step",
+ "expression_mathml": "<ci>time_step</ci>"
+ },
  {
  "id": "behavior_reaction_time",
  "name": "behavior_reaction_time",
@@ -248,37 +254,37 @@
  },
  {
  "id": "link3",
- "source": "treated_fatality_rate",
+ "source": "hospital_capacity_sensitivity",
  "target": "2"
  },
  {
  "id": "link4",
- "source": "infection_duration",
+ "source": "hospital_capacity",
  "target": "2"
  },
  {
  "id": "link5",
- "source": "untreated_fatality_rate",
+ "source": "infection_duration",
  "target": "2"
  },
  {
  "id": "link6",
- "source": "infected",
+ "source": "untreated_fatality_rate",
  "target": "2"
  },
  {
  "id": "link7",
- "source": "hospital_capacity_sensitivity",
+ "source": "treated_fatality_rate",
  "target": "2"
  },
  {
  "id": "link8",
- "source": "fraction_requiring_hospitalization",
+ "source": "infected",
  "target": "2"
  },
  {
  "id": "link9",
- "source": "hospital_capacity",
+ "source": "fraction_requiring_hospitalization",
  "target": "2"
  },
  {
@@ -288,132 +294,132 @@
  },
  {
  "id": "link11",
- "source": "import_time",
+ "source": "n_imported_infections",
  "target": "3"
  },
  {
  "id": "link12",
- "source": "n_imported_infections",
+ "source": "import_time",
  "target": "3"
  },
  {
  "id": "link13",
- "source": "susceptible",
+ "source": "behavior_reaction_time",
  "target": "4"
  },
  {
  "id": "link14",
- "source": "initial_population",
+ "source": "public_health_capacity_sensitivity",
  "target": "4"
  },
  {
  "id": "link15",
- "source": "public_health_capacity_sensitivity",
+ "source": "susceptible",
  "target": "4"
  },
  {
  "id": "link16",
- "source": "seasonal_period",
+ "source": "behavioral_risk_reduction",
  "target": "4"
  },
  {
  "id": "link17",
- "source": "behavioral_risk_reduction",
+ "source": "isolation_reaction_time",
  "target": "4"
  },
  {
  "id": "link18",
- "source": "peak_season",
+ "source": "infected",
  "target": "4"
  },
  {
  "id": "link19",
- "source": "infection_duration",
+ "source": "import_time",
  "target": "4"
  },
  {
  "id": "link20",
- "source": "public_health_strain",
+ "source": "seasonal_amplitude",
  "target": "4"
  },
  {
  "id": "link21",
- "source": "behavior_reaction_time",
+ "source": "infection_duration",
  "target": "4"
  },
  {
  "id": "link22",
- "source": "potential_isolation_effectiveness",
+ "source": "peak_season",
  "target": "4"
  },
  {
  "id": "link23",
- "source": "import_time",
+ "source": "time",
  "target": "4"
  },
  {
  "id": "link24",
- "source": "infected",
+ "source": "potential_isolation_effectiveness",
  "target": "4"
  },
  {
  "id": "link25",
- "source": "r0",
+ "source": "contact_density_decline",
  "target": "4"
  },
  {
  "id": "link26",
- "source": "isolation_reaction_time",
+ "source": "r0",
  "target": "4"
  },
  {
  "id": "link27",
- "source": "seasonal_amplitude",
+ "source": "initial_population",
  "target": "4"
  },
  {
  "id": "link28",
- "source": "contact_density_decline",
+ "source": "public_health_strain",
  "target": "4"
  },
  {
  "id": "link29",
- "source": "time",
+ "source": "seasonal_period",
  "target": "4"
  },
  {
  "id": "link30",
- "source": "treated_fatality_rate",
+ "source": "hospital_capacity_sensitivity",
  "target": "5"
  },
  {
  "id": "link31",
- "source": "infection_duration",
+ "source": "hospital_capacity",
  "target": "5"
  },
  {
  "id": "link32",
- "source": "untreated_fatality_rate",
+ "source": "infection_duration",
  "target": "5"
  },
  {
  "id": "link33",
- "source": "infected",
+ "source": "untreated_fatality_rate",
  "target": "5"
  },
  {
  "id": "link34",
- "source": "hospital_capacity_sensitivity",
+ "source": "treated_fatality_rate",
  "target": "5"
  },
  {
  "id": "link35",
- "source": "fraction_requiring_hospitalization",
+ "source": "infected",
  "target": "5"
  },
  {
  "id": "link36",
- "source": "hospital_capacity",
+ "source": "fraction_requiring_hospitalization",
  "target": "5"
  }
  ]
@@ -490,6 +496,15 @@
  "expression_mathml": "<ci>people</ci>"
  }
  },
+ {
+ "id": "time_step",
+ "description": "The time step for the simulation.",
+ "value": 0.125,
+ "units": {
+ "expression": "day",
+ "expression_mathml": "<ci>day</ci>"
+ }
+ },
  {
  "id": "behavior_reaction_time",
  "description": "Time from first infection for behavioral risk reductions to be fully implemented.",
@@ -587,6 +602,24 @@
  "expression": "people",
  "expression_mathml": "<ci>people</ci>"
  }
+ },
+ {
+ "id": "final_time",
+ "description": "The final time for the simulation.",
+ "value": 300.0,
+ "units": {
+ "expression": "day",
+ "expression_mathml": "<ci>day</ci>"
+ }
+ },
+ {
+ "id": "initial_time",
+ "description": "The initial time for the simulation.",
+ "value": 0.0,
+ "units": {
+ "expression": "day",
+ "expression_mathml": "<ci>day</ci>"
+ }
  }
  ],
  "initials": [