Parameter Revamp - Msuarez/parameters/measles

src/tlo/core.py

@@ -332,7 +332,7 @@ def load_parameters_from_dataframe(self, resource: pd.DataFrame) -> None:
 
         resource.set_index('parameter_name', inplace=True)
         skipped_data_types = ('DATA_FRAME', 'SERIES')
-        acceptable_labels = ['unassigned', 'undetermined', 'universal', 'local', 'scenario']
+        acceptable_labels = ['unassigned', 'undetermined', 'universal', 'local', 'scenario','design feature']
         param_defaults = {'param_label': 'unassigned', 'prior_min': None, 'prior_max': None }
 
         for _col in param_defaults.keys():

src/tlo/methods/measles.py

@@ -70,8 +70,44 @@ class Measles(Module, GenericFirstAppointmentsMixin):
             Types.REAL, "Risk of scheduled death occurring if on treatment for measles complications"),
         "symptom_prob": Parameter(
             Types.DATA_FRAME, "Probability of each symptom with measles infection"),
-        "case_fatality_rate": Parameter(
-            Types.DICT, "Probability that case of measles will result in death if not treated")
+        "odds_ratio_health_seeking_in_children_rash": Parameter(
+            Types.REAL, "Odds ratio seeking care in children rash"),
+        "odds_ratio_health_seeking_in_adults_rash": Parameter(
+            Types.REAL, "Odds ratio seeking care in adults rash"),
+        "odds_ratio_health_seeking_in_children_otitis_media": Parameter(
+            Types.REAL, "Odds ratio seeking care in children otitis media"),
+        "odds_ratio_health_seeking_in_adults_otitis_media": Parameter(
+            Types.REAL, "Odds ratio seeking care in adults otitis media"),
+        "reduction_in_death_risk_measle_treated": Parameter(
+            Types.REAL, "Reduction in death risk when measles are treated"
+        ),
+        "maternal_immunity_age_threshold": Parameter(
+            Types.REAL, "Age threshold below which children are protected by maternal immunity"
+        ),
+        "age_min_symptoms_constant_rate": Parameter(
+            Types.REAL, "Maximum age for measles symptom probability lookup"
+        ),
+        "death_timing_min_days": Parameter(
+            Types.REAL, "Minimum days from symptom onset to death"
+        ),
+        "death_timing_max_days": Parameter(
+            Types.REAL, "Maximum days from symptom onset to death"
+        ),
+        "natural_resolution_min_days": Parameter(
+            Types.REAL, "Minimum days from symptom onset to natural resolution"
+        ),
+        "natural_resolution_max_days": Parameter(
+            Types.REAL, "Maximum days from symptom onset to natural resolution"
+        ),
+        "symptom_onset_min_days": Parameter(
+            Types.REAL, "Minimum days from infection to symptom onset (incubation period)"
+        ),
+        "symptom_onset_max_days": Parameter(
+            Types.REAL, "Maximum days from infection to symptom onset (incubation period)"
+        ),
+        "treatment_followup_days": Parameter(
+            Types.REAL, "Days until follow-up appointment after treatment"
+        )
     }
 
     PROPERTIES = {
@@ -108,6 +144,8 @@ def read_parameters(self, resourcefilepath: Optional[Path] = None):
         self.parameters["case_fatality_rate"] = workbook["cfr"].set_index('age')["probability"].to_dict()
 
         # moderate symptoms all mapped to moderate_measles, pneumonia/encephalitis mapped to severe_measles
+
+        p = self.parameters
         if "HealthBurden" in self.sim.modules.keys():
             self.parameters["daly_wts"] = {
                 "rash": self.sim.modules["HealthBurden"].get_daly_weight(sequlae_code=205),
@@ -122,14 +160,14 @@ def read_parameters(self, resourcefilepath: Optional[Path] = None):
         # Declare symptoms that this module will cause and which are not included in the generic symptoms:
         self.sim.modules['SymptomManager'].register_symptom(
             Symptom(name='rash',
-                    odds_ratio_health_seeking_in_children=2.5,
-                    odds_ratio_health_seeking_in_adults=2.5)  # non-emergencies
+                    odds_ratio_health_seeking_in_children=p['odds_ratio_health_seeking_in_children_rash'],
+                    odds_ratio_health_seeking_in_adults=p['odds_ratio_health_seeking_in_adults_rash'])  # non-emergencies
         )
 
         self.sim.modules['SymptomManager'].register_symptom(
             Symptom(name='otitis_media',
-                    odds_ratio_health_seeking_in_children=2.5,
-                    odds_ratio_health_seeking_in_adults=2.5)  # non-emergencies
+                    odds_ratio_health_seeking_in_children=p['odds_ratio_health_seeking_in_children_otitis_media'],
+                    odds_ratio_health_seeking_in_adults=p['odds_ratio_health_seeking_in_adults_otitis_media'])  # non-emergencies
         )
 
         self.sim.modules['SymptomManager'].register_symptom(Symptom.emergency('encephalitis'))
@@ -149,6 +187,8 @@ def initialise_population(self, population):
 
     def initialise_simulation(self, sim):
         """Schedule measles event to start straight away. Each month it will assign new infections"""
+        p = self.parameters
+
         sim.schedule_event(MeaslesEvent(self), sim.date)
         sim.schedule_event(MeaslesLoggingEvent(self), sim.date)
         sim.schedule_event(MeaslesLoggingFortnightEvent(self), sim.date)
@@ -165,6 +205,7 @@ def initialise_simulation(self, sim):
                                                                               "oxygen cylinders")
         }
 
+
     def on_birth(self, mother_id, child_id):
         """Initialise our properties for a newborn individual
         assume all newborns are uninfected
@@ -196,12 +237,13 @@ def process_parameters(self):
         """Process the parameters (following being read-in) prior to the simulation starting.
         Make `self.symptom_probs` to be a dictionary keyed by age, with values of dictionaries keyed by symptoms and
         the probability of symptom onset."""
+        p = self.parameters
         probs = self.parameters["symptom_prob"].set_index(["age", "symptom"])["probability"]
         self.symptom_probs = {level: probs.loc[(level, slice(None))].to_dict() for level in probs.index.levels[0]}
 
         # Check that a sensible value for a probability of symptom onset is declared for each symptom and for each age
-        # up to and including age 30
-        for _age in range(30 + 1):
+        # up to and including max age for symptom probabilities
+        for _age in range(int(p["age_min_symptoms_constant_rate"]) + 1):
             assert set(self.symptoms) == set(self.symptom_probs.get(_age).keys())
             assert all([0.0 <= x <= 1.0 for x in self.symptom_probs.get(_age).values()])
 
@@ -248,8 +290,8 @@ def apply(self, population):
             protected_by_vaccine.loc[(df.va_measles == 1)] *= (1 - p["vaccine_efficacy_1"])  # partially susceptible
             protected_by_vaccine.loc[(df.va_measles > 1)] *= (1 - p["vaccine_efficacy_2"])  # partially susceptible
 
-        # Find persons to be newly infected (no risk to children under 6 months as protected by maternal immunity)
-        new_inf = df.index[~df.me_has_measles & (df.age_exact_years >= 0.5) &
+        # Find persons to be newly infected (no risk to children under maternal immunity threshold as protected by maternal immunity)
+        new_inf = df.index[~df.me_has_measles & (df.age_exact_years >= p["maternal_immunity_age_threshold"]) &
                            (rng.random_sample(size=len(df)) < (trans_prob * protected_by_vaccine))]
 
         logger.debug(key="MeaslesEvent",
@@ -274,11 +316,12 @@ def apply(self, person_id):
 
         df = self.sim.population.props  # shortcut to the dataframe
         rng = self.module.rng
+        p = self.module.parameters
 
         if not df.at[person_id, "is_alive"]:
             return
 
-        ref_age = df.at[person_id, "age_years"].clip(max=30)  # (For purpose of look-up age limit is 30 years)
+        ref_age = df.at[person_id, "age_years"].clip(max=p["age_min_symptoms_constant_rate"])  # (For purpose of look-up age limit)
 
         # Determine if the person has "untreated HIV", which is defined as a person in any stage of HIV but not on
         # successful treatment currently.
@@ -303,21 +346,22 @@ def apply(self, person_id):
 
             # schedule the death
             self.sim.schedule_event(
-                death_event, symp_onset + DateOffset(days=rng.randint(3, 7)))
+                death_event, symp_onset + DateOffset(days=rng.randint(p["death_timing_min_days"], p["death_timing_max_days"])))
 
         else:
             # schedule symptom resolution without treatment - this only occurs if death doesn't happen first
-            symp_resolve = symp_onset + DateOffset(days=rng.randint(7, 14))
+            symp_resolve = symp_onset + DateOffset(days=rng.randint(p["natural_resolution_min_days"], p["natural_resolution_max_days"]))
             self.sim.schedule_event(MeaslesSymptomResolveEvent(self.module, person_id), symp_resolve)
 
     def assign_symptoms(self, _age):
         """Assign symptoms for this case and returns the date on which symptom onset.
         (Parameter values specify that everybody gets rash, fever and eye complain.)"""
 
         rng = self.module.rng
+        p = self.module.parameters
         person_id = self.target
         symptom_probs_for_this_person = self.module.symptom_probs.get(_age)
-        date_of_symp_onset = self.sim.date + DateOffset(days=rng.randint(7, 21))
+        date_of_symp_onset = self.sim.date + DateOffset(days=rng.randint(p["symptom_onset_min_days"], p["symptom_onset_max_days"]))
 
         symptoms_to_onset = [
             _symp for (_symp, _prob), _rand in zip(
@@ -379,6 +423,7 @@ def __init__(self, module, person_id):
 
     def apply(self, person_id):
         df = self.sim.population.props
+        p = self.sim.parameters
 
         if not df.at[person_id, "is_alive"]:
             return
@@ -389,10 +434,8 @@ def apply(self, person_id):
 
             if df.at[person_id, "me_on_treatment"]:
 
-                reduction_in_death_risk = 0.6
-
                 # Certain death (100%) is reduced by specified amount
-                p_death_with_treatment = 1. - reduction_in_death_risk
+                p_death_with_treatment = 1. - p['reduction_in_death_risk_measle_treated']
 
                 # If below that probability, death goes ahead
                 if self.module.rng.random_sample() < p_death_with_treatment:
@@ -438,6 +481,7 @@ def apply(self, person_id, squeeze_factor):
 
         df = self.sim.population.props
         symptoms = self.sim.modules["SymptomManager"].has_what(person_id=person_id)
+        p = self.module.parameters
 
         # for non-complicated measles
         item_codes = [self.module.consumables['vit_A']]
@@ -463,7 +507,7 @@ def apply(self, person_id, squeeze_factor):
 
             # schedule symptom resolution following treatment
             self.sim.schedule_event(MeaslesSymptomResolveEvent(self.module, person_id),
-                                    self.sim.date + DateOffset(days=7))
+                                    self.sim.date + DateOffset(days=p["treatment_followup_days"]))
 
     def did_not_run(self):
         logger.debug(key="HSI_Measles_Treatment",