PR to record the prevalence of disease/condition, still births, neonatal death, maternal mortality

src/tlo/methods/alri.py

@@ -995,6 +995,14 @@ def report_daly_values(self):
         daly_values_by_pathogen = daly_values_by_pathogen.add_prefix('ALRI_')
         return daly_values_by_pathogen
 
+    def report_prevalence(self):
+        # This returns dataframe that reports on the prevalence of ALRI for all individuals
+        df = self.sim.population.props
+        total_prev = len(
+            df[(df['is_alive']) & (df['ri_current_infection_status'])]
+        ) / len(df[df['is_alive']])
+
+        return total_prev
     def over_ride_availability_of_certain_consumables(self):
         """Over-ride the availability of certain consumables, according the parameter values provided."""
         p = self.parameters

src/tlo/methods/bladder_cancer.py

@@ -594,6 +594,15 @@ def report_daly_values(self):
 
         return disability_series_for_alive_persons
 
+    def report_prevalence(self):
+        # This reports on the prevalence of bladder cancer for all individuals
+
+        df = self.sim.population.props
+        total_prev = len(
+            df[(df.bc_status != 'none') & (df.is_alive)]
+        ) / len(df[df.is_alive])
+        return total_prev
+
     def do_at_generic_first_appt(
         self,
         person_id: int,

src/tlo/methods/breast_cancer.py

@@ -571,6 +571,14 @@ def report_daly_values(self):
 
         return disability_series_for_alive_persons
 
+    def report_prevalence(self):
+        # This returns dataframe that reports on the prevalence of breast cancer for all individuals
+        df = self.sim.population.props
+        total_prev = len(
+            df[(df['is_alive']) & (df['brc_status'] != 'none')]
+        ) / len(df[df['is_alive']])
+
+        return total_prev
     def do_at_generic_first_appt(
         self,
         person_id: int,

src/tlo/methods/cardio_metabolic_disorders.py

@@ -807,6 +807,19 @@ def left_censor(obs, window_open):
 
         return dw
 
+    def report_prevalence(self):
+        """Report prevalence of disease to the HealthBurden module"""
+        df = self.sim.population.props
+        prevalence_dict = {}
+
+        for condition in self.conditions:
+            prevalence = df[f'nc_{condition}'].sum() / len(df)
+            prevalence_dict[condition] = prevalence
+
+        # Create a DataFrame from the prevalence dictionary
+        prevalence_df = pd.DataFrame(prevalence_dict, index=[0])
+        return prevalence_df
+
     def on_hsi_alert(self, person_id, treatment_id):
         """
         This is called whenever there is an HSI event commissioned by one of the other disease modules.

src/tlo/methods/copd.py

@@ -182,6 +182,15 @@ def report_daly_values(self):
         df = self.sim.population.props
         return df.loc[df.is_alive, 'ch_lungfunction'].map(self.models.disability_weight_given_lungfunction)
 
+    def report_prevalence(self):
+        # This returns dataframe that reports on the prevalence of COPD for all individuals
+        df = self.sim.population.props
+        total_prev = len(
+            df[(df['is_alive']) & (df['ch_lungfunction'] > 3)] # 3 is mild COPD
+        ) / len(df[df['is_alive']])
+
+        return total_prev
+
     def define_symptoms(self):
         """Define and register Symptoms"""
         self.sim.modules['SymptomManager'].register_symptom(

src/tlo/methods/demography.py

@@ -383,6 +383,54 @@ def on_birth(self, mother_id, child_id):
                   'mother_age_at_pregnancy': _mother_age_at_pregnancy}
         )
 
+    def report_prevalence(self):
+        """
+        This function reports the prevalence of maternal death and neonatal deaths for this module generated in the previous month.
+        Returns a dataframe with these values.
+        """
+        if 'SimplifiedBirths' in self.sim.modules:
+            neonatal_mortality_rate = None
+            maternal_mortality_rate = None
+            live_births = None
+        else:
+            df = self.sim.population.props
+            if len(df[(df['age_days'] < 29)]) == 0:
+                neonatal_mortality_rate = 0
+                maternal_mortality_rate = 0
+                live_births = 0
+            else:
+                neonatal_deaths = len(df[(df['age_days'] < 29) & (df['age_years'] == 0) & ~(df['is_alive']) & (
+                        df['date_of_death'] >= (self.sim.date - DateOffset(months=1)))])
+                live_births = len(df[(df['age_days'] < 29) & (df['age_years'] == 0)])
+                neonatal_mortality_rate = neonatal_deaths/live_births * 1000
+                maternal_direct_deaths = len(df.loc[
+                                                 (df['cause_of_death'] == 'Maternal Disorders') &
+                                                 (df['date_of_death'] >= (self.sim.date - DateOffset(months=1)))
+                                                 ])
+                indirect_deaths_non_hiv = len(df.loc[
+                                                  (df['is_pregnant'] | df['la_is_postpartum']) &
+                                                  (df['cause_of_death'].str.contains(
+                                                      'Malaria|Suicide|ever_stroke|diabetes|chronic_ischemic_hd|ever_heart_attack|chronic_kidney_disease') |
+                                                   (df['cause_of_death'] == 'TB')) &
+                                                  (df['date_of_death'] >= (self.sim.date - DateOffset(months=1)))
+                                                  ])
+                direct_deaths_non_hiv = len(df.loc[
+                                                (df['is_pregnant'] | df['la_is_postpartum']) &
+                                                df['cause_of_death'].str.contains('AIDS_non_TB|AIDS_TB') &
+                                                (df['date_of_death'] >= (self.sim.date - DateOffset(months=1)))
+                                                ])
+                direct_deaths_non_hiv = direct_deaths_non_hiv * 0.3  # https://www.who.int/publications/i/item/9789240068759
+                maternal_deaths = maternal_direct_deaths + indirect_deaths_non_hiv + direct_deaths_non_hiv
+                maternal_mortality_rate = maternal_deaths/live_births * 1000
+
+        health_values_df = pd.DataFrame({
+            'NMR': [neonatal_mortality_rate],
+            'MMR': [maternal_mortality_rate],
+            'live_births': [live_births]
+        })
+
+        return health_values_df
+
     def _edit_init_pop_to_prevent_persons_greater_than_max_age(self, df, max_age: int):
         """Return an edited version of the `pd.DataFrame` describing the probability of persons in the population being
         created with certain characteristics to reflect the constraint the persons aged greater than `max_age_initial`

src/tlo/methods/depression.py

@@ -554,6 +554,20 @@ def right_censor(obs, window_close):
 
         return av_daly_wt_last_month
 
+    def report_prevalence(self):
+        # This reports on the prevalence of depression for all individuals
+
+        df = self.sim.population.props
+        any_depr_in_the_last_month = df[((df['is_alive']) & (
+            ~pd.isnull(df['de_date_init_most_rec_depr']) & (df['de_date_init_most_rec_depr'] <= self.sim.date)
+        ) & (
+                                         pd.isnull(df['de_date_depr_resolved']) |
+                                         (df['de_date_depr_resolved'] >= (self.sim.date - DateOffset(months=1)))
+                                     ))]
+        total_prev = len(
+            any_depr_in_the_last_month
+        ) / len(df[df.is_alive])
+        return total_prev
     def _check_for_suspected_depression(
         self, symptoms: List[str], treatment_id: str, has_even_been_diagnosed: bool
     ):

src/tlo/methods/diarrhoea.py

@@ -649,6 +649,13 @@ def report_daly_values(self):
         average_daly_weight_in_last_month = pd.Series(values, idx) / days_last_month
         return average_daly_weight_in_last_month.reindex(index=df.loc[df.is_alive].index, fill_value=0.0)
 
+    def report_prevalence(self):
+        df = self.sim.population.props
+        total_prev = len(
+            df[df.gi_has_diarrhoea & df.is_alive]
+        ) / len(df[df.is_alive])
+        return total_prev
+
     def look_up_consumables(self):
         """Look up and store the consumables item codes used in each of the HSI."""
         ic = self.sim.modules['HealthSystem'].get_item_code_from_item_name

src/tlo/methods/epilepsy.py

@@ -241,6 +241,16 @@ def report_daly_values(self):
         df = self.sim.population.props  # shortcut to population properties dataframe
         return df.loc[df.is_alive, 'ep_disability']
 
+    def report_prevalence(self):
+        # This returns dataframe that reports on the prevalence of epilepsy for all individuals
+        df = self.sim.population.props
+        total_prev = len(
+            df[(df['is_alive']) & (df['ep_seiz_stat'] != '0')]
+        ) / len(df[df['is_alive']])
+
+        return total_prev
+
+
     def transition_seizure_stat(self):
         """
         This function handles all transitions in epilepsy seizure status, for those on and off anti epileptics. The