Editing units of consumable required for each HSI

src/scripts/data_file_processing/healthsystem/consumables/consumable_resource_analyses_with_lmis/consumables_availability_estimation.py

@@ -277,14 +277,10 @@ def custom_agg(x):
     return _collapsed_df
 
 # Hold out the dataframe with no naming inconsistencies
-list_of_items_with_inconsistent_names_zipped = list(
-    zip(inconsistent_item_names_mapping.keys(), inconsistent_item_names_mapping.values()))
-list_of_items_with_inconsistent_names = [
-    item for sublist in list_of_items_with_inconsistent_names_zipped for item in sublist]
-df_with_consistent_item_names =  lmis_df_wide_flat[~lmis_df_wide_flat[('item',)].isin(
-    list_of_items_with_inconsistent_names)]
-df_without_consistent_item_names = lmis_df_wide_flat[lmis_df_wide_flat[('item',)].isin(
-    list_of_items_with_inconsistent_names)]
+list_of_items_with_inconsistent_names_zipped = set(zip(inconsistent_item_names_mapping.keys(), inconsistent_item_names_mapping.values()))
+list_of_items_with_inconsistent_names = [item for sublist in list_of_items_with_inconsistent_names_zipped for item in sublist]
+df_with_consistent_item_names =  lmis_df_wide_flat[~lmis_df_wide_flat[('item',)].isin(list_of_items_with_inconsistent_names)]
+df_without_consistent_item_names = lmis_df_wide_flat[lmis_df_wide_flat[('item',)].isin(list_of_items_with_inconsistent_names)]
 # Make inconsistently named drugs uniform across the dataframe
 df_without_consistent_item_names_corrected = rename_items_to_address_inconsistentencies(
     df_without_consistent_item_names, inconsistent_item_names_mapping)

src/scripts/data_file_processing/healthsystem/consumables/processing_data_from_one_health/generate_consumables_item_codes_and_packages.py

@@ -21,7 +21,8 @@
 
 # Set local Dropbox source
 path_to_dropbox = Path(  # <-- point to the TLO dropbox locally
-    '/Users/tbh03/Dropbox (SPH Imperial College)/Thanzi la Onse Theme 1 SHARE')
+   # '/Users/tbh03/Dropbox (SPH Imperial College)/Thanzi la Onse Theme 1 SHARE'
+    '/Users/sm2511/Dropbox/Thanzi La Onse')
 
 resourcefilepath = Path("./resources")
 path_for_new_resourcefiles = resourcefilepath / "healthsystem/consumables"
@@ -245,7 +246,7 @@
 
 def add_record(df: pd.DataFrame, record: Dict):
     """Add a row to the bottom of the dataframe, where the row is specified by a dict keyed by the target columns."""
-    assert list(df.columns) == list(record.keys())
+    assert set(df.columns) == set(record.keys())
     return pd.concat([df, pd.DataFrame.from_records([record])], ignore_index=True)
 
 
@@ -328,6 +329,54 @@ def add_record(df: pd.DataFrame, record: Dict):
     },
 )
 
+cons = add_record(
+    cons,
+    {
+        'Intervention_Cat': "Added by SM (Recommended by TM)",
+        'Intervention_Pkg': "Isoniazid preventative therapy for HIV+ no TB",
+        'Intervention_Pkg_Code': 82,
+        'Items': "Isoniazid/Rifapentine",
+        'Item_Code': 2678,
+        'Expected_Units_Per_Case': 1.0,
+        'Unit_Cost': 1.0
+    },
+)
+
+cons = add_record(
+    cons,
+    {
+    'Intervention_Cat': "Added by SM (Recommended by EJ)",
+    'Intervention_Pkg': "Misc",
+    'Intervention_Pkg_Code': -99,
+    'Items': "Cystoscope",
+    'Item_Code': 285,
+    'Expected_Units_Per_Case': 1.0,
+    'Unit_Cost': np.nan},
+)
+
+cons = add_record(
+    cons,{
+    'Intervention_Cat': "Added by SM (Recommended by EJ)",
+    'Intervention_Pkg': "Misc",
+    'Intervention_Pkg_Code': -99,
+    'Items': "Endoscope",
+    'Item_Code': 280,
+    'Expected_Units_Per_Case': 1.0,
+    'Unit_Cost': np.nan},
+)
+
+cons = add_record(
+    cons,{
+    'Intervention_Cat': "Added by SM (Recommended by EJ)",
+    'Intervention_Pkg': "Misc",
+    'Intervention_Pkg_Code': -99,
+    'Items': "Prostate specific antigen test",
+    'Item_Code': 281,
+    'Expected_Units_Per_Case': 1.0,
+    'Unit_Cost': np.nan},
+)
+
+
 # --------------
 # --------------
 # --------------

src/tlo/methods/alri.py

@@ -21,7 +21,6 @@
 """
 from __future__ import annotations
 
-import types
 from collections import defaultdict
 from itertools import chain
 from pathlib import Path
@@ -1014,139 +1013,85 @@ def look_up_consumables(self):
 
         get_item_code = self.sim.modules['HealthSystem'].get_item_code_from_item_name
 
-        def get_dosage_for_age_in_months(age_in_whole_months: float, doses_by_age_in_months: Dict[int, float]):
-            """Returns the dose corresponding to age, using the lookup provided in `doses`. The format of `doses` is:
-             {<higher_age_boundary_of_age_group_in_months>: <dose>}."""
-
-            for upper_age_bound_in_months, _dose in sorted(doses_by_age_in_months.items()):
-                if age_in_whole_months < upper_age_bound_in_months:
-                    return _dose
-            return _dose
-
-        # # # # # # Dosages by age # # # # # #
+        # # # # # # Dosages by weight # # # # # #
+        # Assuming average weight of 0-5 is 12kg (abstraction). Doses sourced for WHO Pocket book of hospital care for
+        # children: Second edition 2014
 
         # Antibiotic therapy -------------------
-        # Antibiotics for non-severe pneumonia - oral amoxicillin for 5 days
+        # Antibiotics for non-severe pneumonia - oral amoxicillin for 5 days (40mg/kg BD - ((12*40)*2)*5 =4800mg)
         self.consumables_used_in_hsi['Amoxicillin_tablet_or_suspension_5days'] = {
-            get_item_code(item='Amoxycillin 250mg_1000_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {2: 0, 12: 0.006, 36: 0.012, np.inf: 0.018}
-                                                          ),
-            get_item_code(item='Amoxycillin 125mg/5ml suspension, PFR_0.025_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {2: 0, 12: 1, 36: 2, np.inf: 3}
-                                                          ),
-        }
+            get_item_code(item='Amoxycillin 250mg_1000_CMST'): 4800,
+            get_item_code(item='Amoxycillin 125mg/5ml suspension, PFR_0.025_CMST'): 192}  # 25mg/ml - 4800/25
 
-        # Antibiotics for non-severe pneumonia - oral amoxicillin for 3 days
+        # Antibiotics for non-severe pneumonia - oral amoxicillin for 3 days (40mg/kg BD - ((12*40)*2)*3 =2880mg)
         self.consumables_used_in_hsi['Amoxicillin_tablet_or_suspension_3days'] = {
-            get_item_code(item='Amoxycillin 250mg_1000_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {2: 0, 12: 0.01, 36: 0.02, np.inf: 0.03}
-                                                          ),
-            get_item_code(item='Amoxycillin 125mg/5ml suspension, PFR_0.025_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {2: 0, 12: 1, 36: 2, np.inf: 3}
-                                                          ),
-        }
+            get_item_code(item='Amoxycillin 250mg_1000_CMST'): 2880,
+            get_item_code(item='Amoxycillin 125mg/5ml suspension, PFR_0.025_CMST'): 115}  # 25mg/ml - 2880/25
 
-        # Antibiotics for non-severe pneumonia - oral amoxicillin for 7 days for young infants only
+        # Antibiotics for non-severe pneumonia - oral amoxicillin for 7 days for young infants only (40mg/kg BD -
+        # ((12*40)*2)*7 =6720mg)
         self.consumables_used_in_hsi['Amoxicillin_tablet_or_suspension_7days'] = {
-            get_item_code(item='Amoxycillin 250mg_1000_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {1: 0.004, 2: 0.006, np.inf: 0.01}
-                                                          ),
-            get_item_code(item='Amoxycillin 125mg/5ml suspension, PFR_0.025_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {1: 0.4, 2: 0.5, np.inf: 1}
-                                                          ),
-        }
+            get_item_code(item='Amoxycillin 250mg_1000_CMST'): 6720,
+            get_item_code(item='Amoxycillin 125mg/5ml suspension, PFR_0.025_CMST'): 269}  # 25mg/ml - 6720/25
 
         # Antibiotic therapy for severe pneumonia - ampicillin package
+        # Amp. dose - 50mg/KG QDS 5 days = (50*12)*4)*5 = 12_000mg
+        # Gent. dose -7.5mg/kg per day 5 days = (7.5*12)*5 = 450mg
         self.consumables_used_in_hsi['1st_line_IV_antibiotics'] = {
-            get_item_code(item='Ampicillin injection 500mg, PFR_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {1: 3.73, 2: 5.6, 4: 8, 12: 16, 36: 24, np.inf: 40}
-                                                          ),
-            get_item_code(item='Gentamicin Sulphate 40mg/ml, 2ml_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {1: 0.7, 2: 1.4, 4: 2.81, 12: 4.69, 36: 7.03, np.inf: 9.37}
-                                                          ),
+            get_item_code(item='Ampicillin injection 500mg, PFR_each_CMST'): 24,  # 500mg vial -12_000/500
+            get_item_code(item='Gentamicin Sulphate 40mg/ml, 2ml_each_CMST'): 6,  # 80mg/2ml = 450/8
             get_item_code(item='Cannula iv  (winged with injection pot) 16_each_CMST'): 1,
             get_item_code(item='Syringe, Autodisable SoloShot IX '): 1
         }
 
         # # Antibiotic therapy for severe pneumonia - benzylpenicillin package when ampicillin is not available
+        # Benpen dose - 50_000IU/KG QDS 5 days = (50_000*12)*4)*5 = 12_000_000IU = 8g (approx)
+        # Gent. dose -7.5mg/kg per day 5 days = (7.5*12)*5 = 450mg
         self.consumables_used_in_hsi['Benzylpenicillin_gentamicin_therapy_for_severe_pneumonia'] = {
-            get_item_code(item='Benzylpenicillin 3g (5MU), PFR_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {1: 2, 2: 5, 4: 8, 12: 15, 36: 24, np.inf: 34}
-                                                          ),
-            get_item_code(item='Gentamicin Sulphate 40mg/ml, 2ml_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {1: 0.7, 2: 1.4, 4: 2.81, 12: 4.69, 36: 7.03, np.inf: 9.37}
-                                                          ),
+            get_item_code(item='Benzylpenicillin 3g (5MU), PFR_each_CMST'): 8,
+            get_item_code(item='Gentamicin Sulphate 40mg/ml, 2ml_each_CMST'): 6,  # 80mg/2ml = 450/8
             get_item_code(item='Cannula iv  (winged with injection pot) 16_each_CMST'): 1,
             get_item_code(item='Syringe, Autodisable SoloShot IX '): 1
         }
 
         # Second line of antibiotics for severe pneumonia, if Staph not suspected
+        # Ceft. dose = 80mg/kg per day 5 days = (80*12)*5 = 4800mg
         self.consumables_used_in_hsi['Ceftriaxone_therapy_for_severe_pneumonia'] = {
-            get_item_code(item='Ceftriaxone 1g, PFR_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {4: 1.5, 12: 3, 36: 5, np.inf: 7}
-                                                          ),
+            get_item_code(item='Ceftriaxone 1g, PFR_each_CMST'): 1,  # smallest unit is 1g
             get_item_code(item='Cannula iv  (winged with injection pot) 16_each_CMST'): 1,
             get_item_code(item='Syringe, Autodisable SoloShot IX '): 1
         }
 
         # Second line of antibiotics for severe pneumonia, if Staph is suspected
+        # Flucox. dose = 50mg/kg QDS 7 days = ((50*12)*4)*7 = 16_800mg
+        # Oral flucox dose. = same
         self.consumables_used_in_hsi['2nd_line_Antibiotic_therapy_for_severe_staph_pneumonia'] = {
-            get_item_code(item='Flucloxacillin 250mg, vial, PFR_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {2: 21, 4: 22.4, 12: 37.3, 36: 67.2, 60: 93.3, np.inf: 140}
-                                                          ),
-            get_item_code(item='Gentamicin Sulphate 40mg/ml, 2ml_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {4: 2.81, 12: 4.69, 36: 7.03, 60: 9.37, np.inf: 13.6}
-                                                          ),
+            get_item_code(item='Flucloxacillin 250mg, vial, PFR_each_CMST'): 16_800,
+            get_item_code(item='Gentamicin Sulphate 40mg/ml, 2ml_each_CMST'): 6,  # 80mg/2ml = 450/8
             get_item_code(item='Cannula iv  (winged with injection pot) 16_each_CMST'): 1,
             get_item_code(item='Syringe, Autodisable SoloShot IX '): 1,
-            get_item_code(item='Flucloxacillin 250mg_100_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {4: 0.42, 36: 0.84, 60: 1.68, np.inf: 1.68}
-                                                          ),
-        }
+            get_item_code(item='Flucloxacillin 250mg_100_CMST'): 16_800}
 
         # First dose of antibiotic before referral -------------------
-
+        # single dose of 7.5mg gent and 50mg/g amp. given
         # Referral process in iCCM for severe pneumonia, and at health centres for HIV exposed/infected
         self.consumables_used_in_hsi['First_dose_oral_amoxicillin_for_referral'] = {
-            get_item_code(item='Amoxycillin 250mg_1000_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {12: 0.001, 36: 0.002, np.inf: 0.003}
-                                                          ),
+            get_item_code(item='Amoxycillin 250mg_1000_CMST'): 250,
         }
 
         # Referral process at health centres for severe cases
         self.consumables_used_in_hsi['First_dose_IM_antibiotics_for_referral'] = {
-            get_item_code(item='Ampicillin injection 500mg, PFR_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {4: 0.4, 12: 0.8, 36: 1.4, np.inf: 2}
-                                                          ),
-            get_item_code(item='Gentamicin Sulphate 40mg/ml, 2ml_each_CMST'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {4: 0.56, 12: 0.94, 36: 1.41, np.inf: 1.87}
-                                                          ),
+            get_item_code(item='Ampicillin injection 500mg, PFR_each_CMST'): 2,  # 2 x 500mg vial
+            get_item_code(item='Gentamicin Sulphate 40mg/ml, 2ml_each_CMST'): 2,  # assuming single dose at referral
             get_item_code(item='Cannula iv  (winged with injection pot) 16_each_CMST'): 1,
             get_item_code(item='Syringe, Autodisable SoloShot IX '): 1
         }
 
         # Oxygen, pulse oximetry and x-ray -------------------
 
-        # Oxygen for hypoxaemia
+        # Oxygen for hypoxaemia - 5/l per min (Approx) for 3 days ((24*60)*5)*3
         self.consumables_used_in_hsi['Oxygen_Therapy'] = {
-            get_item_code(item='Oxygen, 1000 liters, primarily with oxygen cylinders'): 1,
+            get_item_code(item='Oxygen, 1000 liters, primarily with oxygen cylinders'): 21_600,
         }
 
         # Pulse oximetry
@@ -1162,10 +1107,7 @@ def get_dosage_for_age_in_months(age_in_whole_months: float, doses_by_age_in_mon
         # Optional consumables -------------------
         # Paracetamol
         self.consumables_used_in_hsi['Paracetamol_tablet'] = {
-            get_item_code(item='Paracetamol, tablet, 100 mg'):
-                lambda _age: get_dosage_for_age_in_months(int(_age * 12.0),
-                                                          {36: 12, np.inf: 18}
-                                                          ),
+            get_item_code(item='Paracetamol, tablet, 100 mg'): 240,  # 20mg/kg
         }
 
         # Maintenance of fluids via nasograstric tube
@@ -1178,11 +1120,6 @@ def get_dosage_for_age_in_months(age_in_whole_months: float, doses_by_age_in_mon
             get_item_code(item='Salbutamol sulphate 1mg/ml, 5ml_each_CMST'): 2
         }
 
-        # Bronchodilator - oral
-        self.consumables_used_in_hsi['Oral_Brochodilator'] = {
-            get_item_code(item='Salbutamol, syrup, 2 mg/5 ml'): 1,
-            get_item_code(item='Salbutamol, tablet, 4 mg'): 1
-        }
 
     def end_episode(self, person_id):
         """End the episode infection for a person (i.e. reset all properties to show no current infection or
@@ -2420,11 +2357,7 @@ def _get_cons(self, _arg: Union[str, Tuple[str]]) -> bool:
     def _get_cons_group(self, item_group_str: str) -> bool:
         """True if _all_ of a group of consumables (identified by a string) is available."""
         if item_group_str is not None:
-            return self.get_consumables(
-                item_codes={
-                    k: v(self._age_exact_years) if isinstance(v, types.LambdaType) else v
-                    for k, v in self.module.consumables_used_in_hsi[item_group_str].items()
-                })
+            return self.get_consumables(self.module.consumables_used_in_hsi[item_group_str])
         else:
             raise ValueError('String for the group of consumables not provided')