Update the availability of Xpert (#1725)

* update the availability of Xpert
- to match the average of the last 4 months of 2018 (as per OpenLMIS)

* add explanatory comments to script

Author: sakshimohan

resources/healthsystem/consumables/ResourceFile_Consumables_availability_small.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:f945b15a98e571464b6931f0a3a071c1c90be93d8ba0bd9d1eca751caab34793
-size 55657974
+oid sha256:3bc044868ad9f1c618fc9b3fd6fc0ed23f32b153c8438f52fd4b72e40d8f503f
+size 55831644

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

@@ -765,7 +765,33 @@ def get_inflow_to_outflow_ratio_by_item_and_facilitylevel(_df):
 mwanza_1b = sf.loc[(sf.district_std == 'Mwanza') & (sf.fac_type_tlo == '1a')].copy().assign(fac_type_tlo='1b')
 sf = pd.concat([sf, mwanza_1b], axis=0, ignore_index=True)
 
-# 4) Copy all the results to create a level 0 with an availability equal to half that in the respective 1a
+# 4) Update the availability Xpert (item_code = 187)
+# First add rows for Xpert at level 1b by cloning rows for level 2 -> only if not already present
+xpert_item = sf['item_code'].eq(187)
+level_2    = sf['fac_type_tlo'].eq('2')
+level_1b   = sf['fac_type_tlo'].eq('1b')
+
+# Clone rows from level 2
+base   = sf.loc[level_2 & xpert_item].copy()
+new_rows  = base.copy()
+new_rows['fac_type_tlo'] = '1b'
+
+# Add rows to main availability dataframe and drop duplicates, if any
+sf = pd.concat([sf, new_rows], ignore_index=True)
+id_cols = [c for c in sf.columns if c != 'available_prop']
+dupe_mask = sf.duplicated(subset=id_cols, keep=False)
+dupes = sf.loc[dupe_mask].sort_values(id_cols)
+sf = sf.drop_duplicates(subset=id_cols, keep='first').reset_index(drop=True)
+
+# Compute the average availability Sep–Dec (months >= 9) for level 2, item 187
+sep_to_dec = sf['month'].ge(9)
+new_xpert_availability = sf.loc[level_2 & xpert_item & sep_to_dec, 'available_prop'].mean()
+# Assign new availability to relevant facility levels
+levels_1b_2_or_3 = sf['fac_type_tlo'].isin(['1b', '2', '3'])
+xpert_item = sf['item_code'].eq(187)
+sf.loc[levels_1b_2_or_3 & xpert_item, 'available_prop'] = new_xpert_availability
+
+# 5) Copy all the results to create a level 0 with an availability equal to half that in the respective 1a
 all_1a = sf.loc[sf.fac_type_tlo == '1a']
 all_0 = sf.loc[sf.fac_type_tlo == '1a'].copy().assign(fac_type_tlo='0')
 all_0.available_prop *= 0.5