import pandas as pd from utils.common import read_data steroid_codes = ['0603020T0AAACAC', '0603020T0AABKBK', '0603020T0AAAXAX', '0603020T0AAAGAG', '0603020T0AABHBH', '0603020T0AAACAC', '0603020T0AABKBK', '0603020T0AABNBN', '0603020T0AAAGAG', '0603020T0AABHBH'] antib_codes = ['0501013B0AAAAAA', '0501013B0AAABAB', '0501030I0AAABAB', '0501030I0AAAAAA', '0501050B0AAAAAA', '0501050B0AAADAD', '0501013K0AAAJAJ'] exac_meds = steroid_codes + antib_codes def initialize_presc_data(presc_file): """ Load in prescribing dataset to correct format -------- :param presc_file: prescribing data file name :return: prescribing dataframe with correct column names and types """ print('Loading prescribing data') # Read in data presc_cols = ['SafeHavenID', 'PRESC_DATE', 'PI_Approved_Name', 'PI_BNF_Item_Code'] presc_types = ['int', 'object', 'str', 'str'] df = read_data(presc_file, presc_cols, presc_types) # Drop any nulls or duplicates df = df.dropna() df = df.drop_duplicates() # Convert date df['PRESC_DATE'] = pd.to_datetime(df.PRESC_DATE) return df def track_medication(df): """ Track salbutamol and rescue med prescriptions https://openprescribing.net/bnf/ -------- :param df: dataframe :return: dataframe with tracked meds """ print('Tracking medication') # Extract BNF codes without brand info df['code'] = df.PI_BNF_Item_Code.apply(lambda x: x[0:9]) # Add flag for salbutamol - marked important by Chris df['SALBUTAMOL'] = (df.code == '0301011R0').astype(int) # Track rescue meds df['rescue_meds'] = df.PI_BNF_Item_Code.str.contains( '|'.join(exac_meds)).astype(int) # Track anxiety and depression medication ad_bnf = ('040102', '0403', '0204000R0', '0408010AE') ad_events = df.PI_BNF_Item_Code.str.startswith(ad_bnf).fillna(False) drop_dummy = (df.PI_Approved_Name != 'DUMMY') & (df.PI_Approved_Name != 'DUMMY REJECTED') df['anxiety_depression_presc'] = (drop_dummy & ad_events).astype(int) return df