icds=["icd_0","icd_1","icd_2","icd_3","icd_4","icd_5","icd_6","icd_7","icd_8","icd_9","icd_10","icd_11",
"icd_12","icd_13","icd_14","icd_15","icd_16","icd_17","icd_18","icd_19","icd_20","icd_21","icd_22","icd_23",
"icd_24","icd_25","icd_26","icd_27","icd_28","icd_29","icd_30","icd_31","icd_32","icd_33","icd_34","icd_35","icd_36","icd_37","icd_38"]
#df=diagnoses_1.astype({'HADM_ID': 'int32'})
diagnoses_1=diagnoses_1.fillna('')
#idx="HADM_ID"
#icds=["icd_0","icd_1","icd_2","icd_3","icd_4"]
df=diagnoses_1.sort_values(by=['HADM_ID'])
df=df.fillna('')
df.reset_index(drop=True)
#df.set_index('HADM_ID')
#df=df[['icd_0','icd_1', 'icd_2','icd_3', 'icd_4','HADM_ID']].head(n=1266)
#df=df[['icd_0','icd_1', 'icd_2','icd_3', 'icd_4','HADM_ID']].iloc[1264:1266]
#df['person_id'] = np.arange(len(df))+1
#create dx grouping indicators
comorbidity= icd.icd_to_comorbidities(df, "HADM_ID", icds, mapping="quan_elixhauser9")
#comorbidity.head(n=1)
#df.head(n=1)
comorbidity=comorbidity.reset_index(drop=True)
tt=tt.reset_index(drop=True)
# join the indicators with the patient, admission, and diagnosis codes
adm_w_dxind= pd.merge(tt, comorbidity, on=['HADM_ID'], how='inner')
adm_w_dxind['NEXT_ADM_DATE'] = adm_w_dxind['ADMITTIME'].shift(-1)
adm_w_dxind['DAYS_TO_NEXT_ADM'] = (adm_w_dxind['NEXT_ADM_DATE'] - adm_w_dxind['DISCHTIME']).dt.days
#check data types
adm_w_dxind.dtypes
adm_w_dxind.to_excel("case.xlsx")
def test_custom_mapping():
custom_map = {
"paraplegia_and_hemiplegia": [
'G81', 'G82', 'G041', 'G114', 'G801', 'G802', 'G830', 'G831',
'G832', 'G833', 'G834', 'G839'
],
"renal_disease": [
'N18', 'N19', 'N052', 'N053', 'N054', 'N055', 'N056', 'N057',
'N250', 'I120', 'I131', 'N032', 'N033', 'N034', 'N035', 'N036',
'N037', 'Z490', 'Z491', 'Z492', 'Z940', 'Z992'
],
"cancer": [
'C00', 'C01', 'C02', 'C03', 'C04', 'C05', 'C06', 'C07', 'C08',
'C09', 'C10', 'C11', 'C12', 'C13', 'C14', 'C15', 'C16', 'C17',
'C18', 'C19', 'C20', 'C21', 'C22', 'C23', 'C24', 'C25', 'C26',
'C30', 'C31', 'C32', 'C33', 'C34', 'C37', 'C38', 'C39', 'C40',
'C41', 'C43', 'C45', 'C46', 'C47', 'C48', 'C49', 'C50', 'C51',
'C52', 'C53', 'C54', 'C55', 'C56', 'C57', 'C58', 'C60', 'C61',
'C62', 'C63', 'C64', 'C65', 'C66', 'C67', 'C68', 'C69', 'C70',
'C71', 'C72', 'C73', 'C74', 'C75', 'C76', 'C81', 'C82', 'C83',
'C84', 'C85', 'C88', 'C90', 'C91', 'C92', 'C93', 'C94', 'C95',
'C96', 'C97'
],
"moderate_or_sever_liver_disease": [
'K704', 'K711', 'K721', 'K729', 'K765', 'K766', 'K767', 'I850',
'I859', 'I864', 'I982'
],
"metastitic_carcinoma": ['C77', 'C78', 'C79', 'C80'],
"aids_hiv": ['B20', 'B21', 'B22', 'B24']
}
d = icd.icd_to_comorbidities(df,
"id",
["icd_0", "icd_1", "icd_2", "icd_3", "icd_4"],
mapping=custom_map)
validation_data = {
'aids_hiv': {
1: False,
2: False,
3: False
},
'cancer': {
1: False,
2: False,
3: False
},
'id': {
1: 1,
2: 2,
3: 3
},
'metastitic_carcinoma': {
1: False,
2: True,
3: False
},
'moderate_or_sever_liver_disease': {
1: False,
2: False,
3: False
},
'paraplegia_and_hemiplegia': {
1: False,
2: False,
3: False
},
'renal_disease': {
1: False,
2: False,
3: False
}
}
assert d.to_dict(), validation_data
def test_invalid_stings():
with pytest.raises(Exception):
icd.icd_to_comorbidities(df,
"id",
["icd_0", "icd_1", "icd_2", "icd_3", "icd_4"],
mapping="bad_string")
def test_default_mapping():
d = icd.icd_to_comorbidities(df, "id",
["icd_0", "icd_1", "icd_2", "icd_3", "icd_4"])
validation_data = {
'aids_hiv': {
1: False,
2: False,
3: False
},
'alcohol_abuse': {
1: False,
2: False,
3: False
},
'blood_loss_anemia': {
1: False,
2: False,
3: False
},
'cardiac_arrhythmia': {
1: False,
2: False,
3: False
},
'chronic_pulmonary_disease': {
1: False,
2: False,
3: False
},
'coagulopathy': {
1: False,
2: False,
3: False
},
'congestive_heart_failure': {
1: False,
2: False,
3: False
},
'deficiency_anemia': {
1: False,
2: False,
3: False
},
'depression': {
1: False,
2: True,
3: False
},
'diabetes_complicated': {
1: False,
2: False,
3: False
},
'diabetes_uncomplicated': {
1: False,
2: False,
3: False
},
'drug_abuse': {
1: True,
2: False,
3: False
},
'fluid_and_electrolyte_disorders': {
1: False,
2: False,
3: False
},
'hypertension_complicated': {
1: False,
2: False,
3: False
},
'hypertension_uncomplicated': {
1: False,
2: False,
3: False
},
'hypothyroidism': {
1: False,
2: False,
3: False
},
'id': {
1: 1,
2: 2,
3: 3
},
'liver_disease': {
1: False,
2: False,
3: False
},
'lymphoma': {
1: False,
2: False,
3: False
},
'metastatic_cancer': {
1: False,
2: True,
3: False
},
'obesity': {
1: False,
2: False,
3: False
},
'other_neurological_disorder': {
1: False,
2: False,
3: True
},
'paralysis': {
1: False,
2: False,
3: False
},
'peptic_ulcer_disease_excluding_bleeding': {
1: False,
2: False,
3: False
},
'peripheral vascular_disorder': {
1: False,
2: False,
3: False
},
'psychoses': {
1: False,
2: False,
3: False
},
'pulmonary_circulation_disorder': {
1: False,
2: False,
3: False
},
'renal_failure': {
1: False,
2: False,
3: False
},
'rheumatoid_arhritis': {
1: False,
2: False,
3: False
},
'solid_tumor_wo_metastasis': {
1: False,
2: False,
3: False
},
'valvular_disease': {
1: False,
2: False,
3: False
},
'weight_loss': {
1: True,
2: False,
3: False
}
}
assert d.to_dict(), validation_data
def test_charlson_mapping():
d = icd.icd_to_comorbidities(df,
"id",
["icd_0", "icd_1", "icd_2", "icd_3", "icd_4"],
mapping="charlson10")
validation_data = {
'aids_hiv': {
1: False,
2: False,
3: False
},
'cancer': {
1: False,
2: False,
3: False
},
'cerebrovascular_disease': {
1: False,
2: False,
3: False
},
'chronic_pulmonary_disease': {
1: False,
2: False,
3: False
},
'congestive_heart_failure': {
1: False,
2: False,
3: False
},
'connective_tissue_disease_rheumatic_disease': {
1: False,
2: False,
3: False
},
'dementia': {
1: False,
2: False,
3: False
},
'diabetes_w_complications': {
1: False,
2: False,
3: False
},
'diabetes_wo_complications': {
1: False,
2: False,
3: False
},
'id': {
1: 1,
2: 2,
3: 3
},
'metastitic_carcinoma': {
1: False,
2: True,
3: False
},
'mild_liver_disease': {
1: False,
2: False,
3: False
},
'moderate_or_sever_liver_disease': {
1: False,
2: False,
3: False
},
'myocardial_infarction': {
1: False,
2: False,
3: False
},
'paraplegia_and_hemiplegia': {
1: False,
2: False,
3: False
},
'peptic_ulcer_disease': {
1: False,
2: False,
3: False
},
'periphral_vascular_disease': {
1: False,
2: False,
3: False
},
'renal_disease': {
1: False,
2: False,
3: False
}
}
assert d.to_dict(), validation_data