generated from opensafely/research-template
/
simple_validation_script.py
161 lines (137 loc) · 4.2 KB
/
simple_validation_script.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
from lib_phenotype_validation import *
############################ CONFIGURE OPTIONS HERE ################################
# Import file
input_path = "output/extract_5/input_5.feather"
# Definitions
definitions = [
"ethnicity_5",
"ethnicity_new_5",
"ethnicity_primis_5",
]
definitions_sus = [
"ethnicity_new_5",
"ethnicity_sus_5",
]
# Code dictionary
code_dict = {
"imd": {
0: "Unknown",
1: "1 Most deprived",
2: "2",
3: "3",
4: "4",
5: "5 Least deprived",
},
"ethnicity_5": {1: "White", 2: "Mixed", 3: "Asian", 4: "Black", 5: "Other"},
"ethnicity_new_5": {1: "White", 2: "Mixed", 3: "Asian", 4: "Black", 5: "Other"},
"ethnicity_primis_5": {1: "White", 2: "Mixed", 3: "Asian", 4: "Black", 5: "Other"},
"ethnicity_sus_5": {1: "White", 2: "Mixed", 3: "Asian", 4: "Black", 5: "Other"},
}
# Other variables to include
other_vars = ["white", "mixed", "asian", "black", "other"]
other_vars_combined = [x + "_" + y for x in definitions for y in other_vars]
# Restrict to registered as of index date
registered = True
reg = "fullset"
if registered == True:
reg = "registered"
# Dates
dates = True
date_min = ""
date_max = ""
time_delta = ""
# Min/max range
min_range = 4
max_range = 200
# Null value – could be multiple values in a list [0,'0',NA]
null = [0, "0"]
# Covariates
demographic_covariates = ["age_band", "sex", "region", "imd"]
clinical_covariates = ["dementia", "diabetes", "hypertension", "learning_disability"]
# Output filepath
output_path = "simplified_output"
grouping = "5_group"
########################## SPECIFY ANALYSES TO RUN HERE ##############################
def main():
# combine defintions and other_vars
df_clean = import_clean(
input_path,
definitions,
other_vars_combined,
demographic_covariates,
clinical_covariates,
reg,
null,
date_min,
date_max,
time_delta,
output_path,
grouping,
code_dict,
dates=False,
registered = registered,
dates_check=True,
)
# Count patients with records
simple_patient_counts(
df_clean, definitions,reg, demographic_covariates, clinical_covariates, output_path,grouping,
)
# Count patients by categories
simple_patient_counts(
df_clean,
definitions,
reg,
demographic_covariates,
clinical_covariates,
output_path,
grouping,
categories=True,
)
# # Generate upset plot of overlapping definitions
# upset(df_clean_reg, output_path, definitions[1], definitions[0])
# upset_cat(df_clean, output_path, definitions[1], definitions[0], other_vars)
# Latest v most common
simple_latest_common_comparison(
df_clean, definitions,reg, other_vars_combined, output_path,grouping,
)
simple_latest_common_comparison(
df_clean, definitions,reg, other_vars_combined, output_path,grouping, missing_check=True,
)
# State change
simple_state_change(df_clean, definitions,reg, other_vars_combined, output_path,grouping,)
simple_state_change(
df_clean, definitions,reg, other_vars_combined, output_path,grouping, missing_check=True
)
# # records over time
# records_over_time_perc(
# df_clean, definitions, demographic_covariates, clinical_covariates, output_path, "",grouping,reg
# )
# df_clean_sus=import_clean_sus(
# input_path,
# definitions_sus,
# other_vars_combined,
# demographic_covariates,
# clinical_covariates,
# reg,
# null,
# date_min,
# date_max,
# time_delta,
# output_path,
# grouping,
# code_dict,
# dates=False,
# registered = registered,
# dates_check=True,
# )
# # Count patients with records with SUS
# simple_patient_counts_sus(
# df_clean_sus, definitions_sus,reg, demographic_covariates, clinical_covariates, output_path,grouping,
# )
########################## DO NOT EDIT – RUNS SCRIPT ##############################
if __name__ == "__main__":
main()
# registered = False
# reg = "fullset"
# if __name__ == "__main__":
# main()