/
project.yaml
128 lines (115 loc) · 4.93 KB
/
project.yaml
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
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_ethnicity_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--param end_date="2023-03-01"
--output-dir output/01GV5GNQPG3SDNRVGETDTX1T5Y --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/01GV5GNQPG3SDNRVGETDTX1T5Y/input_ethnicity.csv.gz
generate_study_population_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--param codelist_1_path="codelists/codelist_1.csv"
--param codelist_1_type="medication"
--param codelist_2_path="codelists/codelist_2.csv"
--param codelist_2_type="event"
--param codelist_1_frequency="monthly"
--param time_value="3"
--param time_scale="weeks"
--param time_event="before"
--param codelist_2_comparison_date="end_date"
--param operator="AND"
--param population="all"
--param breakdowns="sex"
--index-date-range="2022-09-02 to 2023-03-01 by month"
--output-dir=output/01GV5GNQPG3SDNRVGETDTX1T5Y
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/01GV5GNQPG3SDNRVGETDTX1T5Y/input_*.csv.gz
join_cohorts_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: >
cohort-joiner:v0.0.38
--lhs output/01GV5GNQPG3SDNRVGETDTX1T5Y/input_20*.csv.gz
--rhs output/01GV5GNQPG3SDNRVGETDTX1T5Y/input_ethnicity.csv.gz
--output-dir output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined
needs: [generate_study_population_01GV5GNQPG3SDNRVGETDTX1T5Y, generate_study_population_ethnicity_01GV5GNQPG3SDNRVGETDTX1T5Y]
outputs:
highly_sensitive:
cohort: output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined/input_20*.csv.gz
generate_measures_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: >
python:latest python -m analysis.measures
--breakdowns="sex"
--input_dir="output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined"
--measure="med_review"
needs: [join_cohorts_01GV5GNQPG3SDNRVGETDTX1T5Y]
outputs:
moderately_sensitive:
measure: output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined/measure*rate.csv
decile_measure: output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined/measure*rate_deciles.csv
top_5_table_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: >
python:latest python analysis/top_5.py
--codelist-1-path="codelists/codelist_1.csv"
--codelist-2-path="codelists/codelist_2.csv"
--output-dir="output/01GV5GNQPG3SDNRVGETDTX1T5Y"
needs: [generate_measures_01GV5GNQPG3SDNRVGETDTX1T5Y]
outputs:
moderately_sensitive:
tables: output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined/top_5*.csv
deciles_chart_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: >
deciles-charts:v0.0.33
--input-files output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined/measure_practice_rate_deciles.csv
--output-dir output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined
config:
show_outer_percentiles: true
tables:
output: true
charts:
output: true
needs: [generate_measures_01GV5GNQPG3SDNRVGETDTX1T5Y]
outputs:
moderately_sensitive:
deciles_charts: output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined/deciles_*.*
plot_measure_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: >
python:latest python analysis/plot_measures.py
--breakdowns="sex"
--output-dir output/01GV5GNQPG3SDNRVGETDTX1T5Y
needs: [generate_measures_01GV5GNQPG3SDNRVGETDTX1T5Y]
outputs:
moderately_sensitive:
measure: output/01GV5GNQPG3SDNRVGETDTX1T5Y/plot_measure*.png
event_counts_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: >
python:latest python analysis/event_counts.py --input_dir="output/01GV5GNQPG3SDNRVGETDTX1T5Y/joined" --output_dir="output/01GV5GNQPG3SDNRVGETDTX1T5Y"
needs: [join_cohorts_01GV5GNQPG3SDNRVGETDTX1T5Y]
outputs:
moderately_sensitive:
measure: output/01GV5GNQPG3SDNRVGETDTX1T5Y/event_counts.json
generate_report_01GV5GNQPG3SDNRVGETDTX1T5Y:
run: >
python:latest python analysis/render_report.py
--report-title="DMARDs & Care planning medication review simple reference set - NHS Digital"
--population="all"
--breakdowns="sex"
--codelist-1-name="DMARDs"
--codelist-2-name="Care planning medication review simple reference set - NHS Digital"
--codelist-1-link="opensafely/dmards/2020-06-23"
--codelist-2-link="opensafely/care-planning-medication-review-simple-reference-set-nhs-digital/61b13c39"
--time-value="3"
--time-scale="weeks"
--time-event="before"
--start-date="2022-09-02"
--end-date="2023-03-01"
--request-id="01GV5GNQPG3SDNRVGETDTX1T5Y"
needs: [event_counts_01GV5GNQPG3SDNRVGETDTX1T5Y, deciles_chart_01GV5GNQPG3SDNRVGETDTX1T5Y, top_5_table_01GV5GNQPG3SDNRVGETDTX1T5Y, plot_measure_01GV5GNQPG3SDNRVGETDTX1T5Y]
outputs:
moderately_sensitive:
notebook: output/01GV5GNQPG3SDNRVGETDTX1T5Y/report.html