generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
project.yaml
108 lines (95 loc) · 3.78 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
version: '3.0'
expectations:
population_size: 1000
actions:
# General population cohort
generate_study_population:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range "2018-03-01 to 2021-12-31 by month"
--output-dir=output/measures
--output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv
generate_study_population_static_2019:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2019-01-01" --output-dir=output/measures/tables --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static_2019-01-01.csv
generate_study_population_static_2020:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2020-01-01" --output-dir=output/measures/tables --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static_2020-01-01.csv
generate_study_population_static_2021:
run: cohortextractor:latest generate_cohort --study-definition study_definition_static --index-date-range "2021-01-01" --output-dir=output/measures/tables --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_static_2021-01-01.csv
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure: output/measures/measure_*_rate.csv
# Diabetes subpopulation
generate_study_population_dm:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_dm
--index-date-range "2018-03-01 to 2021-12-31 by month"
--output-dir=output/measures
--output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_dm_*.csv
calculate_measures_dm:
run: cohortextractor:latest generate_measures --study-definition study_definition_dm --output-dir=output/measures
needs: [generate_study_population_dm]
outputs:
moderately_sensitive:
measure: output/measures/measure_dm*_rate.csv
# Respiratory subpopulation
generate_study_population_resp:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_resp
--index-date-range "2018-03-01 to 2021-12-31 by month"
--output-dir=output/measures
--output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_resp_*.csv
calculate_measures_resp:
run: cohortextractor:latest generate_measures --study-definition study_definition_resp --output-dir=output/measures
needs: [generate_study_population_resp]
outputs:
moderately_sensitive:
measure: output/measures/measure_resp_*_rate.csv
create_baseline_tables:
run: stata-mp:latest analysis/101_baseline_tables.do
needs: [generate_study_population_static_2019, generate_study_population_static_2020, generate_study_population_static_2021]
outputs:
moderately_sensitive:
log: logs/table1_descriptives.log
output: output/tables/baseline_table_*.csv
graphs:
run: stata-mp:latest analysis/102_graphs.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/graphs.log
output: output/graphs/line_*.svg
data: output/graphs/line_*.csv
poisson_prep:
run: stata-mp:latest analysis/103_poisson_prep.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/poisson_prep.log
output: output/cvd/an*.csv
poisson:
run: r:latest analysis/104_poisson.R
needs: [poisson_prep]
outputs:
moderately_sensitive:
output: output/table3.csv