generated from opensafely/research-template
/
project.yaml
137 lines (118 loc) · 5.07 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
129
130
131
132
133
134
135
136
137
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-09-02 to 2020-01-13 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_*.csv.gz
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-20 to 2020-06-01 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input*.csv.gz
generate_study_population_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-06-08 to 2020-10-19 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/inpu*.csv.gz
generate_study_population_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-10-26 to 2021-03-01 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/inp*.csv.gz
generate_study_population_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-03-08 to 2021-06-14 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/in*.csv.gz
generate_study_population_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-06-21 to 2021-09-27 by week" --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/i*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition
needs: [generate_study_population_1, generate_study_population_2, generate_study_population_3, generate_study_population_4, generate_study_population_5, generate_study_population_6]
outputs:
moderately_sensitive:
measure_csv: output/measure_*_rate.csv
run_subgroup_setup:
run: stata-mp:latest analysis/subgroup_data_setup.do
needs: [generate_measures]
outputs:
moderately_sensitive:
subgroup1: output/dva_female.dta
subgroup2: output/dva_male.dta
subgroup3: output/dva_all.dta
subgroup4: output/intdis_sub14.dta
subgroup5: output/intdis_over14.dta
subgroup6: output/intdis_all.dta
subgroup7: output/RCGPsafeguard_sub18.dta
subgroup8: output/CovidNewCaseCounts.dta
run_model_dva_female:
run: stata-mp:latest analysis/model_DVA_female.do
needs: [run_subgroup_setup]
outputs:
moderately_sensitive:
model_dva_female0: output/CITS_dva_female.xlsx
model_dva_female1: output/dva_female2.dta
model_dva_female2: output/dva_female2_ld1.dta
model_dva_female3: output/dva_ratioLoess_f1.svg
model_dva_female4: output/diagnostics/dva_diagnostics_f1.svg
model_dva_female5: output/dva_female_plot1.svg
model_dva_female6: output/dva_female2_ld2.dta
model_dva_female7: output/dva_ratioLoess_f2.svg
model_dva_female8: output/diagnostics/dva_diagnostics_f2.svg
model_dva_female9: output/dva_female_plot2.svg
run_model_dva_male:
run: stata-mp:latest analysis/model_DVA_male.do
needs: [run_subgroup_setup]
outputs:
moderately_sensitive:
model_dva_male0: output/CITS_dva_male.xlsx
model_dva_male1: output/dva_male2.dta
model_dva_male2: output/dva_male2_ld1.dta
model_dva_male3: output/dva_ratioLoess_m1.svg
model_dva_male4: output/diagnostics/dva_diagnostics_m1.svg
model_dva_male5: output/dva_male_plot1.svg
model_dva_male6: output/dva_male2_ld2.dta
model_dva_male7: output/dva_ratioLoess_m2.svg
model_dva_male8: output/diagnostics/dva_diagnostics_m2.svg
model_dva_male9: output/dva_male_plot2.svg
run_model_intdis:
run: stata-mp:latest analysis/model_intdis.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_intdis1: output/intdis_plot1.pdf
model_intdis2: output/intdis_plot2.pdf
run_model_RCGPsafeguard:
run: stata-mp:latest analysis/model_RCGPsafeguard.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_RCGPsafeguard1: output/RCGPsafeguard_plot1.pdf
model_RCGPsafeguard2: output/RCGPsafeguard_plot2.pdf
run_model_safeguard:
run: stata-mp:latest analysis/model_safeguard.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_safeguard1: output/safeguard_plot1.pdf
model_safeguard2: output/safeguard_plot2.pdf
run_model_opioid:
run: stata-mp:latest analysis/model_opioid.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_opioid1: output/opioid_plot1.pdf
model_opioid2: output/opioid_plot2.pdf
run_model_misuse:
run: stata-mp:latest analysis/model_misuse.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_misuse1: output/misuse_plot1.pdf
model_misuse2: output/misuse_plot2.pdf