generated from opensafely/research-template
/
project.yaml
225 lines (203 loc) · 9.14 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
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
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_dva_all:
run: stata-mp:latest analysis/model_dva_all.do
needs: [run_subgroup_setup]
outputs:
moderately_sensitive:
model_dva_all0: output/CITS_dva.xlsx
model_dva_all1: output/dva_all2.dta
model_dva_all2: output/dva_all2_ld1.dta
model_dva_all3: output/dva_ratioLoess1.svg
model_dva_all4: output/diagnostics/dva_diagnostics1.svg
model_dva_all5: output/dva_plot1.svg
model_dva_all6: output/dva2_ld2.dta
model_dva_all7: output/dva_ratioLoess2.svg
model_dva_all8: output/diagnostics/dva_diagnostics2.svg
model_dva_all9: output/dva_plot2.svg
run_model_opioid:
run: stata-mp:latest analysis/model_opioid.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_opioid0: output/CITS_opioid.xlsx
model_opioid1: output/opioid.dta
model_opioid2: output/opioid_ld1.dta
model_opioid3: output/opioid_ratioLoess1.svg
model_opioid4: output/diagnostics/opioid_diagnostics1.svg
model_opioid5: output/opioid_plot1.svg
model_opioid6: output/opioid_ld2.dta
model_opioid7: output/opioid_ratioLoess2.svg
model_opioid8: output/diagnostics/opioid_diagnostics2.svg
model_opioid9: output/opioid_plot2.svg
run_model_alc:
run: stata-mp:latest analysis/model_alc.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_alc0: output/CITS_alc.xlsx
model_alc1: output/alc.dta
model_alc2: output/alc_ld1.dta
model_alc3: output/alc_ratioLoess1.svg
model_alc4: output/diagnostics/alc_diagnostics1.svg
model_alc5: output/alc_plot1.svg
model_alc6: output/alc_ld2.dta
model_alc7: output/alc_ratioLoess2.svg
model_alc8: output/diagnostics/alc_diagnostics2.svg
model_alc9: output/alc_plot2.svg
run_model_drug:
run: stata-mp:latest analysis/model_drug.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_drug0: output/CITS_drug.xlsx
model_drug1: output/drug.dta
model_drug2: output/drug_ld1.dta
model_drug3: output/drug_ratioLoess1.svg
model_drug4: output/diagnostics/drug_diagnostics1.svg
model_drug5: output/drug_plot1.svg
model_drug6: output/drug_ld2.dta
model_drug7: output/drug_ratioLoess2.svg
model_drug8: output/diagnostics/drug_diagnostics2.svg
model_drug9: output/drug_plot2.svg
run_model_misuse:
run: stata-mp:latest analysis/model_misuse.do
needs: [generate_measures]
outputs:
moderately_sensitive:
model_misuse0: output/CITS_misuse.xlsx
model_misuse1: output/misuse.dta
model_misuse2: output/misuse_ld1.dta
model_misuse3: output/misuse_ratioLoess1.svg
model_misuse4: output/diagnostics/misuse_diagnostics1.svg
model_misuse5: output/misuse_plot1.svg
model_misuse6: output/misuse_ld2.dta
model_misuse7: output/misuse_ratioLoess2.svg
model_misuse8: output/diagnostics/misuse_diagnostics2.svg
model_misuse9: output/misuse_plot2.svg
run_model_safeguard:
run: stata-mp:latest analysis/model_RCGPsafeguard.do
needs: [run_subgroup_setup]
outputs:
moderately_sensitive:
model_safeguard0: output/CITS_safeguard.xlsx
model_safeguard1: output/safeguard.dta
model_safeguard2: output/safeguard_ld1.dta
model_safeguard3: output/safeguard_ratioLoess1.svg
model_safeguard4: output/diagnostics/safeguard_diagnostics1.svg
model_safeguard5: output/safeguard_plot1.svg
model_safeguard6: output/safeguard_ld2.dta
model_safeguard7: output/safeguard_ratioLoess2.svg
model_safeguard8: output/diagnostics/safeguard_diagnostics2.svg
model_safeguard9: output/safeguard_plot2.svg
run_model_intdis_sub14:
run: stata-mp:latest analysis/model_intdis_sub14.do
needs: [run_subgroup_setup]
outputs:
moderately_sensitive:
model_intdis_sub0: output/CITS_intdis_sub14.xlsx
model_intdis_sub1: output/intdis_sub14_2.dta
model_intdis_sub2: output/intdis_sub14_2_ld1.dta
model_intdis_sub3: output/intdis_ratioLoess_jr1.svg
model_intdis_sub4: output/diagnostics/intdis_diagnostics_jr1.svg
model_intdis_sub5: output/intdis_sub14_plot1.svg
model_intdis_sub6: output/intdis_sub14_2_ld2.dta
model_intdis_sub7: output/intdis_ratioLoess_jr2.svg
model_intdis_sub8: output/diagnostics/intdis_diagnostics_jr2.svg
model_intdis_sub9: output/intdis_sub14_plot2.svg
run_model_intdis_over14:
run: stata-mp:latest analysis/model_intdis_over14.do
needs: [run_subgroup_setup]
outputs:
moderately_sensitive:
model_intdis_over0: output/CITS_intdis_over14.xlsx
model_intdis_over1: output/intdis_over14_2.dta
model_intdis_over2: output/intdis_over14_2_ld1.dta
model_intdis_over3: output/intdis_ratioLoess_sr1.svg
model_intdis_over4: output/diagnostics/intdis_diagnostics_sr1.svg
model_intdis_over5: output/intdis_over14_plot1.svg
model_intdis_over6: output/intdis_over14_2_ld2.dta
model_intdis_over7: output/intdis_ratioLoess_sr2.svg
model_intdis_over8: output/diagnostics/intdis_diagnostics_sr2.svg
model_intdis_over9: output/intdis_over14_plot2.svg