generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
project.yaml
229 lines (196 loc) · 6.85 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
226
227
228
229
######################################
# This script defines the project pipeline -
# it specifies the execution orders for all the code in this
# repo using a series of actions.
######################################
version: '3.0'
expectations:
population_size: 10000
actions:
generate_dataset_table:
run: ehrql:v0 generate-dataset analysis/define_dataset_table.py
--output output/data/dataset_table.csv.gz
outputs:
highly_sensitive:
cohort: output/data/dataset_table.csv.gz
# Measures - prevalent and new prescribing - overall
measures_overall:
run: ehrql:v0 generate-measures analysis/measures_overall.py
--output output/measures/measures_overall.csv
--
--start-date "2018-01-01"
--intervals 54
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_overall.csv
# Measures - prevalent prescribing - by demographic categories
measures_demo_prev:
run: ehrql:v0 generate-measures analysis/measures_demo_prev.py
--output output/measures/measures_demo_prev.csv
--
--start-date "2018-01-01"
--intervals 3
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_demo_prev.csv
# Measures - new prescribing - by demographic categories
measures_demo_new:
run: ehrql:v0 generate-measures analysis/measures_demo_new.py
--output output/measures/measures_demo_new.csv
--
--start-date "2018-01-01"
--intervals 54
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_demo_new.csv
# Measures - prevalent prescribing - by opioid type
measures_type:
run: ehrql:v0 generate-measures analysis/measures_type.py
--output output/measures/measures_type.csv
--
--start-date "2018-01-01"
--intervals 54
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_type.csv
# Measures - prevalent prescribing - checking overall counts
measures_test:
run: ehrql:v0 generate-measures analysis/measures_test.py
--output output/measures/measures_test.csv
--
--start-date "2019-01-01"
--intervals 36
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_test.csv
# Measures - prevalent and new prescribing - in people in care home
measures_carehome:
run: ehrql:v0 generate-measures analysis/measures_carehome.py
--output output/measures/measures_carehome.csv
--
--start-date "2018-01-01"
--intervals 54
outputs:
moderately_sensitive:
measure_csv: output/measures/measures_carehome.csv
## Process time series data - overall prescribing
process_ts_overall:
run: r:latest analysis/process/process_ts_overall.R
needs: [measures_overall]
outputs:
moderately_sensitive:
timeseries_csv: output/timeseries/ts_overall*.csv
## Process time series data - prescribing by demographics
process_ts_demo:
run: r:latest analysis/process/process_ts_demo.R
needs: [measures_demo_prev, measures_demo_new]
outputs:
moderately_sensitive:
timeseries_csv: output/timeseries/ts_demo*.csv
## Process time series data - prescribing by admin route
process_ts_type:
run: r:latest analysis/process/process_ts_type.R
needs: [measures_type]
outputs:
moderately_sensitive:
timeseries_csv: output/timeseries/ts_type*.csv
## Process time series data - prescribing to people in carehome
process_ts_carehome:
run: r:latest analysis/process/process_ts_carehome.R
needs: [measures_carehome]
outputs:
moderately_sensitive:
timeseries_csv: output/timeseries/ts_carehome*.csv
## Check time series
figures_ts:
run: r:latest analysis/descriptive/ts_figures.R
needs: [process_ts_overall, process_ts_type, process_ts_carehome, process_ts_demo]
outputs:
moderately_sensitive:
plots: output/descriptive/ts_plot*.png
## Results table
table:
run: r:latest analysis/descriptive/table_stand.R
needs: [generate_dataset_table]
outputs:
moderately_sensitive:
table: output/tables/table_*.csv
# OLD COHORTEXTRACTOR CODE
# ## Cohort data
# generate_study_population_1:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2018-01-01 to 2018-12-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/input_*.csv
# generate_study_population_2:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2019-01-01 to 2019-12-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/input*.csv
# generate_study_population_3:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2020-01-01 to 2020-12-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/inpu*.csv
# generate_study_population_4:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2021-01-01 to 2021-12-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/inp*.csv
# generate_study_population_5:
# run: cohortextractor:latest generate_cohort
# --study-definition study_definition
# --index-date-range "2022-01-01 to 2022-03-01 by month"
# --output-dir=output
# --output-format=csv
# outputs:
# highly_sensitive:
# cohort: output/in*.csv
# ## Ethnicity
# generate_ethnicity_cohort:
# run: >
# cohortextractor:latest generate_cohort
# --study-definition study_definition_ethnicity
# outputs:
# highly_sensitive:
# cohort: output/input_ethnicity.csv
# # Data processing ----
# ## Add ethnicity
# join_cohorts:
# run: >
# cohort-joiner:v0.0.48
# --lhs output/input_*.csv
# --rhs output/input_ethnicity.csv
# --output-dir output/data
# needs: [generate_study_population_1, generate_study_population_2,
# generate_study_population_5, generate_study_population_3,
# generate_study_population_4, generate_ethnicity_cohort]
# outputs:
# highly_sensitive:
# cohort: output/data/input_*.csv
# ## Generate measures - full population
# generate_measures:
# run: >
# cohortextractor:latest generate_measures
# --study-definition study_definition
# --output-dir output/data
# needs: [join_cohorts]
# outputs:
# moderately_sensitive:
# measure_csv: output/data/measure_*.csv