generated from opensafely/covid-vaccine-research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
project.yaml
130 lines (101 loc) · 3.67 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
version: '3.0'
expectations:
population_size: 100000
actions:
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
#
# needs: [generate_delivery_cohort]
# outputs:
# moderately_sensitive:
# notebook: output/population_characteristics.html
get_packages:
run: r:latest analysis/R/export_package_names.R
outputs:
moderately_sensitive:
cohort: output/available_packages.csv
## Descriptive info on vaccinated patients
extract_vaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
outputs:
highly_sensitive:
cohort: output/input_vaccinated.csv
data_process_vaccinated:
run: r:latest analysis/R/data_process_vaccinated.R
needs: [extract_vaccinated]
outputs:
highly_sensitive:
cohort: output/data/data_vaccinated.rds
data_properties_vaccinated:
run: r:latest analysis/R/data_properties.R output/data/data_vaccinated.rds output/data_properties
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
summary: output/data_properties/data_vaccinated*.txt
data_summarise_vaccinated:
run: r:latest analysis/R/data_summarise.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
summary1: output/variable_summary/categorical.txt
summary2: output/variable_summary/numeric.txt
summary3: output/variable_summary/date.txt
summarytables: output/variable_summary/tables/categorical_*.csv
summarystats: output/summary_stats.json
vaccine_tables:
run: r:latest analysis/R/vaccine_type.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
tables: output/vaccine_type/tables/vaccine_type_*.csv
tte_tables:
run: r:latest analysis/R/tte_tables.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
tables: output/tte/tables/event_rates_*.csv
tte_plots:
run: r:latest analysis/R/tte_plots.R
needs: [data_process_vaccinated]
outputs:
moderately_sensitive:
plots: output/tte/figures/plot_*.svg
# data for whole cohort
extract_all:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all
outputs:
highly_sensitive:
cohort: output/input_all.csv
data_process_all:
run: r:latest analysis/R/data_process_all.R
needs: [extract_all]
outputs:
highly_sensitive:
data1: output/data/data_all.rds
data2: output/data/data_long_vax_dates.rds
data3: output/data/data_long_admission_dates.rds
data_properties_all:
run: r:latest analysis/R/data_properties.R output/data/data_all.rds output/data_properties
needs: [data_process_all]
outputs:
moderately_sensitive:
datasummary: output/data_properties/data_all*.txt
## VE models in over 80s
models_over80s:
run: r:latest analysis/R/models_over80s.R
needs: [data_process_all]
outputs:
moderately_sensitive:
#datasummary: output/data_properties/data_tte_over80s*.txt
zph: output/models/over80s/zph*.png
forest: output/models/over80s/forest*.svg
tables: output/models/over80s/*.csv
models_under65s:
run: r:latest analysis/R/models_under65s.R
needs: [data_process_all]
outputs:
moderately_sensitive:
#datasummary: output/data_properties/data_tte_over80s*.txt
zph: output/models/under65s/zph*.png
forest: output/models/under65s/forest*.svg
tables: output/models/under65s/*.csv