generated from opensafely/research-template
/
project.yaml
89 lines (78 loc) · 3.36 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
version: '3.0'
expectations:
population_size: 1000
actions:
generate_cohorts_main:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ori
outputs:
highly_sensitive:
cohort: output/input_ori.csv
run_model:
run: r:latest analysis/01-createSDtables.R
needs: [generate_cohorts_main]
outputs:
moderately_sensitive:
log: logs/log-01-createSDtables.txt
#gtpng1: output/tables/gt_ocpop.png
#gtpng2: output/tables/gt_gpcpop.png
rdata1: output/tables/gt_ocpop.RData
rdata2: output/tables/gt_gpcpop.RData
#tb01: output/tables/tb01_gpcr_region.csv
#tb02: output/tables/tb02_gpcr_stp.csv # guidance says to not output identifiable regions
tb04: output/tables/tb04_gpcr_agesex.csv
tb05: output/tables/tb05_gpcr_ethnicity.csv
tb06: output/tables/tb06_gpcr_ruc.csv
tb07: output/tables/tb07_gpcr_care.csv
tb08: output/tables/tb08_gpcr_dis.csv
# https://docs.opensafely.org/en/latest/measures/
generate_cohorts_long:
run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_bycode --index-date-range "2019-01-01 to 2020-12-01 by month" --output-dir=output/measures
outputs:
highly_sensitive:
cohort: output/measures/input_measures_bycode_*.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_measures_bycode --output-dir=output/measures
needs: [generate_cohorts_long]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
run_model_long:
run: r:latest analysis/03-createnattrends_codes.R
needs: [generate_cohorts_long]
outputs:
moderately_sensitive:
log: logs/log-03-createnattrends.txt
tb01: output/tables/sc03_tb01_nattrends.csv
fig01: output/plots/sc03_fig01_nattrends.svg
fig02: output/plots/sc03_fig02_nattrends.svg
fig03: output/plots/sc03_fig03_pracnatcoverage.svg
fig04: output/plots/sc03_fig04_pracbyregcoverage.svg
run_model_measures:
run: r:latest analysis/02-createtemporal.R
needs: [generate_cohorts_long,generate_measures]
outputs:
moderately_sensitive:
log: logs/log-02-createtemporal.txt
red_measures: output/tables/redacted_*.csv
#tb01: output/measures_gpc_pop.csv # redundant into. omit output
fig01: output/plots/plot_overall_gpc_pop.svg
#figall: output/plots/plot_each_OC_*_practice.svg
figquant: output/plots/plot_quantiles_OC_*_practice.svg
run_model_measuresDEBUG:
run: r:latest analysis/02-createtemporal_debug.R
needs: [generate_cohorts_long,generate_measures]
outputs:
moderately_sensitive:
log: logs/log-02-createtemporal-debug.txt
#tb01: output/measures_gpc_pop_debug.csv
#fig01: output/plots/plot_overall_gpc_pop_debug.svg
#figall: output/plots/plot_each_debug_*_practice.svg
#figquant: output/plots/plot_quantiles_debug_*_practice.svg
#figquant2: output/plots/plot_quantiles2_debug_*_practice.svg
run_model_redactedmeasures:
run: r:latest analysis/02a-createredactedmeasure.R
needs: [generate_cohorts_long,generate_measures]
outputs:
moderately_sensitive:
log: logs/log-02a-createredactedmeasure.txt
red_measures: output/tables/redacted2a_*.csv