generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
project.yaml
143 lines (130 loc) · 5.91 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
version: '3.0'
expectations:
population_size: 400000
actions:
generate_study_population_allpts:
run: cohortextractor:latest generate_cohort --study-definition study_definition_allpts
outputs:
highly_sensitive:
cohort: output/input_allpts.csv
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
create_cohorts_allpts:
run: stata-mp:latest analysis/001_define_covariates_allpts.do
needs: [generate_study_population_allpts]
outputs:
highly_sensitive:
log1: logs/cleaning_dataset_allpts.log
data1: output/data/file_eia_allpts.dta
create_cohorts:
run: stata-mp:latest analysis/000_define_covariates.do
needs: [generate_study_population]
outputs:
highly_sensitive:
log1: logs/cleaning_dataset.log
data1: output/data/file_eia_all.dta
run_baseline_tables_allpts:
run: stata-mp:latest analysis/101_baseline_characteristics_allpts.do
needs: [create_cohorts_allpts]
outputs:
moderately_sensitive:
log1: logs/descriptive_tables_allpts.log
doc1: output/tables/baseline_allpts.csv
run_baseline_tables:
run: stata-mp:latest analysis/100_baseline_characteristics.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/descriptive_tables.log
doc1: output/tables/baseline_bydiagnosis.csv
doc2: output/tables/baseline_byyear.csv
doc3: output/tables/referral_bydiag_nomiss.csv
doc4: output/tables/referral_byyear_nomiss.csv
doc5: output/tables/referral_byregion_nomiss.csv
doc6: output/tables/drug_bydiag_miss.csv
doc7: output/tables/drug_byyear_miss.csv
doc8: output/tables/drug_byyear_ra_miss.csv
doc9: output/tables/drug_byyear_psa_miss.csv
doc10: output/tables/drug_byyear_undiff_miss.csv
doc11: output/tables/drug_byyearanddisease.csv
doc12: output/tables/drug_byyearandregion.csv
doc13: output/tables/diag_count_bymonth.csv
doc14: output/tables/diag_count_byyear.csv
doc15: output/tables/appt_count_bymonth.csv
doc16: output/tables/diag_count_byyear_ethn.csv
doc17: output/tables/diag_count_byyear_imd.csv
figure1: output/figures/incidence_twoway_rounded.svg
figure2: output/figures/incidence_twoway_appt.svg
run_itsa_models:
run: stata-mp:latest analysis/200_itsa_models.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/itsa_models.log
figure1: output/figures/ITSA_diagnostic_delay_newey.svg
figure2: output/figures/ITSA_diagnostic_delay_prais.svg
figure3: output/figures/ITSA_diagnostic_delay_GP_newey.svg
figure4: output/figures/ITSA_diagnostic_delay_GP_prais.svg
doc1: output/tables/gp_to_appt_ITSA_table.csv
run_itsa_models_drugs:
run: stata-mp:latest analysis/201_itsa_models_drugs.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/itsa_models_drugs.log
figure1: output/figures/ITSA_csDMARD_delay_newey.svg
figure2: output/figures/ITSA_csDMARD_delay_prais.svg
figure3: output/figures/ITSA_csDMARD_delay_newey_sensitivity.svg
figure4: output/figures/ITSA_csDMARD_delay_prais_sensitivity.svg
doc1: output/tables/appt_to_csdmard_ITSA_table.csv
run_box_plots:
run: stata-mp:latest analysis/300_box_plots.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/box_plots.log
figure 1: output/figures/regional_qs1_bar_overall.svg
figure 2: output/figures/regional_qs1_bar_2019.svg
figure 3: output/figures/regional_qs1_bar_2020.svg
figure 4: output/figures/regional_qs2_bar_overall.svg
figure 5: output/figures/regional_qs2_bar_2019.svg
figure 6: output/figures/regional_qs2_bar_2020.svg
figure 7: output/figures/regional_qs2_bar_GP_overall.svg
figure 8: output/figures/regional_qs2_bar_GP_2019.svg
figure 9: output/figures/regional_qs2_bar_GP_2020.svg
figure 10: output/figures/regional_qs2_bar_GP_merged.svg
figure 11: output/figures/regional_qs2_bar_GP_ethnicity.svg
figure 12: output/figures/regional_qs2_bar_GP_imd.svg
figure 13: output/figures/regional_csdmard_bar_overall.svg
figure 14: output/figures/regional_csdmard_bar_2019.svg
figure 15: output/figures/regional_csdmard_bar_2020.svg
figure 16: output/figures/regional_csdmard_bar_merged.svg
figure 17: output/figures/regional_csdmard_bar_ethnicity.svg
figure 18: output/figures/regional_csdmard_bar_imd.svg
figure 19: output/figures/regional_qs2_bar_GP_compare.svg
run_redacted_tables:
run: stata-mp:latest analysis/400_redacted_tables.do
needs: [create_cohorts]
outputs:
moderately_sensitive:
log1: logs/redacted_tables.log
doc1: output/tables/table_1_rounded_bydiag.csv
doc2: output/tables/table_mean_bydiag_rounded.csv
doc3: output/tables/table_median_bydiag_rounded.csv
doc4: output/tables/table_median_bydiag_rounded_to21.csv
doc5: output/tables/ITSA_tables_appt_delay_rounded.csv
doc6: output/tables/ITSA_tables_csdmard_delay_rounded.csv
doc7: output/tables/drug_byyearanddisease_rounded.csv
doc8: output/tables/first_csdmard_rounded.csv
doc9: output/tables/drug_byyearandregion_rounded.csv
doc10: output/tables/referral_byregion_rounded.csv
run_redacted_tables_allpts:
run: stata-mp:latest analysis/401_redacted_tables_allpts.do
needs: [create_cohorts_allpts]
outputs:
moderately_sensitive:
log1: logs/redacted_tables_allpts.log
doc1: output/tables/table_1_rounded_allpts.csv