generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
project.yaml
780 lines (652 loc) · 27.7 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
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
version: '3.0'
expectations:
population_size: 20000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create_project_actions.R
## Edit and run create_project_actions.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
##
## Part 1. Generate Study Population
##
## Generate dummy data for all eligible population
generate_study_population_all:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_all.feather
## Generate dummy data for study population - vaccinated
generate_study_population_vaccinated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_vaccinated.feather
## Generate dummy data for study population - infected
generate_study_population_infected:
run: cohortextractor:latest generate_cohort --study-definition study_definition_infected
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_infected.feather
## Part 2. Create Analysis Data Sets
## Data Cleaning
## Stage 0 Data Cleaning - all
stage0_data_cleaning_all:
run: r:latest analysis/stage0_data_cleaning.R all
needs:
- generate_study_population_all
outputs:
highly_sensitive:
cohort: output/input_stage0_all.rds
moderately_sensitive:
variable_check_table: output/not_for_review/descriptives/table_0_all.csv
histogram_numerical_variable: output/not_for_review/descriptives/histogram_*_all.svg
table_gp: output/not_for_review/descriptives/table_gp_*_all*
## Stage 0 Data Cleaning - vaccinated
stage0_data_cleaning_vaccinated:
run: r:latest analysis/stage0_data_cleaning.R vaccinated
needs:
- generate_study_population_vaccinated
outputs:
highly_sensitive:
cohort: output/input_stage0_vaccinated.rds
moderately_sensitive:
variable_check_table: output/not_for_review/descriptives/table_0_vaccinated.csv
histogram_numerical_variable: output/not_for_review/descriptives/histogram_*_vaccinated.svg
table_gp: output/not_for_review/descriptives/table_gp_*_vaccinated*
## Stage 0 Data Cleaning - infected
stage0_data_cleaning_infected:
run: r:latest analysis/stage0_data_cleaning.R infected
needs:
- generate_study_population_infected
outputs:
highly_sensitive:
cohort: output/input_stage0_infected.rds
moderately_sensitive:
variable_check_table: output/not_for_review/descriptives/table_0_infected.csv
histogram_numerical_variable: output/not_for_review/descriptives/histogram_*_infected.svg
table_gp: output/not_for_review/descriptives/table_gp_*_infected*
## Define eligible population
## Stage 1 define eligible population - all
stage1_define_eligible_population_all:
run: r:latest analysis/stage1_define_eligible_population.R all
needs:
- stage0_data_cleaning_all
outputs:
highly_sensitive:
cohort: output/input_stage1_all.rds
moderately_sensitive:
table_flow_chart: output/not_for_review/descriptives/flow_chart_all*
table_gp_interactions: output/not_for_review/descriptives/table_quantile_gp*_all*
## Stage 1 define eligible population - vaccinated
stage1_define_eligible_population_vaccinated:
run: r:latest analysis/stage1_define_eligible_population.R vaccinated
needs:
- stage0_data_cleaning_vaccinated
outputs:
highly_sensitive:
cohort: output/input_stage1_vaccinated.rds
moderately_sensitive:
table_flow_chart: output/not_for_review/descriptives/flow_chart_vaccinated*
table_gp_interactions: output/not_for_review/descriptives/table_quantile_gp*_vaccinated*
## Stage 1 define eligible population - infected
stage1_define_eligible_population_infected:
run: r:latest analysis/stage1_define_eligible_population.R infected
needs:
- stage0_data_cleaning_infected
outputs:
highly_sensitive:
cohort: output/input_stage1_infected.rds
moderately_sensitive:
table_flow_chart: output/not_for_review/descriptives/flow_chart_infected*
table_gp_interactions: output/not_for_review/descriptives/table_quantile_gp*_infected*
## Part 3. Figures and tables
## Table 1. Patient Characteristics - all
table_1_all:
run: r:latest analysis/table_1.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
descriptive_table: output/review/descriptives/table_1_all.csv
## Table 1. Patient Characteristics - vaccinated
table_1_vaccinated:
run: r:latest analysis/table_1.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
descriptive_table: output/review/descriptives/table_1_vaccinated.csv
## Table 1. Patient Characteristics - infected
table_1_infected:
run: r:latest analysis/table_1.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
descriptive_table: output/review/descriptives/table_1_infected.csv
## Table_1_combined - all table 1 combined
table_1_combined:
run: r:latest analysis/table_1_combined.R
needs:
- table_1_all
- table_1_vaccinated
- table_1_infected
outputs:
moderately_sensitive:
table: output/review/descriptives/table_1_combined*
## Table 2 event count
## Table 2. Event count - all
table_2_all:
run: r:latest analysis/table_2.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
event_count_table: output/review/descriptives/table_2_all*
## Table 2. Event count - all_vax_c
table_2_all_vax_c:
run: r:latest analysis/table_2.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
event_count_table: output/review/descriptives/table_2_all_vax_c*
## Table 2. Event count - vaccinated
table_2_vaccinated:
run: r:latest analysis/table_2.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
event_count_table: output/review/descriptives/table_2_vaccinated*
## Table 2. Event count - infected
table_2_infected:
run: r:latest analysis/table_2.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
event_count_table: output/review/descriptives/table_2_infected*
## Table_2_combined - all table 2 combined
table_2_combined:
run: r:latest analysis/table_2_combined.R
needs:
- table_2_all
- table_2_all_vax_c
- table_2_vaccinated
- table_2_infected
outputs:
moderately_sensitive:
table: output/review/descriptives/table_2_combined*
## Table - sequence count
## Table. Sequence count - all
table_sequence_all:
run: r:latest analysis/table_sequence.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
sequence_count_table: output/review/descriptives/table_sequence_all*
## Table. Sequence count - vaccinated
table_sequence_vaccinated:
run: r:latest analysis/table_sequence.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
sequence_count_table: output/review/descriptives/table_sequence_vaccinated*
## Table. Sequence count - infected
table_sequence_infected:
run: r:latest analysis/table_sequence.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
sequence_count_table: output/review/descriptives/table_sequence_infected*
## Table sequence combined - all tables for sequence count combined
table_sequence_combined:
run: r:latest analysis/table_sequence_combined.R
needs:
- table_sequence_all
- table_sequence_vaccinated
- table_sequence_infected
outputs:
moderately_sensitive:
table: output/review/descriptives/table_sequence_combined*
## Figure - long covid count
figure_long_covid_count_all:
run: r:latest analysis/figure_long_covid_count.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
long_covid_count_all: output/review/descriptives/long_covid_count_*_all*
## Figure_hist - Histogram of days from covid to long covid
figure_hist_all:
run: r:latest analysis/figure_hist.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
days_covid_to_long: output/review/descriptives/days_c_to_long*
table_bin_count: output/review/descriptives/supporting_doc_hist_*
## Figure - Kaplan Meier plot
figure_km_all:
run: r:latest analysis/figure_kaplan_meier.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
plot_km: output/review/descriptives/figure_kaplan_meier_*
data_km: output/review/descriptives/supporting_doc_km_*
## Table - frequencies of snomed code for long covid diagnosis
table_snomed_codes_all:
run: r:latest analysis/table_snomed_code.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
snomed_code: output/not_for_review/descriptives/snomed_code*
## Summarise survival data
summarise_survival_data_all:
run: r:latest analysis/stage2_summarise_survival_data.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
summary_survival_data: output/review/descriptives/summarise_survival_data*
## Part 4. Modelling
## Development Cox model
## post-viral fatigue
development_cox_model_fatigue:
run: r:latest analysis/stage3_fatigue_survival_analysis.R
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
summary_survival_data: output/review/model/analysis_data_summary_fatigue*
cox_model_output: output/review/model/HR_fatigue*
## Development Cox Model - all
development_cox_model_all:
run: r:latest analysis/stage3_model_development.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
supporting_document: output/review/model/analysis_data_summary_all*
hazard_ratios: output/review/model/HR_*_all*
selected_variables: output/not_for_review/model/selected_variables_all.csv
model_selection: output/not_for_review/model/model_selection_all.csv
AIC: output/review/model/AIC_all.csv
fit_cox_model: output/not_for_review/model/fit_cox_model_*_all*
## Development Cox Model - all_vax_c
development_cox_model_all_vax_c:
run: r:latest analysis/stage3_model_development.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
supporting_document: output/review/model/analysis_data_summary_all_vax_c*
hazard_ratios: output/review/model/HR_*_all_vax_c*
selected_variables: output/not_for_review/model/selected_variables_all_vax_c.csv
model_selection: output/not_for_review/model/model_selection_all_vax_c.csv
AIC: output/review/model/AIC_all_vax_c.csv
fit_cox_model: output/not_for_review/model/fit_cox_model_*_all_vax_c*
## Development Cox Model - vaccinated
development_cox_model_vaccinated:
run: r:latest analysis/stage3_model_development.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
supporting_document: output/review/model/analysis_data_summary_vaccinated*
hazard_ratios: output/review/model/HR_*_vaccinated*
selected_variables: output/not_for_review/model/selected_variables_vaccinated.csv
model_selection: output/not_for_review/model/model_selection_vaccinated.csv
AIC: output/review/model/AIC_vaccinated.csv
fit_cox_model: output/not_for_review/model/fit_cox_model_*_vaccinated*
## Development Cox Model - all_vax_td
development_cox_model_all_vax_td:
run: r:latest analysis/stage3_model_development.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
supporting_document: output/review/model/analysis_data_summary_all_vax_td*
hazard_ratios: output/review/model/HR_*_all_vax_td*
selected_variables: output/not_for_review/model/selected_variables_all_vax_td.csv
model_selection: output/not_for_review/model/model_selection_all_vax_td.csv
AIC: output/review/model/AIC_all_vax_td.csv
fit_cox_model: output/not_for_review/model/fit_cox_model_*_all_vax_td*
## Development Cox Model - infected
development_cox_model_infected:
run: r:latest analysis/stage3_model_development.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
supporting_document: output/review/model/analysis_data_summary_infected*
hazard_ratios: output/review/model/HR_*_infected*
selected_variables: output/not_for_review/model/selected_variables_infected.csv
model_selection: output/not_for_review/model/model_selection_infected.csv
AIC: output/review/model/AIC_infected.csv
fit_cox_model: output/not_for_review/model/fit_cox_model_*_infected*
## Development Cox Model - all
development_model_age_sex_all:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
age_sex_model: output/not_for_review/model/fit_cox_model_age_sex_model_*_all*
full_model: output/not_for_review/model/fit_cox_model_full_model_*_all*
hazard_ratios: output/review/model/HR_age_sex_*_all*
hazard_ratios_full_model: output/review/model/HR_full_model_*_all*
performance_measure: output/review/model/PM_age_sex_*_all*
performance_measure_full_model: output/review/model/PM_full_model_*_all*
survival_plot: output/not_for_review/model/survival_plot_*_age_sex_*_all.svg
## Development Cox Model - all_vax_c
development_model_age_sex_all_vax_c:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
age_sex_model: output/not_for_review/model/fit_cox_model_age_sex_model_*_all_vax_c*
full_model: output/not_for_review/model/fit_cox_model_full_model_*_all_vax_c*
hazard_ratios: output/review/model/HR_age_sex_*_all_vax_c*
hazard_ratios_full_model: output/review/model/HR_full_model_*_all_vax_c*
performance_measure: output/review/model/PM_age_sex_*_all_vax_c*
performance_measure_full_model: output/review/model/PM_full_model_*_all_vax_c*
survival_plot: output/not_for_review/model/survival_plot_*_age_sex_*_all_vax_c.svg
## Development Cox Model - vaccinated
development_model_age_sex_vaccinated:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
age_sex_model: output/not_for_review/model/fit_cox_model_age_sex_model_*_vaccinated*
full_model: output/not_for_review/model/fit_cox_model_full_model_*_vaccinated*
hazard_ratios: output/review/model/HR_age_sex_*_vaccinated*
hazard_ratios_full_model: output/review/model/HR_full_model_*_vaccinated*
performance_measure: output/review/model/PM_age_sex_*_vaccinated*
performance_measure_full_model: output/review/model/PM_full_model_*_vaccinated*
survival_plot: output/not_for_review/model/survival_plot_*_age_sex_*_vaccinated.svg
## Development Cox Model - all_vax_td
development_model_age_sex_all_vax_td:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
age_sex_model: output/not_for_review/model/fit_cox_model_age_sex_model_*_all_vax_td*
full_model: output/not_for_review/model/fit_cox_model_full_model_*_all_vax_td*
hazard_ratios: output/review/model/HR_age_sex_*_all_vax_td*
hazard_ratios_full_model: output/review/model/HR_full_model_*_all_vax_td*
performance_measure: output/review/model/PM_age_sex_*_all_vax_td*
performance_measure_full_model: output/review/model/PM_full_model_*_all_vax_td*
survival_plot: output/not_for_review/model/survival_plot_*_age_sex_*_all_vax_td.svg
## Development Cox Model - infected
development_model_age_sex_infected:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
age_sex_model: output/not_for_review/model/fit_cox_model_age_sex_model_*_infected*
full_model: output/not_for_review/model/fit_cox_model_full_model_*_infected*
hazard_ratios: output/review/model/HR_age_sex_*_infected*
hazard_ratios_full_model: output/review/model/HR_full_model_*_infected*
performance_measure: output/review/model/PM_age_sex_*_infected*
performance_measure_full_model: output/review/model/PM_full_model_*_infected*
survival_plot: output/not_for_review/model/survival_plot_*_age_sex_*_infected.svg
## Development Cox Model - all
development_model_age_sex_adjusted_all:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_adjusted*_all*
hazard_ratios: output/review/model/HR_age_sex_adjusted_all*
performance_measure: output/review/model/PM_age_sex_adjusted_all*
## Development Cox Model - all_vax_c
development_model_age_sex_adjusted_all_vax_c:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_adjusted*_all_vax_c*
hazard_ratios: output/review/model/HR_age_sex_adjusted_all_vax_c*
performance_measure: output/review/model/PM_age_sex_adjusted_all_vax_c*
## Development Cox Model - vaccinated
development_model_age_sex_adjusted_vaccinated:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_adjusted*_vaccinated*
hazard_ratios: output/review/model/HR_age_sex_adjusted_vaccinated*
performance_measure: output/review/model/PM_age_sex_adjusted_vaccinated*
## Development Cox Model - all_vax_td
development_model_age_sex_adjusted_all_vax_td:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_adjusted*_all_vax_td*
hazard_ratios: output/review/model/HR_age_sex_adjusted_all_vax_td*
performance_measure: output/review/model/PM_age_sex_adjusted_all_vax_td*
## Development Cox Model - infected
development_model_age_sex_adjusted_infected:
run: r:latest analysis/stage3_4_model_dev_eval_age_sex_adjusted.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
fit_cox_model: output/not_for_review/model/fit_cox_model_age_sex_adjusted*_infected*
hazard_ratios: output/review/model/HR_age_sex_adjusted_infected*
performance_measure: output/review/model/PM_age_sex_adjusted_infected*
## Subset variables
identify_subset_variables:
run: r:latest analysis/stage3_identify_subset_variables.R
needs:
- development_cox_model_all
- development_cox_model_all_vax_c
- development_cox_model_all_vax_td
- development_cox_model_vaccinated
- development_cox_model_infected
outputs:
moderately_sensitive:
subset_variables: output/review/model/selected_vars.csv
## Development Cox Model using a subset of variables - all
model_subset_variables_all:
run: r:latest analysis/stage3_model_subset_variables.R all
needs:
- identify_subset_variables
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
hazard_ratios: output/review/model/HR_subset*_all*
performance_measure: output/review/model/PM_subset*_all*
## Development Cox Model using a subset of variables - all_vax_c
model_subset_variables_all_vax_c:
run: r:latest analysis/stage3_model_subset_variables.R all_vax_c
needs:
- identify_subset_variables
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
hazard_ratios: output/review/model/HR_subset*_all_vax_c*
performance_measure: output/review/model/PM_subset*_all_vax_c*
## Development Cox Model using a subset of variables - vaccinated
model_subset_variables_vaccinated:
run: r:latest analysis/stage3_model_subset_variables.R vaccinated
needs:
- identify_subset_variables
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
hazard_ratios: output/review/model/HR_subset*_vaccinated*
performance_measure: output/review/model/PM_subset*_vaccinated*
## Development Cox Model using a subset of variables - all_vax_td
model_subset_variables_all_vax_td:
run: r:latest analysis/stage3_model_subset_variables.R all_vax_td
needs:
- identify_subset_variables
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
hazard_ratios: output/review/model/HR_subset*_all_vax_td*
performance_measure: output/review/model/PM_subset*_all_vax_td*
## Development Cox Model using a subset of variables - infected
model_subset_variables_infected:
run: r:latest analysis/stage3_model_subset_variables.R infected
needs:
- identify_subset_variables
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
hazard_ratios: output/review/model/HR_subset*_infected*
performance_measure: output/review/model/PM_subset*_infected*
## Figure - log hazard ratio against continuous age
## Figure. Log hazard ratio against age - all
figure_loghr_age_all:
run: r:latest analysis/figure_log_hr_vs_age.R all
needs:
- development_cox_model_all
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
figure_loghr_age: output/review/model/figure_loghr_age_all*
## Figure. Log hazard ratio against age - all_vax_c
figure_loghr_age_all_vax_c:
run: r:latest analysis/figure_log_hr_vs_age.R all_vax_c
needs:
- development_cox_model_all_vax_c
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
figure_loghr_age: output/review/model/figure_loghr_age_all_vax_c*
## Figure. Log hazard ratio against age - vaccinated
figure_loghr_age_vaccinated:
run: r:latest analysis/figure_log_hr_vs_age.R vaccinated
needs:
- development_cox_model_vaccinated
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
figure_loghr_age: output/review/model/figure_loghr_age_vaccinated*
## Figure. Log hazard ratio against age - all_vax_td
figure_loghr_age_all_vax_td:
run: r:latest analysis/figure_log_hr_vs_age.R all_vax_td
needs:
- development_cox_model_all_vax_td
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
figure_loghr_age: output/review/model/figure_loghr_age_all_vax_td*
## Figure. Log hazard ratio against age - infected
figure_loghr_age_infected:
run: r:latest analysis/figure_log_hr_vs_age.R infected
needs:
- development_cox_model_infected
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
figure_loghr_age: output/review/model/figure_loghr_age_infected*
## Figure - hazard ratio against continuous age
## Figure. Hazard ratio against age - all
figure_hr_age_all:
run: r:latest analysis/figure_hr_vs_age.R all
needs:
- development_cox_model_all
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
plot_hr_age: output/review/model/plot_HR_vs_age_all*
## Figure. Hazard ratio against age - all_vax_c
figure_hr_age_all_vax_c:
run: r:latest analysis/figure_hr_vs_age.R all_vax_c
needs:
- development_cox_model_all_vax_c
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
plot_hr_age: output/review/model/plot_HR_vs_age_all_vax_c*
## Figure. Hazard ratio against age - vaccinated
figure_hr_age_vaccinated:
run: r:latest analysis/figure_hr_vs_age.R vaccinated
needs:
- development_cox_model_vaccinated
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
plot_hr_age: output/review/model/plot_HR_vs_age_vaccinated*
## Figure. Hazard ratio against age - all_vax_td
figure_hr_age_all_vax_td:
run: r:latest analysis/figure_hr_vs_age.R all_vax_td
needs:
- development_cox_model_all_vax_td
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
plot_hr_age: output/review/model/plot_HR_vs_age_all_vax_td*
## Figure. Hazard ratio against age - infected
figure_hr_age_infected:
run: r:latest analysis/figure_hr_vs_age.R infected
needs:
- development_cox_model_infected
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
plot_hr_age: output/review/model/plot_HR_vs_age_infected*
## Evaluation Cox model
evaluation_cox_model_all:
run: r:latest analysis/stage4_model_evaluation.R all
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/PM_*_all.csv
survival_plot: output/not_for_review/model/survival_plot_*_all.svg
evaluation_cox_model_all_vax_c:
run: r:latest analysis/stage4_model_evaluation.R all_vax_c
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/PM_*_all_vax_c.csv
survival_plot: output/not_for_review/model/survival_plot_*_all_vax_c.svg
evaluation_cox_model_vaccinated:
run: r:latest analysis/stage4_model_evaluation.R vaccinated
needs:
- stage1_define_eligible_population_vaccinated
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/PM_*_vaccinated.csv
survival_plot: output/not_for_review/model/survival_plot_*_vaccinated.svg
evaluation_cox_model_all_vax_td:
run: r:latest analysis/stage4_model_evaluation.R all_vax_td
needs:
- stage1_define_eligible_population_all
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/PM_*_all_vax_td.csv
survival_plot: output/not_for_review/model/survival_plot_*_all_vax_td.svg
evaluation_cox_model_infected:
run: r:latest analysis/stage4_model_evaluation.R infected
needs:
- stage1_define_eligible_population_infected
outputs:
moderately_sensitive:
performance_measure_CSV: output/review/model/PM_*_infected.csv
survival_plot: output/not_for_review/model/survival_plot_*_infected.svg