generated from opensafely/research-template
/
an_cox_models.do
590 lines (407 loc) · 18.4 KB
/
an_cox_models.do
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
********************************************************************************
*
* Do-file: an_cox_models.do
*
* Project: SGTF CFR
*
* Programmed by: Daniel Grint
*
* Data used: output/cr_analysis_new.dta
*
* Data created:
*
* Other output: an_cox_models.log containing:
* 1-Unadjusted Cox models for SGTF
* 2-Adjusted Cox models for SGTF
*
********************************************************************************
*
* Purpose: This do-file runs Cox PH models, calculating HR for VOC
* vs. non-VOC
*
********************************************************************************
* Open a log file
cap log close
log using ./logs/an_cox_models, replace t
clear
use ./output/cr_analysis_new.dta
* DROP MISSING UTLA
noi di "DROPPING MISSING UTLA DATA"
drop if utla_group==""
* DROP IF NO DATA ON SGTF
noi di "DROPPING NO SGTF DATA"
drop if has_sgtf==0
noi di "SUBSETTING ON COX CENSORED POPULATION"
keep if cox_pop==1
tab sgtf cox_death, row
*Set up output file
cap file close tablecontent
file open tablecontent using ./output/table2_hr.txt, write text replace
file write tablecontent ("Table 2: Hazard ratios for VOC vs. non-VOC") _n _n
file write tablecontent ("Estimate") _tab ///
("HR (95% CI)") _tab ///
("P-value") _n
*******************
/* Unadjusted HR */
*******************
stset stime_death, origin(study_start) fail(cox_death) scale(1) id(patient_id)
stcox i.sgtf
* Stratified by STP
stcox i.sgtf, strata(stp)
* Stratified by region
stcox i.sgtf, strata(region)
* Stratified by UTLA
stcox i.sgtf, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
* Output unadjusted
lincom 1.sgtf, eform
file write tablecontent _n ("Unadjusted") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Interaction with time
stcox i.sgtf, tvc(i.sgtf) strata(utla_group)
* Interaction with time excluding November
stcox i.sgtf if study_start >= date("01dec2020", "DMY"), strata(utla_group)
estat phtest, d
stcox i.sgtf if study_start >= date("01dec2020", "DMY"), tvc(i.sgtf) strata(utla_group)
************************
/* Age as spline only */
************************
* Stratified by region
stcox i.sgtf age1 age2 age3 ///
, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Age adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Age grouped only
stcox i.sgtf ib2.agegroupA ///
, strata(utla_group)
***************************
/* Age and comorbidities */
***************************
* Stratified by region
stcox i.sgtf age1 age2 age3 ib0.comorb_cat ib1.smoke_nomiss2 ib1.obese4cat ///
, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Age + comorb adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
*********************************************************************
/* Demographically adjusted HR - age as spline, cat hh size */
/* Not adjusting for comorbidities, obesity, or smoking status */
*********************************************************************
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.hh_total_cat i.home_bin ///
ib1.rural_urban5 ib1.start_week age1 age2 age3 ///
if eth2 != 6 ///
, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Demographically adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
*********************************************************************
/* Demographically adjusted HR - age grouped, cat hh size */
/* Not adjusting for comorbidities, obesity, or smoking status */
*********************************************************************
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.hh_total_cat i.home_bin ///
ib1.rural_urban5 ib1.start_week ib2.agegroupA ///
if eth2 != 6 ///
, strata(utla_group)
****************************************************
/* Fully adjusted HR - age as spline, cat hh size */
****************************************************
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_no_int
* N (events)
bysort start_weekA: tab sgtf cox_death if e(sample)
bysort comorb_cat: tab sgtf cox_death if e(sample)
bysort eth2: tab sgtf cox_death if e(sample)
bysort imd: tab sgtf cox_death if e(sample)
bysort agegroupA: tab sgtf cox_death if e(sample)
estat phtest, d
lincom 1.sgtf, eform
file write tablecontent ("Fully adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Plot scaled schoenfeld residuals
estat phtest, plot(1.sgtf)
graph export ./output/cox_shoen.svg, as(svg) replace
* KM plot
sts graph, surv by(sgtf) ci risktable(, order(1 "non-VOC" 2 "VOC") size(small)) ///
ylabel(0.994(0.001)1, format(%5.3f)) ///
legend(order(2 4) label(2 "non-VOC") label(4 "VOC") rows(1))
graph export ./output/cox_km.svg, as(svg) replace
* Cumulative hazard plot
sts graph, cumhaz by(sgtf) ci ///
ylabel(minmax, format(%5.3f)) ///
legend(order(2 4) label(2 "non-VOC") label(4 "VOC") rows(1))
graph export ./output/cox_cumhaz.svg, as(svg) replace
* Smoothed hazard plot
sts graph, haz by(sgtf) ///
legend(label(1 "non-VOC") label(2 "VOC"))
graph export ./output/cox_haz.svg, as(svg) replace
/* Subgroup analyses */
* Epi week
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib2.start_weekA age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_week
stcox i.sgtf##ib2.start_weekA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_weekX
* Test for interaction
lrtest e_week e_weekX
file write tablecontent _n ("Subgroup analyses") _n
file write tablecontent _n ("Epi. week") _tab _tab %6.4f (r(p)) _n
* Epi week VOC vs. non-VOC HR
lincom 1.sgtf + 1.sgtf#2.start_weekA, eform // week 1/2
file write tablecontent ("16Nov-29Nov") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#3.start_weekA, eform // week 3
file write tablecontent ("30Nov-06Dec") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#4.start_weekA, eform // week 4
file write tablecontent ("07Dec-13Dec") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#5.start_weekA, eform // week 5
file write tablecontent ("14Dec-20Dec") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#6.start_weekA, eform // week 6
file write tablecontent ("21Dec-27Dec") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#7.start_weekA, eform // week 7
file write tablecontent ("28Dec-03Jan") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#8.start_weekA, eform // week 8
file write tablecontent ("04Jan-11Jan") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Comorbidities
stcox i.sgtf##ib0.comorb_cat i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_comorbX
* Test for interaction
lrtest e_no_int e_comorbX
file write tablecontent _n ("Comorbidities") _tab _tab %6.4f (r(p)) _n
* Comorbidities VOC vs. non-VOC HR
lincom 1.sgtf, eform // no comorbs
file write tablecontent ("None") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#1.comorb_cat, eform // 1 comorb
file write tablecontent ("1") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#2.comorb_cat, eform // 2+ comorbs
file write tablecontent ("2+") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Test for trend
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 c.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_linco
stcox i.sgtf##c.comorb_cat i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_lincoX
lrtest e_linco e_lincoX
local lin_lr_p = r(p)
lincom 1.sgtf#c.comorb_cat, eform
file write tablecontent ("Per unit increase") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (`lin_lr_p') _n
* Ethnicity
stcox i.sgtf##ib1.eth2 i.male ib1.imd ib0.comorb_cat ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_eth2X
* Test for interaction
lrtest e_no_int e_eth2X
file write tablecontent _n ("Ethnicity") _tab _tab %6.4f (r(p)) _n
* Ethnicity VOC vs. non-VOC HR
lincom 1.sgtf, eform // White
file write tablecontent ("White") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
*lincom 1.sgtf + 1.sgtf#2.eth5, eform // S Asian
*lincom 1.sgtf + 1.sgtf#3.eth5, eform // Black
*lincom 1.sgtf + 1.sgtf#4.eth5, eform // Mixed
lincom 1.sgtf + 1.sgtf#5.eth2, eform // Other
file write tablecontent ("Not white") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
*lincom 1.sgtf + 1.sgtf#6.eth2, eform // Missing
* IMD
stcox i.sgtf##ib1.imd i.male ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib1.start_week ib0.comorb_cat age1 age2 age3 i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_imdX
* Test for interaction
lrtest e_no_int e_imdX
file write tablecontent _n ("IMD") _tab _tab %6.4f (r(p)) _n
* IMD VOC vs. non-VOC HR
lincom 1.sgtf, eform // 1
file write tablecontent ("1 Least deprived") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#2.imd, eform // 2
file write tablecontent ("2") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#3.imd, eform // 3
file write tablecontent ("3") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#4.imd, eform // 4
file write tablecontent ("4") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#5.imd, eform // 5
file write tablecontent ("5 Most deprived") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Age group
stcox i.sgtf ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_age
stcox i.sgtf##ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_ageX
* Test for interaction
lrtest e_age e_ageX
file write tablecontent _n ("Age group") _tab _tab %6.4f (r(p)) _n
* Age group VOC vs. non-VOC HR
lincom 1.sgtf + 1.sgtf#1.agegroupA, eform // 0-<65
file write tablecontent ("0-<65") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#2.agegroupA, eform // 65-<75
file write tablecontent ("65-<75") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#3.agegroupA, eform // 75-<85
file write tablecontent ("75-<85") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
lincom 1.sgtf + 1.sgtf#4.agegroupA, eform // 85+
file write tablecontent ("85+") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Test for trend
stcox i.sgtf c.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_cage
stcox i.sgtf##c.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
est store e_cageX
lrtest e_cage e_cageX
local lin_age_p = r(p)
lincom 1.sgtf#c.agegroupA, eform
file write tablecontent ("Per group increase") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (`lin_age_p') _n
**************************
/* Sensitivity analyses */
**************************
* 28-days follow-up censor
stset stime_death28, origin(study_start) fail(cox_death28) scale(1) id(patient_id)
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 & risk_pop==1 ///
, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
file write tablecontent _n ("Sensitivity analyses") _n
lincom 1.sgtf, eform
file write tablecontent ("28-day follow-up censor") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
tab risk_pop risk_pop_40
stset stime_death, origin(study_start) fail(cox_death) scale(1) id(patient_id)
* Include with 40-days follow-up
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 & risk_pop_40==1 ///
, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Min. 40-days follow-up") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Excluding week 1
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib2.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 & start_week!=1 ///
, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Excluding week 1") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* No adjustment for care home
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib2.start_week age1 age2 age3 ///
if eth2 != 6 ///
, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("No care home adj.") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* NHS England coverage - exclude SE and NE
* Stratified by region
stcox i.sgtf i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ib1.hh_total_cat ///
ib1.rural_urban5 ib0.comorb_cat ib1.start_week age1 age2 age3 i.home_bin ///
if eth2 != 6 & !inlist(region,3,5) ///
, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
tab region if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Exluding NE/SE") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
**************************************************
/* Fully adjusted HR - age grouped, cat hh size */
**************************************************
* Stratified by region
stcox i.sgtf ib2.agegroupA i.male ib1.imd ib1.eth2 ib1.smoke_nomiss2 ib1.obese4cat ///
ib1.hh_total_cat ib1.rural_urban5 ib0.comorb_cat ib1.start_week i.home_bin ///
if eth2 != 6 ///
, strata(utla_group)
*********************************************************************
/* Causal min adjustment set - age as spline, comorbidities, */
/* deprivation index, and smoking status */
*********************************************************************
stcox i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 age1 age2 age3 i.home_bin
* Stratified by STP
stcox i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 age1 age2 age3 i.home_bin, strata(stp)
* Stratified by region
stcox i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss2 age1 age2 age3 i.home_bin, strata(utla_group)
* N (events)
tab sgtf cox_death if e(sample)
lincom 1.sgtf, eform
file write tablecontent ("Causal min. adjustment") _tab
file write tablecontent %4.2f (r(estimate)) (" (") %4.2f (r(lb)) ("-") %4.2f (r(ub)) (")") _tab %6.4f (r(p)) _n
* Interaction with time
stcox i.sgtf i.comorb_cat ib1.imd i.smoke_nomiss age1 age2 age3 ///
if eth2 != 6 ///
, strata(utla_group) tvc(i.sgtf)
* Close output table
file write tablecontent _n _n
file close tablecontent
log close
clear
insheet using ./output/table2_hr.txt, clear
export excel using ./output/table2_hr.xlsx, replace