Update phplots_2020.do

opensafely · Jun 19, 2024 · 199f348 · 199f348
1 parent d05802b
commit 199f348
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/analysis/phplots_2020.do b/analysis/phplots_2020.do
@@ -73,17 +73,19 @@ gen follow_up_esrd = follow_up_time_esrd
 recode follow_up_esrd	min/89=1 	///
 						90/max=2
 stset exit_date_esrd, fail(esrd_date) origin(index_date_esrd) id(unique) scale(365.25)
-stcox i.case i.ethnicity i.ckd_stage i.aki_baseline i.diabetes i.bmi i.smoking i.admissions i.covid_vax, vce(cluster practice_id) strata(set_id)
+drop age1 age2 age3
+mkspline age = age if _st==1&sex!=.&ethnicity!=.&imd!=.&urban!=.&region!=.&bmi!=.&smoking!=., cubic nknots(4)
+stcox i.case age1 age2 age3 i.sex i.stp i.ethnicity i.ckd_stage i.aki_baseline i.diabetes i.bmi i.smoking i.admissions i.covid_vax, vce(cluster practice_id)
 estat phtest, d
-stcox i.case##i.follow_up_esrd i.ethnicity i.ckd_stage i.aki_baseline i.diabetes i.bmi i.smoking i.admissions i.covid_vax, vce(cluster practice_id) strata(set_id)
+stcox i.case##i.follow_up_esrd age1 age2 age3 i.sex i.stp i.ethnicity i.ckd_stage i.aki_baseline i.diabetes i.bmi i.smoking i.admissions i.covid_vax, vce(cluster practice_id)
 lincom 1.case, eform
 lincom 1.case + 1.case#2.follow_up_esrd, eform
 estat phtest, d
 drop if ckd_stage==5
 replace ckd_stage=5 if ckd_stage==6
 label define ckd_stage2 1 "No CKD" 2 "CKD 3A" 3 "CKD 3B" 4 "CKD 4" 5 "No baseline eGFR measurement"
 label values ckd_stage ckd_stage2
-stcox i.case##i.follow_up_esrd i.ethnicity i.ckd_stage##i.follow_up_esrd i.aki_baseline##i.follow_up_esrd i.diabetes##i.follow_up_esrd i.imd i.urban i.bmi i.smoking i.cardiovascular i.hypertension i.immunosuppressed i.non_haem_cancer i.gp_consults i.admissions i.covid_vax, vce(cluster practice_id) strata(set_id)
+stcox i.case##i.follow_up_esrd age1 age2 age3 i.sex i.stp i.ethnicity i.ckd_stage##i.follow_up_esrd i.aki_baseline##i.follow_up_esrd i.diabetes##i.follow_up_esrd i.imd i.urban i.bmi i.smoking i.cardiovascular i.hypertension i.immunosuppressed i.non_haem_cancer i.gp_consults i.admissions i.covid_vax, vce(cluster practice_id)
 lincom 1.case, eform
 lincom 1.case + 1.case#2.follow_up_esrd, eform
 estat phtest, d