updated

01 Hazard ratios.R

@@ -59,7 +59,7 @@ cohort <- add_surv_vars(cohort, main_only=TRUE)
 
 cohort <- cohort %>%
 
-  select(patid, malesex, ethnicity_5cat_decoded, imd2015_10, regstartdate, gp_record_end, death_date, drugclass, studydrug, dstartdate, dstopdate, drugline_all, drugsubstances, ncurrtx, DPP4, GLP1, MFN, SGLT2, SU, TZD, INS, dstartdate_age, dstartdate_dm_dur_all, preweight, prehba1c, prebmi, prehdl, preldl, pretriglyceride, pretotalcholesterol, prealt, presbp, preegfr, preckdstage, contains("cens"), qrisk2_5yr_score, last_sglt2_stop)
+  select(patid, malesex, ethnicity_5cat_decoded, imd2015_10, regstartdate, gp_record_end, death_date, drugclass, studydrug, dstartdate, dstopdate, drugline_all, drugsubstances, ncurrtx, DPP4, GLP1, MFN, SGLT2, SU, TZD, INS, dstartdate_age, dstartdate_dm_dur_all, preweight, prehba1c, prebmi, prehdl, preldl, pretriglyceride, pretotalcholesterol, prealt, presbp, preegfr, preckdstage, contains("cens"), starts_with("ckdpc"), qrisk2_5yr_score, last_sglt2_stop)
 
 rm(list=setdiff(ls(), "cohort"))
 
@@ -182,3 +182,105 @@ all_hrs <- rbind(all_hrs, outcome_hr)
 
 
 flextable(all_hrs)
+
+
+
+# Test CKD with CKD risk scores
+
+## CKD 345
+
+ckd60_cohort <- cohort %>% filter(!is.na(ckdpc_egfr60_risk_confirmed_score))
+
+count <- ckd60_cohort %>%
+  group_by(studydrug) %>%
+  summarise(count=n()) %>%
+  pivot_wider(names_from=studydrug,
+              names_glue="{studydrug}_count",
+              values_from=count)
+
+followup <- ckd60_cohort %>%
+  group_by(studydrug) %>%
+  summarise(time=round(median(ckd_345_censtime_yrs), 2)) %>%
+  pivot_wider(names_from=studydrug,
+              names_glue="{studydrug}_followup",
+              values_from=time)
+
+events <- ckd60_cohort %>%
+  group_by(studydrug) %>%
+  summarise(event_count=sum(ckd_345_censvar),
+            drug_count=n()) %>%
+  mutate(events_perc=round(event_count*100/drug_count, 1),
+         events=paste0(event_count, " (", events_perc, "%)")) %>%
+  select(studydrug, events) %>%
+  pivot_wider(names_from=studydrug,
+              names_glue="{studydrug}_events",
+              values_from=events)
+
+unadjusted <- coxph(Surv(ckd_345_censtime_yrs, ckd_345_censvar) ~  studydrug, ckd60_cohort) %>%
+  tidy(conf.int=TRUE, exponentiate=TRUE) %>%
+  filter(term=="studydrugSGLT2") %>%
+  mutate(unadjusted_HR=paste0(round(estimate, 2), " (", round(conf.low, 2), ", ", round(conf.high, 2), ")")) %>%
+  select(unadjusted_HR)
+
+adjusted <- coxph(Surv(ckd_345_censtime_yrs, ckd_345_censvar) ~  studydrug + dstartdate_age + malesex + dstartdate_dm_dur_all + imd2015_10 + ckdpc_egfr60_risk_confirmed_score + drugline_all + ncurrtx, ckd60_cohort) %>%
+  tidy(conf.int=TRUE, exponentiate=TRUE) %>%
+  filter(term=="studydrugSGLT2") %>%
+  mutate(adjusted_HR=paste0(round(estimate, 2), " (", round(conf.low, 2), ", ", round(conf.high, 2), ")")) %>%
+  select(adjusted_HR)
+
+
+outcome_hr <- cbind(count, followup, events, unadjusted, adjusted)
+
+flextable(outcome_hr)
+
+
+## 40% decline in eGFR
+
+ckd40_cohort <- cohort %>% filter(!is.na(ckdpc_40egfr_risk_score))
+
+count <- ckd40_cohort %>%
+  group_by(studydrug) %>%
+  summarise(count=n()) %>%
+  pivot_wider(names_from=studydrug,
+              names_glue="{studydrug}_count",
+              values_from=count)
+
+followup <- ckd40_cohort %>%
+  group_by(studydrug) %>%
+  summarise(time=round(median(ckd_egfr40_censtime_yrs), 2)) %>%
+  pivot_wider(names_from=studydrug,
+              names_glue="{studydrug}_followup",
+              values_from=time)
+
+events <- ckd40_cohort %>%
+  group_by(studydrug) %>%
+  summarise(event_count=sum(ckd_egfr40_censvar),
+            drug_count=n()) %>%
+  mutate(events_perc=round(event_count*100/drug_count, 1),
+         events=paste0(event_count, " (", events_perc, "%)")) %>%
+  select(studydrug, events) %>%
+  pivot_wider(names_from=studydrug,
+              names_glue="{studydrug}_events",
+              values_from=events)
+
+unadjusted <- coxph(Surv(ckd_egfr40_censtime_yrs, ckd_egfr40_censvar) ~  studydrug, ckd60_cohort) %>%
+  tidy(conf.int=TRUE, exponentiate=TRUE) %>%
+  filter(term=="studydrugSGLT2") %>%
+  mutate(unadjusted_HR=paste0(round(estimate, 2), " (", round(conf.low, 2), ", ", round(conf.high, 2), ")")) %>%
+  select(unadjusted_HR)
+
+adjusted <- coxph(Surv(ckd_egfr40_censtime_yrs, ckd_egfr40_censvar) ~  studydrug + dstartdate_age + malesex + dstartdate_dm_dur_all + imd2015_10 + ckdpc_40egfr_risk_score + drugline_all + ncurrtx, ckd60_cohort) %>%
+  tidy(conf.int=TRUE, exponentiate=TRUE) %>%
+  filter(term=="studydrugSGLT2") %>%
+  mutate(adjusted_HR=paste0(round(estimate, 2), " (", round(conf.low, 2), ", ", round(conf.high, 2), ")")) %>%
+  select(adjusted_HR)
+
+
+outcome_hr <- cbind(count, followup, events, unadjusted, adjusted)
+
+flextable(outcome_hr)
+
+
+
+
+