Ethnicity mediators

analysis/cox_forest_2017_ethnicity_esrd_mediators.do

@@ -0,0 +1,80 @@
+clear
+sysdir set PLUS ./analysis/adofiles
+sysdir set PERSONAL ./analysis/adofiles
+pwd
+cap log close
+macro drop hr
+log using ./logs/cox_forest_2017_ethnicity_esrd_mediators.log, replace t
+cap file close tablecontent
+file open tablecontent using ./output/cox_forest_2017_ethnicity_esrd_mediators.csv, write text replace
+file write tablecontent _tab ("HR (95% CI)") _tab ("hr") _tab ("ll") _tab ("ul") _n
+
+use ./output/analysis_complete_2017.dta, clear
+
+qui stset exit_date_esrd, fail(esrd_date) origin(index_date_esrd) id(unique) scale(365.25)
+
+file write tablecontent ("Minimally-adjusted") _n
+forvalues i=1/5 {
+local label_`i': label ethnicity `i'
+}
+qui stcox i.case##i.ethnicity, strata(set_id)
+qui lincom 1.case, eform
+local int_1b = r(estimate)
+local int_1ll = r(lb)
+local int_1ul = r(ub)
+forvalues i=2/5 {
+qui lincom 1.case + 1.case#`i'.ethnicity, eform
+local int_`i'b = r(estimate)
+local int_`i'll = r(lb)
+local int_`i'ul = r(ub)
+}
+file write tablecontent ("`label_1'")
+file write tablecontent _tab %4.2f (`int_1b') (" (") %4.2f (`int_1ll') ("-") %4.2f (`int_1ul') (")") _tab %4.2f (`int_1b') _tab %4.2f (`int_1ll') _tab %4.2f (`int_1ul') _n
+forvalues i=2/5 {
+file write tablecontent ("`label_`i''")
+file write tablecontent _tab %4.2f (`int_`i'b') (" (") %4.2f (`int_`i'll') ("-") %4.2f (`int_`i'ul') (")") _tab %4.2f (`int_`i'b') _tab %4.2f (`int_`i'll') _tab %4.2f (`int_`i'ul') _n
+}
+
+local mediators "imd urban bmi smoking ckd_stage aki_baseline cardiovascular diabetes hypertension immunosuppressed non_haem_cancer gp_consults admissions"
+
+local imd_lab "IMD"
+local urban_lab "rural/urban"
+local bmi_lab "BMI"
+local smoking_lab "smoking"
+local ckd_stage_lab "CKD stage"
+local aki_baseline_lab "previous AKI"
+local cardiovascular_lab "cardiovascular diseases"
+local diabetes_lab "diabetes"
+local hypertension_lab "hypertension"
+local immunosuppressed_lab "immunosuppressed"
+local non_haem_cancer_lab "non-haematological cancer"
+local gp_consults_lab "GP consultations"
+local admissions_lab "previous hospital admissions"
+
+foreach med of local mediators {
+
+file write tablecontent ("After adjustment for ``med'_lab'") _n
+forvalues i=1/5 {
+local label_`i': label ethnicity `i'
+}
+
+qui stcox i.case##i.ethnicity i.`med', strata(set_id)
+qui lincom 1.case, eform
+local int_1b = r(estimate)
+local int_1ll = r(lb)
+local int_1ul = r(ub)
+forvalues i=2/5 {
+qui lincom 1.case + 1.case#`i'.ethnicity, eform
+local int_`i'b = r(estimate)
+local int_`i'll = r(lb)
+local int_`i'ul = r(ub)
+}
+file write tablecontent ("`label_1'")
+file write tablecontent _tab %4.2f (`int_1b') (" (") %4.2f (`int_1ll') ("-") %4.2f (`int_1ul') (")") _tab %4.2f (`int_1b') _tab %4.2f (`int_1ll') _tab %4.2f (`int_1ul') _n
+forvalues i=2/5 {
+file write tablecontent ("`label_`i''")
+file write tablecontent _tab %4.2f (`int_`i'b') (" (") %4.2f (`int_`i'll') ("-") %4.2f (`int_`i'ul') (")") _tab %4.2f (`int_`i'b') _tab %4.2f (`int_`i'll') _tab %4.2f (`int_`i'ul') _n
+}
+}
+
+file close tablecontent

analysis/cox_forest_2020_ethnicity_esrd_mediators.do

@@ -0,0 +1,81 @@
+clear
+sysdir set PLUS ./analysis/adofiles
+sysdir set PERSONAL ./analysis/adofiles
+pwd
+cap log close
+macro drop hr
+log using ./logs/cox_forest_2020_ethnicity_esrd_mediators.log, replace t
+cap file close tablecontent
+file open tablecontent using ./output/cox_forest_2020_ethnicity_esrd_mediators.csv, write text replace
+file write tablecontent _tab ("HR (95% CI)") _tab ("hr") _tab ("ll") _tab ("ul") _n
+
+use ./output/analysis_complete_2020.dta, clear
+
+qui stset exit_date_esrd, fail(esrd_date) origin(index_date_esrd) id(unique) scale(365.25)
+
+file write tablecontent ("Minimally-adjusted") _n
+forvalues i=1/5 {
+local label_`i': label ethnicity `i'
+}
+qui stcox i.case##i.ethnicity, strata(set_id)
+qui lincom 1.case, eform
+local int_1b = r(estimate)
+local int_1ll = r(lb)
+local int_1ul = r(ub)
+forvalues i=2/5 {
+qui lincom 1.case + 1.case#`i'.ethnicity, eform
+local int_`i'b = r(estimate)
+local int_`i'll = r(lb)
+local int_`i'ul = r(ub)
+}
+file write tablecontent ("`label_1'")
+file write tablecontent _tab %4.2f (`int_1b') (" (") %4.2f (`int_1ll') ("-") %4.2f (`int_1ul') (")") _tab %4.2f (`int_1b') _tab %4.2f (`int_1ll') _tab %4.2f (`int_1ul') _n
+forvalues i=2/5 {
+file write tablecontent ("`label_`i''")
+file write tablecontent _tab %4.2f (`int_`i'b') (" (") %4.2f (`int_`i'll') ("-") %4.2f (`int_`i'ul') (")") _tab %4.2f (`int_`i'b') _tab %4.2f (`int_`i'll') _tab %4.2f (`int_`i'ul') _n
+}
+
+local mediators "imd urban bmi smoking ckd_stage aki_baseline cardiovascular diabetes hypertension immunosuppressed non_haem_cancer gp_consults admissions covid_vax"
+
+local imd_lab "IMD"
+local urban_lab "rural/urban"
+local bmi_lab "BMI"
+local smoking_lab "smoking"
+local ckd_stage_lab "CKD stage"
+local aki_baseline_lab "previous AKI"
+local cardiovascular_lab "cardiovascular diseases"
+local diabetes_lab "diabetes"
+local hypertension_lab "hypertension"
+local immunosuppressed_lab "immunosuppressed"
+local non_haem_cancer_lab "non-haematological cancer"
+local gp_consults_lab "GP consultations"
+local admissions_lab "previous hospital admissions"
+local covid_vax_lab "COVID-19 vaccination"
+
+foreach med of local mediators {
+
+file write tablecontent ("After adjustment for ``med'_lab'") _n
+forvalues i=1/5 {
+local label_`i': label ethnicity `i'
+}
+
+qui stcox i.case##i.ethnicity i.`med', strata(set_id)
+qui lincom 1.case, eform
+local int_1b = r(estimate)
+local int_1ll = r(lb)
+local int_1ul = r(ub)
+forvalues i=2/5 {
+qui lincom 1.case + 1.case#`i'.ethnicity, eform
+local int_`i'b = r(estimate)
+local int_`i'll = r(lb)
+local int_`i'ul = r(ub)
+}
+file write tablecontent ("`label_1'")
+file write tablecontent _tab %4.2f (`int_1b') (" (") %4.2f (`int_1ll') ("-") %4.2f (`int_1ul') (")") _tab %4.2f (`int_1b') _tab %4.2f (`int_1ll') _tab %4.2f (`int_1ul') _n
+forvalues i=2/5 {
+file write tablecontent ("`label_`i''")
+file write tablecontent _tab %4.2f (`int_`i'b') (" (") %4.2f (`int_`i'll') ("-") %4.2f (`int_`i'ul') (")") _tab %4.2f (`int_`i'b') _tab %4.2f (`int_`i'll') _tab %4.2f (`int_`i'ul') _n
+}
+}
+
+file close tablecontent

project.yaml

@@ -1571,7 +1571,23 @@ actions:
     outputs:
       moderately_sensitive:
         log: logs/cox_forest_2020_ethnicity_esrd.log
-        output: output/cox_forest_2020_ethnicity_esrd.csv     
+        output: output/cox_forest_2020_ethnicity_esrd.csv
+
+  cox_forest_2017_ethnicity_esrd_mediators:
+    run: stata-mp:latest analysis/cox_forest_2017_ethnicity_esrd_mediators.do
+    needs: [analysis_complete]
+    outputs:
+      moderately_sensitive:
+        log: logs/cox_forest_2017_ethnicity_esrd_mediators.log
+        output: output/cox_forest_2017_ethnicity_esrd_mediators.csv
+
+  cox_forest_2020_ethnicity_esrd_mediators:
+    run: stata-mp:latest analysis/cox_forest_2020_ethnicity_esrd_mediators.do
+    needs: [analysis_complete]
+    outputs:
+      moderately_sensitive:
+        log: logs/cox_forest_2020_ethnicity_esrd_mediators.log
+        output: output/cox_forest_2020_ethnicity_esrd_mediators.csv    
 
   events_cca_2017:
     run: stata-mp:latest analysis/events_cca_2017.do