Time stratified event counts

analysis/covariate_events_2020.do

@@ -0,0 +1,102 @@
+sysdir set PLUS ./analysis/adofiles
+sysdir set PERSONAL ./analysis/adofiles
+pwd
+cap log close
+macro drop hr
+log using ./logs/covariate_events_2020.log, replace t
+
+use ./output/analysis_complete_2020.dta, clear
+
+cap file close tablecontent
+file open tablecontent using ./output/covariate_events_2020.csv, write text replace
+
+file write tablecontent _tab ("Matched") _tab _tab _tab ("Non-hospitalised COVID-19") _tab _tab _tab ("Hospitalised_COVID-19") _n
+file write tablecontent _tab ("0-29 days") _tab ("30-89 days") _tab ("90-179 days") _tab ("180 days+") _tab ("0-29 days") _tab ("30-89 days") _tab ("90-179 days") _tab ("180 days+") _tab ("0-29 days") _tab ("30-89 days") _tab ("90-179 days") _tab ("180 days+") _n
+
+gen follow_up_esrd = follow_up_time_esrd
+recode follow_up_esrd	min/29=1 	///
+						30/89=2 	///
+						90/179=3			///
+						180/max=4 
+stset exit_date_esrd, fail(esrd_date) origin(index_date_esrd) id(unique) scale(365.25)
+
+*COVID severity
+
+file write tablecontent ("Overall") _n
+forvalues i=0/2 {
+forvalues j=1/4 {
+qui safecount if covid_severity==`i' & _d==1 & follow_up_esrd==`j'
+local followup_`j' = round(r(N),5)
+}
+file write tablecontent %9.0f (`followup_1') _tab %9.0f (`followup_2') _tab %9.0f (`followup_3') _tab %9.0f (`followup_4') _tab
+}
+file write tablecontent _n
+
+
+
+*IMD
+file write tablecontent ("Index of multiple deprivation") _n
+forvalues imd=1/5 {
+local label_`imd': label imd `imd'
+file write tablecontent ("`label_`imd''") _tab
+forvalues i=0/2 {
+forvalues j=1/4 {
+qui safecount if imd==`imd' & covid_severity==`i' & _d==1 & follow_up_esrd==`j'
+local followup_`j' = round(r(N),5)
+}
+file write tablecontent %9.0f (`followup_1') _tab %9.0f (`followup_2') _tab %9.0f (`followup_3') _tab %9.0f (`followup_4') _tab
+}
+file write tablecontent _n
+}
+
+*Ethnicity
+file write tablecontent ("Ethnicity") _n
+forvalues ethnicity=1/5 {
+local label_`ethnicity': label ethnicity `ethnicity'
+file write tablecontent ("`label_`ethnicity''") _tab
+forvalues i=0/2 {
+forvalues j=1/4 {
+qui safecount if ethnicity==`ethnicity' & covid_severity==`i' & _d==1 & follow_up_esrd==`j'
+local followup_`j' = round(r(N),5)
+}
+file write tablecontent %9.0f (`followup_1') _tab %9.0f (`followup_2') _tab %9.0f (`followup_3') _tab %9.0f (`followup_4') _tab
+}
+file write tablecontent _n
+}
+
+*CKD stage
+file write tablecontent ("CKD stage") _n
+forvalues ckd_stage =1/6 {
+local label_`ckd_stage': label ckd_stage `ckd_stage'
+file write tablecontent ("`label_`ckd_stage''") _tab
+forvalues i=0/2 {
+forvalues j=1/4 {
+qui safecount if ckd_stage==`ckd_stage' & covid_severity==`i' & _d==1 & follow_up_esrd==`j'
+local followup_`j' = round(r(N),5)
+}
+file write tablecontent %9.0f (`followup_1') _tab %9.0f (`followup_2') _tab %9.0f (`followup_3') _tab %9.0f (`followup_4') _tab
+}
+file write tablecontent _n
+}
+
+*AKI
+file write tablecontent ("Previous acute kidney injury") _tab
+forvalues i=0/2 {
+forvalues j=1/4 {
+qui safecount if aki_baseline==1 & covid_severity==`i' & _d==1 & follow_up_esrd==`j'
+local followup_`j' = round(r(N),5)
+}
+file write tablecontent %9.0f (`followup_1') _tab %9.0f (`followup_2') _tab %9.0f (`followup_3') _tab %9.0f (`followup_4') _tab
+}
+file write tablecontent _n
+
+*Diabetes
+file write tablecontent ("Diabetes") _tab
+forvalues i=0/2 {
+forvalues j=1/4 {
+qui safecount if diabetes==1 & covid_severity==`i' & _d==1 & follow_up_esrd==`j'
+local followup_`j' = round(r(N),5)
+}
+file write tablecontent %9.0f (`followup_1') _tab %9.0f (`followup_2') _tab %9.0f (`followup_3') _tab %9.0f (`followup_4') _tab
+}
+

project.yaml

@@ -2476,4 +2476,11 @@ actions:
         phplot_2020_severity_esrd_ckd_stage5: phplot_2020_severity_esrd_ckd_stage5.png
         phplot_2020_severity_esrd_ckd_stage6: phplot_2020_severity_esrd_ckd_stage6.png
         phplot_2020_severity_esrd_aki_baseline: phplot_2020_severity_esrd_aki_baseline.png
-        phplot_2020_severity_esrd_diabetes: phplot_2020_severity_esrd_diabetes.png
+        phplot_2020_severity_esrd_diabetes: phplot_2020_severity_esrd_diabetes.png
+
+  covariate_events_2020:
+    run: stata-mp:latest analysis/covariate_events_2020.do
+    needs: [analysis_complete]
+    outputs:
+      moderately_sensitive:
+        output: output/covariate_events_2020.csv