graph axis updates

opensafely · May 10, 2023 · a24c623 · a24c623
1 parent 672da7d
commit a24c623
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Showing 2 changed files with 116 additions and 179 deletions.
diff --git a/analysis/305_cox_ph.do b/analysis/305_cox_ph.do
@@ -15,14 +15,13 @@ cap mkdir ./output/graphs
 foreach period in pre pandemic /*wave1 easing1 wave2 easing2 wave3 easing3*/ {
     use ./output/prep_survival_`period', clear
     describe
-    foreach outcome in stroke mi hf vte dm_keto depress anx asthma {
+    foreach outcome in stroke mi hf vte dm_keto depress anx {
         * Drop events that occur on index date
         drop if `outcome'_admit_date==index_date
 
         * Update study population for diabetes and respiratory outcomes
         drop if diabetes_subgroup==0 & "`outcome'"== "dm_keto"
-        drop if has_asthma==0 & "`outcome'"== "asthma"
-
+
         * Cox model for each outcome category
         * Generate flags and end dates for each outcome
         gen `outcome'_admit=(`outcome'_admit_date!=.)
@@ -34,7 +33,7 @@ foreach period in pre pandemic /*wave1 easing1 wave2 easing2 wave3 easing3*/ {
 
                 stset `outcome'_end, fail(`outcome'_admit) id(patient_id) enter(index_date) origin(index_date) 
                 * Kaplan-Meier plot
-                sts graph, by(eth5) ylabel(.99(.002)1) title("`period'") graphregion(fcolor(white))
+                sts graph, by(eth5) ylabel(.99(0.01)1) title("`period'") graphregion(fcolor(white))
                 graph export ./output/graphs/km_`outcome'_`period'.svg, as(svg) replace
                 /*qui stcox eth5, strata(stp)
                 estat phtest 
@@ -78,37 +77,40 @@ foreach period in pre pandemic wave1 easing1 wave2 easing2 wave3 easing3 {
     }
 } */
 
-* T2 DM plots 
+* T2 DM and asthma plots 
 foreach period in pre pandemic /*wave1 easing1 wave2 easing2 wave3 easing3*/ {
     use ./output/prep_survival_`period', clear
     describe
+    foreach outcome in asthma t2dm {
     * Drop events that occur on index date
-    drop if t2dm_admit_date==index_date
+        drop if `outcome'_admit_date==index_date 
 
-    * Update study population for diabetes and respiratory outcomes
-    drop if has_t2_diabetes==0
+        * Update study population for diabetes and respiratory outcomes
+        drop if has_t2_diabetes==0 & "`outcome'"== "t2dm"
+        drop if has_asthma==0 & "`outcome'"== "asthma"
 
-    * Cox model for each outcome category
-    * Generate flags and end dates for each outcome
-    gen t2dm_admit=(t2dm_admit_date!=.)
-    tab t2dm_admit
-    count if t2dm_admit_date!=.
-    if r(N) > 10 {
-            gen t2dm_end = end_date
-            replace t2dm_end = t2dm_admit_date if t2dm_admit==1
+        * Cox model for each outcome category
+        * Generate flags and end dates for each outcome
+        gen `outcome'_admit=(`outcome'_admit_date!=.)
+        tab `outcome'_admit
+        count if `outcome'_admit_date!=.
+        if r(N) > 10 {
+                gen `outcome'_end = end_date
+                replace `outcome'_end = `outcome'_admit_date if `outcome'_admit==1
 
-            stset t2dm_end, fail(t2dm_admit) id(patient_id) enter(index_date) origin(index_date) 
-            * Kaplan-Meier plot
-            sts graph, by(eth5) ylabel(.95(.01)1) title("`period'") graphregion(fcolor(white))
-            graph export ./output/graphs/km_t2dm_`period'.svg, as(svg) replace
-            /*qui stcox eth5, strata(stp)
-            estat phtest 
-            qui stcox eth5 i.age_cat i.male, strata(stp)
-            estat phtest 
-            qui stcox eth5 i.age_cat i.male i.urban_rural_bin i.imd i.shielded, strata(stp)
-            estat phtest*/
-    }
-} 
+                stset `outcome'_end, fail(`outcome'_admit) id(patient_id) enter(index_date) origin(index_date) 
+                * Kaplan-Meier plot
+                sts graph, by(eth5) ylabel(.95(.01)1) title("`period'") graphregion(fcolor(white))
+                graph export ./output/graphs/km_`outcome'_`period'.svg, as(svg) replace
+                /*qui stcox eth5, strata(stp)
+                estat phtest 
+                qui stcox eth5 i.age_cat i.male, strata(stp)
+                estat phtest 
+                qui stcox eth5 i.age_cat i.male i.urban_rural_bin i.imd i.shielded, strata(stp)
+                estat phtest*/
+        }
+    } 
+}
 
 /* COPD plots
 foreach period in pre pandemic wave1 easing1 wave2 easing2 wave3 easing3 {