remove "atrisk" stratification from history report

analysis/dataset_definition_varying.py

@@ -69,7 +69,7 @@
 
     # primis variables
 #    primis_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix)
-    dataset.add_column(f"primis_atrisk_{i}", primis_atrisk(current_vax.date)) # at risk 
+#    dataset.add_column(f"primis_atrisk_{i}", primis_atrisk(current_vax.date)) # at risk 
 
     # other clinical variables
 #    other_cx_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix)

analysis/process.R

@@ -109,17 +109,17 @@ data_vax <-
     matches("imd_\\d+"),
     matches("imd_quintile_\\d+"),
     # ... more clinical (PRIMIS) characteristics here
-    matches("primis_atrisk_\\d+") #, # Clinically vulnerable
-#    matches("crd_\\d+"), #chronic respiratory disease
-#    matches("chd_\\d+"), #chronic heart disease
-#    matches("ckd_\\d+"), #chronic kidney disease
+#    matches("primis_atrisk_\\d+") #, # Clinically vulnerable
+#    matches("crd_\\d+"), # chronic respiratory disease
+#    matches("chd_\\d+"), # chronic heart disease
+#    matches("ckd_\\d+"), # chronic kidney disease
 #    matches("cld_\\d+"), # chronic liver disease
 #    matches("cns_\\d+"), # chronic neurological disease
 #    matches("learndis_\\d+"), # learning Disability
-#    matches("diabetes_\\d+"), #diabetes
-#    matches("immunosuppressed_\\d+"), #immunosuppress grouped
+#    matches("diabetes_\\d+"), # diabetes
+#    matches("immunosuppressed_\\d+"), # immunosuppressed
 #    matches("asplenia_\\d+"), # asplenia or dysfunction of the spleen
-#    matches("severe_obesity_\\d+"), #immunosuppress grouped
+#    matches("severe_obesity_\\d+"), # obesity
 #    matches("smi_\\d+"), #severe mental illness
   ) %>%
   pivot_longer(

analysis/report_history.R

@@ -173,7 +173,7 @@ summary_stratified <-
     sex, ageband, ethnicity5, region, imd_quintile,
     # PRIMIS
  #   crd, chd, ckd, cld, cns, learndis, diabetes, immunosuppressed, asplenia, severe_obesity, smi, 
- primis_atrisk
+ #   primis_atrisk
   ) %>%
   summarise(
     n = ceiling_any(n(), 100)
@@ -270,14 +270,14 @@ plot_vax_dates(vax_dosenumber, all)
 #plot_vax_dates(chd, all) # chronic heart disease
 #plot_vax_dates(ckd, all) # chronic kidney disease
 #plot_vax_dates(cld, all) # chronic liver disease
-# plot_vax_dates(cns, all) #chronic neurological
-# plot_vax_dates(learndis, all) # learning disability
-# plot_vax_dates(diabetes, all) # diabetes
-# plot_vax_dates(immunosuppressed, all) # immunosuppressed
-# plot_vax_dates(asplenia, all) # asplenia or dysfunction of the spleen
-# plot_vax_dates(severe_obesity, all) # obesity
-# plot_vax_dates(smi, all) # severe mental illness
-plot_vax_dates(primis_atrisk, all) # clinically vulnerable 
+#plot_vax_dates(cns, all) #chronic neurological
+#plot_vax_dates(learndis, all) # learning disability
+#plot_vax_dates(diabetes, all) # diabetes
+#plot_vax_dates(immunosuppressed, all) # immunosuppressed
+#plot_vax_dates(asplenia, all) # asplenia or dysfunction of the spleen
+#plot_vax_dates(severe_obesity, all) # obesity
+#plot_vax_dates(smi, all) # severe mental illness
+#plot_vax_dates(primis_atrisk, all) # clinically vulnerable 
 
 
 plot_vax_dates(sex, vax_dosenumber)
@@ -289,16 +289,16 @@ plot_vax_dates(vax_campaign, vax_dosenumber)
 #PRIMIS
 #plot_vax_dates(crd, vax_dosenumber) # chronic respiratory disease
 #plot_vax_dates(chd, vax_dosenumber) # chronic heart disease
-# plot_vax_dates(ckd, vax_dosenumber) # chronic kidney disease
-# plot_vax_dates(cld, vax_dosenumber) # chronic liver disease
-# plot_vax_dates(cns, vax_dosenumber) # chronic neurological disease
-# plot_vax_dates(learndis, vax_dosenumber) # learning Disability
-# plot_vax_dates(diabetes, vax_dosenumber) # diabetes
-# plot_vax_dates(immunosuppressed, vax_dosenumber) # immunosuppressed
-# plot_vax_dates(asplenia, vax_dosenumber) # asplenia or dysfunction of the spleen
-# plot_vax_dates(severe_obesity, vax_dosenumber) # obesity
-# plot_vax_dates(smi, vax_dosenumber) # severe mental illness
-plot_vax_dates(primis_atrisk, vax_dosenumber) # Clinically vulnerable
+#plot_vax_dates(ckd, vax_dosenumber) # chronic kidney disease
+#plot_vax_dates(cld, vax_dosenumber) # chronic liver disease
+#plot_vax_dates(cns, vax_dosenumber) # chronic neurological disease
+#plot_vax_dates(learndis, vax_dosenumber) # learning Disability
+#plot_vax_dates(diabetes, vax_dosenumber) # diabetes
+#plot_vax_dates(immunosuppressed, vax_dosenumber) # immunosuppressed
+#plot_vax_dates(asplenia, vax_dosenumber) # asplenia or dysfunction of the spleen
+#plot_vax_dates(severe_obesity, vax_dosenumber) # obesity
+#plot_vax_dates(smi, vax_dosenumber) # severe mental illness
+#plot_vax_dates(primis_atrisk, vax_dosenumber) # Clinically vulnerable
 
 ## output plots of time since previous vaccination by type, dose number, and other characteristics ----
 
@@ -391,4 +391,4 @@ plot_vax_intervals(vax_dosenumber, all)
 # plot_vax_intervals(asplenia, vax_dosenumber) # asplenia or dysfunction of the spleen
 # plot_vax_intervals(severe_obesity, vax_dosenumber) # obesity
 # plot_vax_intervals(smi, vax_dosenumber) # severe mental illness
-plot_vax_intervals(primis_atrisk, vax_dosenumber) # Clinically vulnerable
+# plot_vax_intervals(primis_atrisk, vax_dosenumber) # Clinically vulnerable