Removed primis_variables() and fixed related bugs

analysis/dataset_definition_snapshot.py

@@ -65,4 +65,4 @@
 
 demographic_variables(dataset = dataset, index_date = snapshot_date)
 primis_variables(dataset = dataset, index_date = snapshot_date)
-other_cx_variables(dataset = dataset, index_date = snapshot_date)
+# other_cx_variables(dataset = dataset, index_date = snapshot_date)

analysis/dataset_definition_varying.py

@@ -68,10 +68,11 @@
     demographic_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix)
 
     # primis variables
-    primis_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix)
+#    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 
 
-    # primis variables
-    other_cx_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix)
+    # other clinical variables
+#    other_cx_variables(dataset = dataset, index_date = current_vax.date, var_name_suffix = suffix)
 
     previous_vax_date = current_vax.date
 

analysis/process.R

@@ -109,18 +109,18 @@ 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("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("asplenia_\\d+"), # asplenia or dysfunction of the spleen
-    matches("severe_obesity_\\d+"), #immunosuppress grouped
-    matches("smi_\\d+"), #severe mental illness
+    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("asplenia_\\d+"), # asplenia or dysfunction of the spleen
+#    matches("severe_obesity_\\d+"), #immunosuppress grouped
+#    matches("smi_\\d+"), #severe mental illness
   ) %>%
   pivot_longer(
     cols = -patient_id,

analysis/report_history.R

@@ -172,7 +172,8 @@ summary_stratified <-
     vax_dosenumber, vax_type8, vax_campaign,
     sex, ageband, ethnicity5, region, imd_quintile,
     # PRIMIS
-    crd, chd, ckd, cld, cns, learndis, diabetes, immunosuppressed, asplenia, severe_obesity, smi, primis_atrisk
+ #   crd, chd, ckd, cld, cns, learndis, diabetes, immunosuppressed, asplenia, severe_obesity, smi, 
+ primis_atrisk
   ) %>%
   summarise(
     n = ceiling_any(n(), 100)
@@ -265,17 +266,17 @@ plot_vax_dates(vax_campaign, all)
 plot_vax_dates(vax_dosenumber, all)
 
 #PRIMIS
-plot_vax_dates(crd, all) # chronic respiratory disease
-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(crd, all) # chronic respiratory disease
+#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 
 
 
@@ -286,17 +287,17 @@ plot_vax_dates(region, vax_dosenumber)
 plot_vax_dates(imd_quintile, vax_dosenumber)
 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(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
 
 ## output plots of time since previous vaccination by type, dose number, and other characteristics ----
@@ -379,15 +380,15 @@ plot_vax_intervals(vax_dosenumber, all)
 
 #PRIMIS
 
-plot_vax_intervals(crd, vax_dosenumber) # chronic respiratory disease
-plot_vax_intervals(chd, vax_dosenumber) # chronic heart disease
-plot_vax_intervals(ckd, vax_dosenumber) # chronic kidney disease
-plot_vax_intervals(cld, vax_dosenumber) # chronic liver disease
-plot_vax_intervals(cns, vax_dosenumber) # chronic neurological
-plot_vax_intervals(learndis, vax_dosenumber) # learning disability
-plot_vax_intervals(diabetes, vax_dosenumber) # diabetes
-plot_vax_intervals(immunosuppressed, vax_dosenumber) # immunosuppressed
-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(crd, vax_dosenumber) # chronic respiratory disease
+# plot_vax_intervals(chd, vax_dosenumber) # chronic heart disease
+# plot_vax_intervals(ckd, vax_dosenumber) # chronic kidney disease
+# plot_vax_intervals(cld, vax_dosenumber) # chronic liver disease
+# plot_vax_intervals(cns, vax_dosenumber) # chronic neurological
+# plot_vax_intervals(learndis, vax_dosenumber) # learning disability
+# plot_vax_intervals(diabetes, vax_dosenumber) # diabetes
+# plot_vax_intervals(immunosuppressed, vax_dosenumber) # immunosuppressed
+# 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

analysis/variables_function.py

@@ -148,7 +148,11 @@ def has_severe_obesity(index_date):
     event_bmi = last_prior_event(
         bmi, 
         index_date,
-        where=(clinical_events.numeric_value.is_not_null())
+        where=(
+            clinical_events.numeric_value.is_not_null() & 
+            (clinical_events.numeric_value > 4) & 
+            (clinical_events.numeric_value < 200)
+        )
     )
     # Severe obesity
     severe_obesity = case(
@@ -308,14 +312,14 @@ def primis_variables(dataset, index_date, var_name_suffix=""):
 ##################################################################
 
 
-def other_cx_variables(dataset, index_date, var_name_suffix=""):
+# def other_cx_variables(dataset, index_date, var_name_suffix=""):
     ## others of interest
-    dataset.add_column(f"sol_org_trans{var_name_suffix}", has_prior_event(solid_organ_transplant, index_date)) # Organs transplant
-    dataset.add_column(f"hiv{var_name_suffix}", has_prior_event(hiv_aids, index_date)) #HIV/AIDS
-    dataset.add_column(f"cancer{var_name_suffix}", 
-                       has_prior_event(cancer_nonhaem_snomed, index_date, where=clinical_events.date.is_after(index_date - days(int(3 * 365.25))))|
-                       has_prior_event(cancer_haem_snomed, index_date, where=clinical_events.date.is_after(index_date - days(int(3 * 365.25))))
-                       ) #cancer   
+#    dataset.add_column(f"sol_org_trans{var_name_suffix}", has_prior_event(solid_organ_transplant, index_date)) # Organs transplant
+#    dataset.add_column(f"hiv{var_name_suffix}", has_prior_event(hiv_aids, index_date)) #HIV/AIDS
+#    dataset.add_column(f"cancer{var_name_suffix}", 
+#                       has_prior_event(cancer_nonhaem_snomed, index_date, where=clinical_events.date.is_after(index_date - days(int(3 * 365.25))))|
+#                       has_prior_event(cancer_haem_snomed, index_date, where=clinical_events.date.is_after(index_date - days(int(3 * 365.25))))
+#                       ) #cancer