Update data_processing.R

analysis/data_processing.R

@@ -46,6 +46,9 @@ df_input <- merge(df_input, household_comp_vars, by = "patient_id")
 
 #create time dependency
 if(cohort == "infants" | cohort == "infants_subgroup") {
+  print(nrow(df_input))
+  print(class(study_start_date))
+  print(class(study_end_date))
   df_input <- df_input %>%
     mutate(
       date = map2(study_start_date, study_end_date, ~seq(.x, .y, by = 30.44))
@@ -176,6 +179,22 @@ if (cohort != "infants" & cohort != "infants_subgroup") {
   )
 }
 
+#define two vaccinations categories for each outcome type, set vaccination to null
+#if immunity date occurs after outcome date 
+if (cohort != "infants" & cohort != "infants_subgroup") {
+  df_input <- df_input %>%
+    mutate(
+      #define flu_vaccination_mild
+      flu_vaccination_mild = factor(if_else(
+        flu_vaccination_immunity_date <= flu_primary_date, "Yes", "No"
+      )),
+      #define flu_vaccination severe 
+      flu_vaccination_severe = factor(ifelse(
+        flu_vaccination_immunity_date <= flu_secondary_date, "Yes", "No"
+      ))
+    )
+}
+
 #covid vaccination 
 if (study_start_date >= covid_prior_vacc_min & cohort != "infants" & cohort != "infants_subgroup") {
   df_input <- df_input %>%
@@ -205,6 +224,22 @@ if (study_start_date >= covid_current_vacc_min & cohort != "infants" & cohort !=
     )
 }
 
+#define two vaccinations categories for each outcome type, set vaccination to null
+#if immunity date occurs after outcome date 
+if (study_start_date >= covid_current_vacc_min & cohort != "infants" & cohort != "infants_subgroup") {
+  df_input <- df_input %>%
+    mutate(
+      #define covid_vaccination_mild
+      covid_vaccination_mild = factor(if_else(
+        covid_vaccination_immunity_date <= covid_primary_date, "Yes", "No"
+      )),
+      #define covid_vaccination severe 
+      covid_vaccination_severe = factor(ifelse(
+        covid_vaccination_immunity_date <= covid_secondary_date, "Yes", "No"
+      ))
+    )
+}
+
 # #re-level factors so they have reference categories for the regression models
 # df_input <- df_input %>% 
 #   mutate(