corrected bug in recombination of imputed with known dead individuals

imputation-report.Rmd

@@ -202,6 +202,7 @@ tbl_posteriors <- tibble(
 ```
 
 ```{r final-imputations}
+# start by adding confirmed <= 180d deaths back in
 tbl_final_imputations <- readr::read_csv(
         sprintf('%s/tbl_gose_imputation.csv', config$datapath),
         col_types = "cinncD"
@@ -209,7 +210,7 @@ tbl_final_imputations <- readr::read_csv(
     select(gupi, Subject.DeathDate) %>% 
     distinct %>% 
     transmute(
-        gupi = gupi,
+        gupi       = gupi,
         death_days = difftime(Subject.DeathDate, "1970-01-01", unit = "days") %>% as.numeric
     ) %>% 
     left_join(tbl_posteriors, by = "gupi") %>% 
@@ -220,7 +221,7 @@ tbl_final_imputations <- readr::read_csv(
     ) %>% 
     mutate(
         probability = ifelse(
-            is.na(death_days),
+            is.na(death_days) | (death_days > 180),
             probability,
             ifelse(gose != "gose_1_probability", 0.0, 1.0)
         )