Merge pull request #1369 from cmu-delphi/contingency-missing-val-tables

Don't report contingency table if responses for supporting items are all `NA`

Author: krivard

facebook/delphiFacebook/R/contingency_aggregate.R

@@ -158,15 +158,20 @@ post_process_aggs <- function(df, aggregations, cw_list) {
   metric_cols <- unique(aggregations$metric)
 
   cols_check_available <- unique(c(group_vars[group_vars != "geo_id"], metric_cols))
-  available <- cols_check_available %in% names(df)
+  available <- unlist(
+    lapply(cols_check_available, function(col) {
+      # Exists in dataframe and column is not only NAs
+      col %in% names(df) && !all(is.na( unique(df[[col]] )))
+    })
+  )
   cols_not_available <- cols_check_available[ !available ]
   for (col_var in cols_not_available) {
     # Remove from aggregations
     aggregations <- aggregations[aggregations$metric != col_var &
                                    !mapply(aggregations$group_by,
                                            FUN=function(x) {col_var %in% x}), ]
     msg_plain(paste0(
-        col_var, " is not defined. Removing all aggregations that use it. ",
+        col_var, " is not available or not defined. Removing all aggregations that use it. ",
         nrow(aggregations), " remaining")
     )
   }