Merge pull request #58 from zoyafuso-NOAA/main

Quick fixes after 10/17/24 run
afsc-gap-products · Oct 18, 2024 · 5c2c3fd · 5c2c3fd
2 parents 90f25c2 + 16ebbb5
commit 5c2c3fd
Show file tree

Hide file tree

Showing 3 changed files with 40 additions and 16 deletions.
diff --git a/code/utility_scripts/taxonomic_groupings.R b/code/utility_scripts/taxonomic_groupings.R
@@ -281,11 +281,12 @@ test_check <- merge(x = updated_gp_taxon_groups,
 ## Reorder columns
 test_check <- 
   test_check[, c("SPECIES_CODE", 
-                 as.vector(sapply(X = names(current_gp_taxon_groups)[-2], 
+                 as.vector(sapply(X = names(current_gp_taxon_groups)[-1], 
                                   FUN = function(x) 
                                     paste0(x, c("_UPDATE", "_CURRENT")))))]
+
 ## Check for differences in each non-key field
-for (icol in names(current_gp_taxon_groups)[-2]) {
+for (icol in names(current_gp_taxon_groups)[-1]) {
   test_check[, paste0(icol, "_DIFF")] <- 
     test_check[, paste0(icol, "_UPDATE")] != 
     test_check[, paste0(icol, "_CURRENT")]
@@ -294,7 +295,7 @@ for (icol in names(current_gp_taxon_groups)[-2]) {
 ## Reorder columns
 test_check <- 
   test_check[, c("SPECIES_CODE", 
-                 as.vector(sapply(X = names(current_gp_taxon_groups)[-2], 
+                 as.vector(sapply(X = names(current_gp_taxon_groups)[-1], 
                                   FUN = function(x) 
                                     paste0(x, c("_UPDATE", 
                                                 "_CURRENT",

diff --git a/functions/calc_diff.R b/functions/calc_diff.R
@@ -14,7 +14,7 @@ calc_diff <- function(v1, v2, percent = T) {
                                "DIFF" = v2 - v1)
   data.table::setnames(x = df, c("v1", "v2", "DIFF"))
 
-  df[, v2 := ifelse(test = v2 == 0, 1, v2)]
+  df[, v1 := ifelse(test = v1 == 0, 1, v1)]
   df[, PERC_DIFF := 100 * DIFF / v1]
 
   return(df[, ifelse(percent == T, "PERC_DIFF", "DIFF"), with = F])

diff --git a/functions/compare_tables.R b/functions/compare_tables.R
@@ -62,22 +62,22 @@ compare_tables <- function(x = NULL,
 
   for (icol in 1:nrow(x = cols_to_check)) {
     x[, paste0(cols_to_check$colname[icol], "_DIFF") := 
-      round(x = calc_diff(v1 = x[, paste0(cols_to_check$colname[icol], 
-                                          base_table_suffix), with = F],
-                          v2 = x[, paste0(cols_to_check$colname[icol], 
-                                          update_table_suffix), with = F],
-                          percent = cols_to_check$percent[icol]) ,
-            digits = cols_to_check$decplaces[icol])]
+        round(x = calc_diff(v1 = x[, paste0(cols_to_check$colname[icol], 
+                                            base_table_suffix), with = F],
+                            v2 = x[, paste0(cols_to_check$colname[icol], 
+                                            update_table_suffix), with = F],
+                            percent = cols_to_check$percent[icol]) ,
+              digits = cols_to_check$decplaces[icol])]
   }
-
+  
   new_records_stmt <- 
     paste0("x[",
            paste0(sapply(X = cols_to_check$colname, 
                          FUN = function(x) 
                            paste0("(is.na(x = ", x, base_table_suffix, 
                                   ") & !is.na(x = ", x, update_table_suffix, 
                                   "))")), 
-                  collapse = "|"), 
+                  collapse = "&"), 
            "]")
   new_records <- eval(parse(text = new_records_stmt))
   new_records <- new_records[, c(key_columns, col_order), with = F]
@@ -94,16 +94,39 @@ compare_tables <- function(x = NULL,
   removed_records <- eval(parse(text = removed_records_stmt))
   removed_records <- removed_records[, c(key_columns, col_order), with = F]
 
-  modified_records_stmt <- 
+  ## modified records consist of two types:
+  ## 1) non-zero differences
+  ## 2) instances where 
+  modified_records_stmt1 <- 
     paste0("x[",
            paste0(sapply(X = cols_to_check$colname, 
                          FUN = function(x) 
                            paste0(x, "_DIFF != 0")), 
                   collapse = " | "), 
            "]")
-  modified_records <- eval(parse(text = modified_records_stmt))
-  modified_records <- modified_records[, c(key_columns, col_order), with = F]
-
+  modified_records1 <- eval(parse(text = modified_records_stmt1))
+
+  modified_records_stmt2 <- 
+    paste0("x[",
+           paste0(sapply(X = cols_to_check$colname, 
+                         FUN = function(x) 
+                           paste0("(is.na(x = ", x, base_table_suffix, 
+                                  ") & !is.na(x = ", x, update_table_suffix, 
+                                  "))")), 
+                  collapse = "|"), 
+           "]")
+  modified_records2 <- eval(parse(text = modified_records_stmt2))
+  modified_records2 <- modified_records2[
+    apply(X = modified_records2[, 
+                                paste0(cols_to_check$colname, "_DIFF"), 
+                                with = F],
+          MARGIN = 1,
+          FUN = function(x) !all(is.na(x)))]
+
+
+  modified_records <- rbind(modified_records1, modified_records2)
+  modified_records <- modified_records[, c(key_columns, col_order), with = F]  
+
   return(do.call(what = list,
                  args = list(new_records = new_records, 
                              removed_records = removed_records,