fixes #5 (hydrophytes should be NA when wetland indicators are not li…

…sted in regional db)
ifoxfoot · Aug 24, 2023 · 2be2268 · 2be2268
1 parent e39d4df
commit 2be2268
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Showing 2 changed files with 25 additions and 18 deletions.
diff --git a/R/cover_metrics.R b/R/cover_metrics.R
@@ -241,17 +241,21 @@ transect_summary <- function(x, key = "name", db, cover_class = "percent_cover",
     # Native Mean Wetness
     mean(dplyr::filter(unique_entries, .data$nativity == "native")$w, na.rm = TRUE),
     #% hydrophytes
-    if(db %in% c("dakotas_excluding_black_hills_2017",
-                 "delaware_2013",
-                 "illinois_2020",
-                 "iowa_2001","louisiana_coastal_prairie_2006",
-                 "mid_atlantic_allegheny_plateau_glaciated_2012",
-                 "mid_atlantic_allegheny_plateau_nonglaciated_2012",
-                 "mid_atlantic_ridge_valley_2012",
-                 "minnesota_wetlands_2007",
-                 "pennsylvania_piedmont_2013")) {
-      (sum(entries$w < -1, na.rm = TRUE )/length(entries$w))*100
-    } else {(sum(entries$w < 0, na.rm = TRUE )/length(entries$w))*100}
+    if (all(is.na(entries$w))) {
+      NA
+    } else {
+      if(db %in% c("dakotas_excluding_black_hills_2017",
+                   "delaware_2013",
+                   "illinois_2020",
+                   "iowa_2001","louisiana_coastal_prairie_2006",
+                   "mid_atlantic_allegheny_plateau_glaciated_2012",
+                   "mid_atlantic_allegheny_plateau_nonglaciated_2012",
+                   "mid_atlantic_ridge_valley_2012",
+                   "minnesota_wetlands_2007",
+                   "pennsylvania_piedmont_2013")) {
+        (sum(entries$w < -1, na.rm = TRUE )/length(entries$w))*100
+      } else {(sum(entries$w < 0, na.rm = TRUE )/length(entries$w))*100}
+    }
   )
 
   #bind metrics and values into data frame

diff --git a/R/fqi_metrics.R b/R/fqi_metrics.R
@@ -241,13 +241,16 @@ all_metrics <- function(x, key = "name", db, allow_no_c = TRUE) {
     # Native Mean Wetness
     mean(dplyr::filter(entries, .data$nativity == "native")$w, na.rm = TRUE),
     #% hydrophytes
-    if(db %in% c("dakotas_excluding_black_hills_2017", "delaware_2013", "illinois_2020",
-                 "iowa_2001","louisiana_coastal_prairie_2006", "mid_atlantic_allegheny_plateau_glaciated_2012",
-                 "mid_atlantic_allegheny_plateau_nonglaciated_2012", "mid_atlantic_ridge_valley_2012",
-                 "minnesota_wetlands_2007", "pennsylvania_piedmont_2013")) {
-      (sum(entries$w < -1, na.rm = TRUE)/length(entries$w))*100
-    } else {(sum(entries$w < 0, na.rm = TRUE)/length(entries$w))*100}
-
+    if (all(is.na(entries$w))) {
+      NA
+    } else {
+      if(db %in% c("dakotas_excluding_black_hills_2017", "delaware_2013", "illinois_2020",
+                   "iowa_2001","louisiana_coastal_prairie_2006", "mid_atlantic_allegheny_plateau_glaciated_2012",
+                   "mid_atlantic_allegheny_plateau_nonglaciated_2012", "mid_atlantic_ridge_valley_2012",
+                   "minnesota_wetlands_2007", "pennsylvania_piedmont_2013")) {
+        (sum(entries$w < -1, na.rm = TRUE)/length(entries$w))*100
+      } else {(sum(entries$w < 0, na.rm = TRUE)/length(entries$w))*100}
+    }
   )
 
   #bind metrics and values into data frame