fix opacity

ironwood_plots.R

@@ -57,11 +57,27 @@ text(x = barplot(percentage, plot = FALSE),
 # 2. Create a stacked barchart that represents all site and their health data
 ##
 
-# Create data
+# Convert tree_health_index to factor for correct ordering in the barplot
-set.seed(1124)
+df$tree_health_index <- factor(df$tree_health_index, levels = 0:4, ordered = TRUE)
+
+# Create a new data frame with counts of each health index for each site
+health_counts <- df %>%
+  group_by(site_num, tree_health_index) %>%
+  summarise(count = n())
+
+# Pivot the data frame to wide format for ggplot
+health_counts_wide <- pivot_wider(health_counts, names_from = tree_health_index, values_from = count, values_fill = list(count = 0))
+
+ggplot(health_counts_wide, aes(x = site_num)) +
+  geom_bar(aes(fill = `0`), position = "stack", width = 0.5) +
+  geom_bar(aes(fill = `1`), position = "stack", width = 0.5) +
+  geom_bar(aes(fill = `2`), position = "stack", width = 0.5) +
+  geom_bar(aes(fill = `3`), position = "stack", width = 0.5) +
+  geom_bar(aes(fill = `4`), position = "stack", width = 0.5) +
+  labs(x = "Site Number", y = "Count", fill = "Health Index") +
+  scale_fill_manual(values = c("#1b9e77", "#d95f02", "#7570b3", "#e7298a", "#66a61e")) +  # Custom colors for each health index
+  theme_minimal()
 
-# for each site i need a table like this:
-#table(df$tree_health_index[1:14])
 
 colnames(health_data) <- paste("Site", seq(1,20), sep=" ")
 rownames(health_data) <- condition_names
@@ -108,12 +124,17 @@ map <- leaflet() %>%
   setView(lng = population_lon,
           lat = population_lat,
           zoom = 16) %>%
-  addTiles() %>%
+  addProviderTiles(
+    provider = "Esri.WorldImagery",
+    options = providerTileOptions(
+      opacity = 0.5
+    )  
+  ) %>%
   addCircleMarkers(
     data = df,
     lng = ~tree_lon,
     lat = ~tree_lat,
-    radius = 2,
+    radius = 1,
     color = ~condition_colors[tree_health_index+1],
     opacity = 1,
     fillOpacity = 1
@@ -122,10 +143,10 @@ map <- leaflet() %>%
     data = sites,
     lng = ~site_lon,
     lat = ~site_lat,
-    radius = 25,
+    radius = 40,
     fill = FALSE,
-    color = "green",
+    color = "black",
-    opacity = 0.1
+    opacity = 0.5
   )
 
 # show map