Merge branch 'feature/35_feature' into develop

02_Cleaning_scripts/WQ_GTMNERR.R

@@ -79,7 +79,9 @@ WQ_locations <- WQ %>%
   mutate(Year = year(SampleDate)) %>% 
   select(site_friendly, Year, site_acronym, lat, long, wbid, location) %>% 
   group_by(site_friendly, site_acronym, lat, long, wbid, location) %>% 
-  summarize(maxYear = max(Year), minYear = min(Year)) 
+  summarize(maxYear = max(Year), minYear = min(Year)) %>% 
+  mutate(type = "Water quality",
+         dataset = "Guana Water Quality Monitoring (GTMNERR)")
 
 WQ_data_available <- WQ %>% 
   mutate(Year = year(SampleDate)) %>% 

02_Cleaning_scripts/shapefile_cleanup.R

@@ -55,7 +55,7 @@ pt4 <- st_point(c(xmax, ymax))
 # Put together as sf object and get bounding box
 bound_box <- st_bbox(st_sfc(pt1, pt3, pt4, pt2, crs = st_crs(GTMNERR)))
 
-##### Counties #####
+#### Counties #####
 counties <- st_read("01_Data_raw/shapefiles/countyshore_areas_sep15/countyshore_areas_sep15.shp")
 # CRS: Albers Conical Equal Area
 counties <- st_transform(counties, crs = st_crs(GTMNERR))
@@ -79,7 +79,7 @@ st_write(counties_select, "03_Data_for_app/shapefiles_new/counties_GTMNERR.shp",
          append = FALSE)
 # Ignore warnings when writing data: checked saved shapefile and it is correct
 
-##### Salt marshes #####
+#### Salt marshes #####
 salt_marsh <- st_read("01_Data_raw/shapefiles/salt_marsh_2020/salt_marsh_2020.shp")
 # CRS: NAD83(HARN) / Florida GDL Albers -> for visualization this is not a problem,
 # for consistency I am still changing the CRS
@@ -95,7 +95,7 @@ ggplot()+
 st_write(salt_marsh, "03_Data_for_app/shapefiles_new/salt_marsh_GTMNERR.shp",
          append = FALSE)
 
-##### Hydrology (several shapefiles) #####
+#### Hydrology (several shapefiles) #####
 hydro_6 <- st_read("01_Data_raw/shapefiles/nhdwbd_huc6_dec17/nhdwbd_huc6_dec17.shp")
 # CRS: Albers Conical Equal Area 
 hydro_6 <- st_transform(hydro_6, crs = st_crs(GTMNERR))
@@ -159,8 +159,7 @@ ggplot()+
 # Look up differences between HUCs to add to metadata
 st_write(hydro_10_select, "03_Data_for_app/shapefiles_new/nhdwbd_huc10_dec17_GTMNERR.shp", append = FALSE)
 st_write(hydro_12_select, "03_Data_for_app/shapefiles_new/nhdwbd_huc12_dec17_GTMNERR.shp", append = FALSE)
-#### CHECK WARNINGS of some values not being written (too long) #####
-
+#### Checked warnings of some values not being written (too long): looks fine
 
 #### Water bodies ####
 waterbodies <- st_read("01_Data_raw/shapefiles/nhd24waterbody_dec17/nhd24waterbody_dec17.shp")

04_Tests/leaflet_test.R

@@ -15,7 +15,18 @@ GTMNERR <- st_read("03_Data_for_app/shapefiles_new/GTMNERR.shp")# CRS: Albers Co
 
 GTMNERR <- st_transform(GTMNERR, crs = 4326)
 
-m <- leaflet(data = GTMNERR, options = leafletOptions(minZoom = 9, maxZoom = 18)) %>%
+# Leaflet uses EPSG 3857, change this
+# https://gis.stackexchange.com/questions/48949/epsg-3857-or-4326-for-web-mapping
+epsg4326 <- leafletCRS(crsClass = "L.CRS.EPSG4326")
+# BUT! It actually seems that Leaflet does still want shapefiles in 4326, see
+# https://github.com/Leaflet/Leaflet/issues/4146 I also tried to change GTMNERR 
+# to crs 3857 but that threw errors. See second paragraph here: 
+# https://rstudio.github.io/leaflet/articles/projections.html
+
+m <- leaflet(data = GTMNERR, 
+             options = leafletOptions(#crs = epsg4326,
+                                      minZoom = 9, 
+                                      maxZoom = 18)) %>%
   #setView(lng=-81.347388, lat=30.075, zoom = 11) %>% 
   clearBounds() %>% 
   addTiles() %>%  # Add default OpenStreetMap map tiles
@@ -32,7 +43,7 @@ HAB_data_locations <- HAB_data %>%
   distinct() %>% 
   st_as_sf(coords = c("Longitude", "Latitude"), crs = 4326)
 
-leaflet(options = leafletOptions(minZoom = 9, maxZoom = 18)) %>%
+leaflet(options = leafletOptions(crs = epsg4326, minZoom = 9, maxZoom = 18)) %>%
   setView(lng=-81.347388, lat=30.075, zoom = 11) %>% 
   # Base map
   addTiles() %>%  # Add default OpenStreetMap map tiles

global.R

@@ -40,10 +40,23 @@ try({
   print(paste0("Working dir: ", getwd()))
 }, silent = FALSE) # Setting silent = FALSE will print the error message to the console
 
-#### GTMNERR shapefile ------------------------------------------------
-GTMNERR <- st_read("./03_Data_for_app/shapefiles_new/GTMNERR.shp")
-GTMNERR <- st_transform(GTMNERR, crs = 4326)
+### Load shapefiles ------------------------------------------------
 
-#### county shapefiles ------------------------------------------------
+##### GTMNERR shapefile ------------------------------------------------
+GTMNERR <- st_read("./03_Data_for_app/shapefiles_new/GTMNERR_small_nosea.shp")
+
+##### county shapefiles ------------------------------------------------
 counties_select <- st_read("./03_Data_for_app/shapefiles_new/counties_GTMNERR.shp")
-counties_select <- st_transform(counties_select, crs = 4326)
+
+##### HUC shapefiles ------------------------------------------------
+HUC10 <- st_read("./03_Data_for_app/shapefiles_new/nhdwbd_huc10_dec17_GTMNERR.shp")
+HUC12 <- st_read("./03_Data_for_app/shapefiles_new/nhdwbd_huc12_dec17_GTMNERR.shp")
+
+##### Outstanding Florida Waters (OFW) shapefiles ------------------------------
+ofw <- st_read("./03_Data_for_app/shapefiles_new/ofw_GTMNERR.shp")
+
+##### mangrove shapefiles -----------------------------------------------------
+mangroves <- st_read("./03_Data_for_app/shapefiles_new/mangrove_GTMNERR.shp")
+
+##### salt marsh shapefiles -----------------------------------------------------
+saltmarsh <- st_read("./03_Data_for_app/shapefiles_new/salt_marsh_GTMNERR.shp")

modules/main_page.R

@@ -1,17 +1,56 @@
+
+#### Get WIN data locations
+# I am putting this here right now, but I feel we should move this to a cleaning
+# script so it doesn't need to be run every time someone uses the app (as with
+# WQ locations)
+WIN_df <- readRDS("./03_Data_for_app/WIN.Rds")
+
+WIN_data_locations = WIN_df %>%
+  filter(variable %in% c("geometry", 
+                         "HUC12.Name", 
+                         "Start.Date",
+                         "latitude",
+                         "longitude")
+  ) %>%
+  select(c(RowID, variable, value)) %>%
+  distinct(RowID, variable, value) %>%
+  pivot_wider(
+    names_from = variable,
+    values_from = value,
+    values_fill = list(value = NA)
+  ) %>%
+  distinct(geometry, HUC12.Name, Start.Date, latitude, longitude) %>%
+  mutate(
+    lat = as.numeric(latitude),
+    long = as.numeric(longitude),
+    type = "Water quality",
+    dataset = "Watershed Information Network (DEP)"
+  ) %>% 
+  select(-geometry, - latitude, -longitude)
+
+#### WQ locations data ------------------------------------------------
+WQ_data_locations <- readRDS("./03_Data_for_app/WQ_locations.Rds")
+
+# For now, for testing, make WQ_locations the dataframe to be used for filtering
+datasets_location <- full_join(WQ_data_locations, WIN_data_locations)
+datasets_location <- st_as_sf(datasets_location, coords = c("long", "lat"), crs = 4326)
+
+color_palette <- colorFactor(palette = c("red"), #, "blue", "green", "purple"
+                             domain = datasets_location$type)
+
+### Define the UI -------------------------------------------------------------
 mainPageUI <- function(id) {
   ns <- NS(id) # This is an important part to add to all subpages so they use the
   # correct sessions / ID's that connect the ui and server here
   tagList(
     h2("Main Page"),
     p("This is the main page of the Guana River Data Dashboard."),
+    # Dropdown menu for markers is above the map
     fluidRow(
-      # Map occupies 1st column
-      column(width = 10, leafletOutput(ns("map"), height=750)),
-      # histogram occupies rows in the 2nd column
-      # column(width = 5, plotOutput(ns("distPlot")),
-      #        sliderInput(ns("bins"), "Number of bins:", 
-      #                    min = 1, max = 50, value = 30)
-      # )
+      column(width = 7, uiOutput(ns("dropdown_ui"))),
+    ),
+    fluidRow(
+      column(width = 10, leafletOutput(ns("map"), height="500px")),
     ),
     # fluidRow(
     #   column(12, 
@@ -21,23 +60,21 @@ mainPageUI <- function(id) {
   )
 }
 
+### Define the server logic ----------------------------------------------------
 
 mainPageServer <- function(input, output, session) {
   ns <- session$ns
 
-  # Create the histogram
-  # output$distPlot <- renderPlot({
-  #   # generate bins based on input$bins from ui.R
-  #   x    <- filter(WQ,  ComponentShort == "ATEMP") %>% select(Result) %>% pull()
-  #   x <- as.numeric(x) # stop-gap measure because everything is characters
-  #   bins <- seq(min(x, na.rm = TRUE), max(x, na.rm = TRUE),
-  #               length.out = input$bins + 1)
-  #   
-  #   # draw the histogram with the specified number of bins
-  #   hist(x, breaks = bins, col = 'darkgray', border = 'white',
-  #        xlab = 'Air temperature (degrees Celsius)',
-  #        main = 'Histogram of air temperatures')
-  # })
+  # Create the dropdown UI
+  output$dropdown_ui <- renderUI({
+    print("Rendering dropdown UI")
+    selectInput(
+      inputId = ns("datatype_selector"),
+      label = "Select a type of data to see locations with data availability",
+      choices = unique(datasets_location$type),
+      selected = unique(datasets_location$type)[1]
+    )
+  })
 
   # Create the map
   output$map <- renderLeaflet({
@@ -55,22 +92,61 @@ mainPageServer <- function(input, output, session) {
                   highlightOptions = highlightOptions(color = "white", weight = 2,
                                                       bringToFront = TRUE),
                   group = "Counties", popup = ~NAME) %>% 
-      # addMarkers(data = HAB_data_locations,
-      #            popup = ~paste("Site: ", Site, "<br>",
-      #                           "County: ", County),
-      #            group = "HAB") %>% 
-      addMarkers(data = WQ_data_locations,
-                 popup = ~paste("Station: ", site_friendly, "<br>",
-                                "Location: ", wbid, "<br>",
-                                "Latest year of sampling: ", maxYear, "<br",
-                                "Sampling start year: ", minYear, "<br"),
-                 group = "WQ") %>% 
-      # # Layers control (turning layers on and off)
-      addLayersControl(overlayGroups = c("Counties", "GTMNERR boundaries", "WQ"),
-                       options = layersControlOptions(collapsed = FALSE)) %>%
+      addPolygons(data = mangroves, 
+                  color = "darkgreen", weight = 2, opacity = 1,
+                  fill = TRUE, fillColor = "darkgreen", fillOpacity = 0.4,
+                  group = "Mangroves") %>% #, popup = ~Area_ha
+      addPolygons(data = ofw, 
+                  color = "darkorange", weight = 2, opacity = 1,
+                  fill = TRUE, fillColor = "darkorange", fillOpacity = 0.4,
+                  group = "Outstanding Florida Waters") %>%
+      addPolygons(data = saltmarsh, 
+                  color = "darkslateblue", weight = 2, opacity = 1,
+                  fill = TRUE, fillColor = "darkslateblue", fillOpacity = 0.4,
+                  group = "Salt marshes") %>%
+      addPolygons(data = HUC10, 
+                  color = "royalblue", weight = 2, opacity = 1,
+                  fill = TRUE, fillColor = "royalblue", fillOpacity = 0.2,
+                  group = "HUC10", popup = ~NAME) %>%
+      addPolygons(data = HUC12, 
+                  color = "darkblue", weight = 2, opacity = 1,
+                  fill = TRUE, fillColor = "darkblue", fillOpacity = 0.2,
+                  group = "HUC12", popup = ~NAME) %>%
+      # Layers control (turning layers on and off)
+      addLayersControl(overlayGroups = c("GTMNERR boundaries", "Counties", 
+                                         "Mangroves", "Salt marshes",
+                                         "Outstanding Florida Waters", "HUC10",
+                                         "HUC12"),
+                       options = layersControlOptions(collapsed = TRUE)) %>%
+      hideGroup(c("Counties", "Mangroves", "Salt marshes",
+                  "Outstanding Florida Waters", "HUC10", "HUC12")) %>% 
       addMeasure(primaryLengthUnit = "miles", primaryAreaUnit = "sqmiles")
   })
 
+  # Select dataset to add markers to the plot
+  observeEvent(input$datatype_selector, {
+    # Filter data based on selected group
+    filtered_data <- datasets_location[datasets_location$type == input$datatype_selector,]
+
+    # Add markers to the map - commented out the popup bc this only works for WQ data
+    print("Adding markers")
+    leafletProxy(ns("map")) %>%
+      clearMarkers() %>%
+      addCircleMarkers(
+        data = filtered_data,
+        color = ~color_palette(type),
+        opacity = 1,
+        fillOpacity = 0.5,
+        fillColor = ~color_palette(type),
+        fill = TRUE,
+        weight = 3,
+        radius = 8,
+        # popup = ~paste("Station: ", site_friendly, "<br>",
+        #                                           "Location: ", wbid, "<br>",
+        #                                           "Latest year of sampling: ", maxYear, "<br",
+        #                                           "Sampling start year: ", minYear, "<br")
+      )
+  })
   # Add buttons to go to other pages
   # observeEvent(input[[ns("go_to_subpage")]], {
   #   print("Go to subpage button clicked")