Map of Kelp Abundances

Load Libraries

library(googlesheets4) #handles data
library(dplyr) #for data manipulation
library(sf) #geospatial processing
library(measurements) #to make lat/long into decimal degrees
library(leaflet) #pretty scrollable Maps
library(leaflet.extras)

Load the Data

# Load in the data and turn degree/minute/second into latlong
kelp_labels <- read_sheet("https://docs.google.com/spreadsheets/d/1-fJVqQ6jRDgsIIi4C9FggdzqTQY2GRCy3Ic_pqtnhTs/edit?usp=sharing") |>
  mutate(Latitude = gsub("[(,)]", "", Latitude),
         Longitude = gsub("[(,)]", "", Longitude),
         Latitude = gsub("\\.0 ", " ", Latitude),
         Longitude = gsub("\\.0 ", " ", Longitude),
         Longitude = gsub("70 ", "-70 ", Longitude),
         ) |>
  mutate(Latitude = conv_unit(Latitude, 
                              from = "deg_min_sec", 
                              to = "dec_deg"),
         Longitude = conv_unit(Longitude, 
                              from = "deg_min_sec", 
                              to = "dec_deg"),
         )

# Convert the data into a sf spatial object with
# a coordinate reference system of lat/long with WGS84 
# https://epsg.io/4326
kelp_labels <- kelp_labels |>
  st_as_sf(coords = c("Longitude", "Latitude"),
           crs = 4326)

kelp_labels_filtered <- 
  kelp_labels |>
  filter(!is.na(`Kelp % Cover`))

Plot Kelp

First, a basic map for later use

base_map <- leaflet(kelp_labels_filtered) |>
    #the setup
      addProviderTiles(providers$Esri.WorldTopoMap, 
                       group = "Topo Map") |>
      addProviderTiles(providers$Esri.WorldImagery, 
                       group = "World Imagery") |>
      addProviderTiles(providers$Esri.WorldGrayCanvas, 
                       group = "ESRI World Gray Canvas",
                       options = providerTileOptions(noWrap = TRUE)) |>
      setView(lat = 42.5264892, lng = -70.8222588, zoom = 12) |>       addLayersControl(
        baseGroups = c("Topo Map", "ESRI World Gray Canvas", 
                       "World Imagery"),
        options = layersControlOptions(collapsed = FALSE)
      ) |>
    addFullscreenControl()

Now plot kelp

pal <- colorNumeric(
  palette = viridis::viridis_pal(option = "D")(5),
  domain = kelp_labels_filtered$`Kelp % Cover`)

base_map |>
  addCircleMarkers(radius = 5,
                   color = ~pal(`Kelp % Cover`)) |>
        addLegend("bottomright",
                pal = pal,
                values = kelp_labels_filtered$`Kelp % Cover`,
                title = "Kelp % Cover",
                opacity = 1
      ) 

Plot Vegetation

pal_veg <- colorNumeric(
  palette = viridis::viridis_pal(option = "G")(5),
  domain = kelp_labels_filtered$`Kelp % Cover`)

base_map |>
  addCircleMarkers(radius = 5,
                   color = ~pal_veg(`Non-Kelp Vegetation % Cover`)) |>
        addLegend("bottomright",
                pal = pal_veg,
                values = kelp_labels_filtered$`Non-Kelp Vegetation % Cover`,
                title = "Non-Kelp Vegetation % Cover",
                opacity = 1
      ) 

Warning in pal(c(r[1], cuts, r[2])): Some values were outside the color scale
and will be treated as NA

Warning in pal_veg(`Non-Kelp Vegetation % Cover`): Some values were outside the
color scale and will be treated as NA

Warning in pal_veg(`Non-Kelp Vegetation % Cover`): Some values were outside the
color scale and will be treated as NA

Plot Substrate

pal_veg <- colorNumeric(
  palette = viridis::viridis_pal(option = "E")(5),
  domain = kelp_labels_filtered$`Substrate % Cover`)

base_map |>
  addCircleMarkers(radius = 5,
                   color = ~pal_veg(`Substrate % Cover`)) |>
        addLegend("bottomright",
                pal = pal_veg,
                values = kelp_labels_filtered$`Substrate % Cover`,
                title = "Substrate % Cover",
                opacity = 1
      )