Lab5

Doing this on hawks actually

Getting data

stern_observations <- occ_search(
  scientificName = "Sterna dougallii",
  country = "US",
  hasCoordinate = TRUE,
  limit = 2000
)$data


#or if you want a specific dataset you can do

stern_gbif <- occ_download_get(key = "0013929-260226173443078", overwrite = TRUE) %>%
occ_download_import(stern_gbif_download, na.strings = c("", NA))

## Download file size: 0.11 MB

## On disk at C:\Users\emles\EEB4100\hw_labs\0013929-260226173443078.zip

#Summarizing?

stern_gbif %>% count(occurrenceStatus, sort = TRUE)

## # A tibble: 1 × 2
##   occurrenceStatus     n
##   <chr>            <int>
## 1 PRESENT           3463

testing<- stern_gbif[1:100, ]

MApping

library(raster)

## Loading required package: sp

## 
## Attaching package: 'raster'

## The following object is masked from 'package:MASS':
## 
##     select

## The following object is masked from 'package:dplyr':
## 
##     select

temperature_raster <- raster("temperature/temperature.tif")
downsampled_temp <- aggregate(temperature_raster, fact = 4)


nyc_coords <- c(40.7128, -74.0060)
# Latitude and Longitude for Santo Domingo
santo_domingo_coords <- c(18.4861, -69.9312)
# Latitude and Longitude for Nassau
nassau_coords <- c(25.0343, -77.3963)

#more complex
map <- leaflet() %>% setView(lng = -79, lat = 37.8, zoom = 5) %>% addTiles() %>%
    addProviderTiles(providers$Esri.NatGeoWorldMap) %>%
    addProviderTiles(providers$OpenTopoMap) %>%
  
addCircleMarkers(data = stern_observations,
        ~decimalLongitude, ~decimalLatitude,
        color = "#FFB6C1", fillOpacity = 1, radius = 3,
        popup = ~paste(scientificName, "<br>", eventDate),
        group = "Stern observations") %>%
  
addRasterImage(downsampled_temp, colors = "cyan", opacity = 0.7, group = "Temperature") %>%
  
addLayersControl(
    overlayGroups = c("Sterna dougallii observations", "Temperature"),
    options = layersControlOptions(collapsed = FALSE)) %>%
    addLegend(position = "bottomright",
        colors = c("#FFB6C1", "cyan"),
        labels = c("Sterna dougallii observations", "Temperature"), opacity = 1) %>%

  addLegend("bottomleft", title = "Elevation",
      pal = colorNumeric(palette = c("lightgreen", "green", "darkgreen", "yellow","orange", "red"), domain = c(0, 2000)),
values = c(0, 2000),
labels = c("0-200m", "201-400m", "401-600m", "601-800m", "801-1000m", "1001-
2000m"),opacity = 1) %>%
  
  addMarkers(lng = nyc_coords[2], lat = nyc_coords[1], label = "New York City", labelOptions = labelOptions(noHide = TRUE)) %>%
  addMarkers(lng = santo_domingo_coords[2], lat = santo_domingo_coords[1], label = "Santo Domingo", labelOptions = labelOptions(noHide = TRUE)) %>%
  addMarkers(lng = nassau_coords[2], lat = nassau_coords[1], label = "Nassau", labelOptions = labelOptions(noHide = TRUE))

map