Spatial Data

Species Occurrences Map

A colleague of yours is working on a project on banner-tailed kangaroo rats (Dipodomys spectabilis) and is interested in what elevations these mice tend to occupy in the continental United States. You offer to help them out by getting some coordinates for specimens of this species and looking up the elevation of these coordinates.

1. Get banner-tailed kangaroo rat occurrences from GBIF, the Global Biodiversity Information Facility, using the spocc R package, which is designed to retrieve species occurrence data from various openly available data resources. Use the following code to do so:

    dipo_df = occ(query = "Dipodomys spectabilis", 
                from = "gbif",
                limit = 1000,
                has_coords = TRUE)
    dipo_df = data.frame(dipo_df$gbif$data)
   

2. Clean up the data by:
   • Using the rename function from dplyr to rename the second and third columns of this dataset to longitude and latitude
   • Filter the data to only include those specimens with Dipodomys_spectabilis.basisOfRecord that is PRESERVED_SPECIMEN and a Dipodomys_spectabilis.countryCode that is US
   • Remove points with values of 0 for latitude or longitude
   • Remove all of the columns from the dataset except latitude and longitude using select
   • Use head() function to show the top few rows of this cleaned dataset
3. Do the following to display the locations of these points on a map of the United States:
   • Get data for a US map using usmap = map_data("usa")
   • Plot it using geom_polygon. In the aesthetic use group = group to avoid weird lines cross your graph. Use fill = "white" and color = "black".
   • Plot the kangaroo rat locations
   • Use coord_quickmap() to automatically use a reasonable spatial projection

[click here for output] [click here for output]