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.

Start by getting 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)
```

Clean up the data by:
- 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 Dipodomys_spectabilis.latitude or Dipodomys_spectabilis.longitude
- Remove all of the columns from the dataset except Dipodomys_spectabilis.latitude and Dipodomys_spectabilis.longitude and rename these columns to latitude and longitude using select. You can rename while selecting columns using a format like this one select(new_column_name = old_column_name)
- Use the head() function to show the top few rows of this cleaned dataset
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]

Data Science for Biologists

Spatial Data

Species Occurrences Map