Mapping and geographic data analysis with the simple features package in R

Introducing sf and simple features in R

The simple features or sf R package allows geodata to be imported as objects with the type sf, which are essentially R data frames with the map geometry stored as coordinates in a variable called geometry. This allows you to work with geodata as you would with regular data frames or tibbles, using functions from the dplyr package and the rest of the tidyverse, including the charting package ggplot2 for making maps.

Load the packages we will use today

If you are working in the computers provided at the NICAR meeting, the packages listed in the code chunk below should already be installed. If you are working on your own computer, you will first need to install these packages. For sf to work correctly, you must also have the Geospatial Data Abstraction Library, or GDAL, installed on your computer. If you routinely work with QGIS, this should already be installed. If it is not, follow the instructions to install GDAL for your operating system given on the sf package home page.

Also if working on your own computer, click on the Materials link in the top navigation bar to download a zipped folder containing the data, notes, and code for this class, which is in the file r-sf-mapping-geo-analysis.Rmd. Open that file in RStudio, and switch to the Visual Markdown Editing view, by clicking the Visual button at top left above.

With the required packages all installed, run the code below to load them for use in the current session:

# load required packages
library(sf)
library(tidyverse)
library(tidygeocoder)

Import and examine geodata

First we will import the file seismic.geojson using the function st_read. The data contains a single variable ValueRange giving ranges for the annual percentage chance of experiencing a damaging earthquake across the continental US, as calculated by the US Geological Survey, plus the geometry for a map. The coordinates define polygons, or two-dimensional shapes.

# load geojson file
seismic <- st_read("seismic.geojson")

# examine the data
glimpse(seismic)
view(seismic)

Convert between geodata formats

sf objects can be exported to other common geodata formats using the st_write function, as shown in the following code chunk:

# save as kml
st_write(seismic, "seismic.kml", delete_dsn = TRUE)

# save as shapefile
dir.create("seismic")
st_write(seismic, "seismic/seismic.shp", delete_dsn = TRUE)

Including delete_dsn = TRUE in the st_write function allows any previously saved version to be overwritten, so exclude this from the code if you do not wish to allow this behavior. Shapefiles consist of multiple files, so the code to save as a shapefile first creates a folder to hold those files, and then writes the files into that folder.

Geocode addresses

Next we will use the tidygeocoder package to geocode the list of San Francisco addresses using the ArcGIS geocoder. The data is in the file addresses.tsv, which contains a single column with the header address.

# load addresses data
addresses <- read_tsv("addresses.tsv")

# geocode
addresses <- geocode(addresses,
                     address = address,
                     method = "arcgis",
                     full_results = TRUE)

# look at the geocoded data
view(addresses)

Including full_results = TRUE in this code provides some information about the estimated accuracy of the geocoding.

Convert a data frame with latitude and longitude coordinates into an sf object

We can now convert the geocoded data frame of San Francisco addresses to an sf object with the following code:

# convert to sf object with equirectangular projection (EPSG:4326)
addresses <- addresses %>%
  st_as_sf(coords = c("long","lat"),
           crs = st_crs("EPSG:4326"))

# examine data
view(addresses)

The function st_as_sf converts a regular data frame with latitude and longitude coordinates into an sf object. In this code "long" and "lat" are the names of the variables containing longitude and latitude coordinates. The sf object now has a geometry column containing the point coordinates.

Notice also that the st_as_sf function includes st_crs("EPSG:4326"). This sets the projection, or coordinate reference system, for the geometry.

Because the Earth is roughly spherical, any map other than a globe is a distortion of reality. Just as you can’t peel an orange and arrange the skin as a perfect rectangle, circle, or ellipse, it is impossible to plot the Earth’s surface in two dimensions and accurately represent distances, areas, shapes and directions. So maps rely on a projection or coordinate reference system to convert locations on a sphere to two-dimensional maps. Some projections are optimized to minimize the distortion of area; others aim to preserve shape or distance; yet others keep directions constant.

Projections have numeric codes, defined originally by the European Petroleum Survey Group.

Here are the codes for some common projections:

  • Equirectangular: EPSG:4326 Plots degrees of latitude against degrees of longitude. Used in the code above.

  • Web Mercator: EPSG:3857 Used for OpenStreetMap and other web maps. Mercator was originally designed for navigation and keeps direction/compass bearing constant.

  • Albers Equal Area Conic, centered on continental US: EPSG:5070 Keeps areas constant, widely used for maps of the entire US.

  • Mollweide: ESRI:54009 Equal area projection suitable for mapping the entire world.

  • Robinson: ESRI:54030 A “compromise” projection for showing the entire world, minimizes distortion across each of area, shape, distance, and compass bearing but represents none of them perfectly.

Search here for projection codes.

Change the projection of an sf object

You can change the projection of an sf object with the function st_transform and check the projection of an sf object with the function st_crs:

# change projection to Web Mercator
addresses <- addresses %>%
  st_transform("EPSG:3857")

# what is the projection?
st_crs(addresses)
# change projection back to equirectangular
addresses <- addresses %>%
  st_transform("EPSG:4326")

# what is the projection?
st_crs(addresses)

Make a map showing the annual risk of damaging quakes in the continental US

Before making a map from the seismic data, we will convert the ValueRange variable from text to a categorical variable, or factor, with the values arranged in increasing order of risk. This will ensure that the colors get applied to the values in the ascending order of risk.

This is achieved with the following code:

# convert to ordered factor/categorical variable
seismic <- seismic %>%
  mutate(ValueRange = factor(ValueRange,
                             levels = c("< 1","1 - 2","2 - 5","5 - 10","10 - 14")))

Let’s also check the projection of the data:

# what is the projection of the seismic risk data?
st_crs(seismic)

This reveals that the data is in EPSG:4326.

The following code creates a map of the annual risk of experiencing a damaging quake with ggplot2:

# make a map of the annual risk of experiencing a damaging quake in the continental US
ggplot() +
  geom_sf(data = seismic,
          aes(fill = ValueRange), 
          linewidth = 0,
          color = NA) +
  scale_fill_brewer(palette = "Reds",
                    name = "% chance") +
  coord_sf(crs = "EPSG:5070",
           default_crs = "EPSG:4326") +
  theme_void()

geom_sf will add a layer to a ggplot2 map from an sf object, plotting points, lines, or polygons (i.e. two-dimensional shapes that can be filled with color) depending on the coordinates stored in the geometry variable.

In the code above, the seismic risk data is added inside the geom_sf function and then the color to fill the polygons with is set to the values in ValueRange using an aes function. linewidth = 0 sets the size of boundary lines between the different seismic risk zones to zero, so they do not appear; color = NA should be redundant, but ensures that any line has no color.

The scale_fill_brewer function is then used to apply a ColorBrewer palette to the data.

coord_sf applies a custom projection to the map. crs = "EPSG:5070" applies an Albers Equal Area Conic projection, centered on the continental US; default_crs = "EPSG:4326" defines the pre-existing projection of the data, so that the conversion is handled correctly.

theme_void is a ggplot2 theme that is good for maps because it omits grid lines, axes, and so on.

Add data on historical earthquakes to the map

Now we will add data on earthquakes to the map. The code below loads GeoJSON returned from the US Geological Survey earthquakes search API for quakes larger than magnitude 5.5 since the beginning of 1960 within 3,000 kilometers of the geographic center of the continental US:

# load quakes data from USGS earthquakes API
quakes <- st_read("https://earthquake.usgs.gov/fdsnws/event/1/query?starttime=1960-01-01T00:00:00&minmagnitude=5.5&format=geojson&latitude=39.828175&longitude=-98.5795&maxradiuskm=3000&orderby=magnitude") 

# examine the data
view(quakes)

Looking at the data, the geometry column contains three coordinates. The first two give latitude and longitude in degrees. The third is depth of the quake in kilometers and may create a problem when we try to map the points. This can be solved by removing that dimension from the coordinates with the function st_zm.

# remove the depth dimension from the coordinates
quakes <- quakes %>%
  st_zm()

We should also check the projection:

# what is the projection of the quakes data?
st_crs(quakes)

Again, the projection is EPSG:4326. Before making a map in ggplot2 with multiple sf layers, make sure they are all in the same projection so that they can all be handled in the same way by the coord_sf function. I would recommend EPSG:4326.

Now we can add the quakes to the map:

# add the historical quakes to the map
ggplot() +
  geom_sf(data = seismic,
          aes(fill = ValueRange), 
          linewidth = 0,
          color = NA) +
  geom_sf(data = quakes,
          alpha = 0.1,
          aes(size = 10^mag)) +
  scale_fill_brewer(palette = "Reds",
                    name = "% chance" ) +
  scale_size_area(max_size = 20, guide = "none") +
  coord_sf(crs = "EPSG:5070",
           default_crs = "EPSG:4326") +
  theme_void()

The code above adds the quakes using another geom_sf layer, making them 90% transparent by setting their opacity with alpha = 0.1. The points are sized using an aes function according to the values of 10 raised to the power of mag, or the magnitude of each quake. Using this formula is a quirk of working with earthquakes, where magnitude is measured on a logarithmic scale, so that a difference of 1 corresponds to a 10-fold difference in earth movement, as recorded on a seismograph. Raising 10 to the power of the earthquake magnitude correctly scales the circles according to the amount of shaking they caused.

When scaling circles on a map for most forms of data you would simply set size to correspond to the values of a variable in the data.

The maximum size for the resulting circles is then set using the scale_size_area function; guide = "none" prevents a legend for size being drawn for the size of the circles. Using scale_size_area also ensures that the circles scale correctly by area right down to a value of zero; without this there will be a minimum size below which the points will not scale with the data values.

Add a basemap showing neighboring countries, and zoom into the continental US

The map as it currently stands has no wider context for the positions of nearby quakes that occurred outside of the boundaries of the continental US, and is now zoomed out to the 3,000km-radius circle containing all of the quakes we pulled from the USGS API. So now we will add data for the world’s nations and change the zoom of the map.

The data used is from Natural Earth, a widely used repository of geodata, converted to a local GeoJSON file. It can also be accessed from R directly using the rnaturalearth package.

# load a world map of country boundaries
countries <- st_read("countries.geojson")

Now we can add this layer to the map beneath the seismic risk and quakes layers with a third geom_sf function, setting the fill to a light gray defined by the hex code #cccccc and the country borders to white. Altering size for this geom_sf layer will change the thickness of the border lines.

# add the countries layer and zoom into the continental US
ggplot() +
  geom_sf(data = countries,
          fill = "#cccccc",
          color = "white",
          linewidth = 0.3) +
  geom_sf(data = seismic,
          aes(fill = ValueRange), 
          linewidth = 0,
          color = NA) +
  geom_sf(data = quakes,
          alpha = 0.1,
          aes(size = 10^mag)) +
  scale_fill_brewer(palette = "Reds",
                    name = "% chance") +
  scale_size_area(max_size = 20, guide = "none") +
  coord_sf(crs = "EPSG:5070",
           default_crs = "EPSG:4326",
           xlim = c(-135,-65),
           ylim = c(20,55)) +
  theme_void()