This vignette demonstrates some subtleties of spatial subsetting of sf objects using base R and tidyvers methods.

The starting point is to load necessary packages:

library(sf)
library(spData)
library(tidyverse)

And subsetting canterbury and nz_height features in the region (as per Chapter 4 of the book):

canterbury = nz %>% filter(Name == "Canterbury")
canterbury_height = nz_height[canterbury, ]

Subsetting with intermediary objects

We can see how to get a list representation for subsetting:

sel_sgbp = st_intersects(x = nz_height, y = canterbury)
class(sel_sgbp)
## [1] "sgbp"
sel_logical = lengths(sel_sgbp) > 0
canterbury_height2 = nz_height[sel_logical, ]

And use the result with the tidyverse:

canterbury_height3 = nz_height %>% filter(sel_logical)

Dplyr changes row names

We can test whether the subsetted objects are identical as follows:

identical(x = canterbury_height, y = canterbury_height2)
## [1] TRUE
identical(x = canterbury_height, y = canterbury_height3)
## [1] FALSE

What is different about canterbury_height3? The only difference is that filter() changed the row names:

row.names(canterbury_height)[1:3]
## [1] "5" "6" "7"
row.names(canterbury_height3)[1:3]
## [1] "1" "2" "3"

If the row names are re-set, the objects become identical:

attr(canterbury_height3, "row.names") = attr(x = canterbury_height, "row.names")
identical(canterbury_height, canterbury_height3)
## [1] TRUE

This discarding of row names is not something that is specific to spatial data, as illustrated in the code chunk below. dplyr discards row names by design. For further discussion of this decision, and some controversy, see the (closed) issue #366 in the package’s issue tracker.

Dense matrices from spatial predicates

In the code below a dense matrix is created. sel is not, as one might imagine, a logical vector (although it behaves as one as it only has one column) but a logical matrix:

sel = st_intersects(nz_height, canterbury, sparse = FALSE)
class(sel)
## [1] "matrix"
typeof(sel)
## [1] "logical"
dim(sel)
## [1] 101   1

The dimensions of sel (returned by the base R command dim()) show one row per feature in the target object (nz_height) and a column per feature in the subsetting object (canterbury). The general pattern here is that sel[i, j] is TRUE if the ith feature in the target object intersects with the jth feature in the subsetting object. If there is more than one feature in y the resulting selection matrix must be converted into a vector before it is used for subsetting, e.g. with rowSums(sel_matrix) > 0. Another solution is to convert the default sparse matrix (list) output from st_intersects() to a logical vector using the function lengths(). This approach to spatial subsetting, used internally by sf (see the source code of sf:::`[.sf`), is illustrated in the code chunk below:

co = filter(nz, grepl("Canter|Otag", Name))
sel_sparse = st_intersects(nz_height, co)
sel_vector = lengths(sel_sparse) > 0
heights_co = nz_height[sel_vector, ]

The above code chunk results in an object, heights_co, that represents the high points that intersect with either Canterbury or Otago region (hence the object name co). It did this in four stages:

  1. Subset the regions of nz containing “Canter” or “Otago” in their names. This was done using the pattern matching function grepl() in combination with the | character, which means ‘or’, resulting in the subsetting object co.
  2. Create a sparse geometry binary predicate sgbp object, a list representing which features of nz_height intersect with the regions in co.
  3. Convert the selection list into a logical ‘selection vector’. lengths() finds the features in nz_height matching any features in co.
  4. Use the result to subset nz_heights, creating a new object heights_co.

More on subsetting in base R

Another spatial subsetting example will use an object representing the countries of Africa, created using attribute subsetting as follows:1

africa_wgs = world %>% filter(continent == "Africa")

To further prepare the input data, we will reproject the data to the coordinate reference system (CRS) 32630, its EPSG code (explained in Chapter 6):

africa = st_transform(africa_wgs, crs = 32630)

We can also use the [ operator for Spatial subsetting. The difference is that we use another spatial object inside the square brackets instead of an integer or logical vector. This is a concise and consistent syntax, as shown in the next code chunk. Let’s test it with a hypothetical scenario: we want to subset all countries within 2000 km of the point where the equator (where latitude = 0 degrees) intersects the prime meridian (longitude = 0 degrees), as illustrated in Figure @ref(fig:globe). The subsetting object is created below. Note that this must have the same CRS as the target object (set with the crs argument):

center_wgs = st_sf(geometry = st_sfc(st_point(c(0, 0)), crs = 4326))
center = st_transform(center_wgs, 32630)
buff = st_buffer(center, dist = 2e6)
Subsetting scenario: which countries intersect with a circle of 2000 km in radius located at zero degrees longitude and zero degrees latitude? Figure created with the globe package.

Subsetting scenario: which countries intersect with a circle of 2000 km in radius located at zero degrees longitude and zero degrees latitude? Figure created with the globe package.

The data to be subset, or ‘target layer’, is the africa object created above, which has a projected CRS (32630). Subsequently, spatial subsetting can be done with a single, concise command:

africa_buf = africa[buff, ]
If we were using geographic (‘lon/lat’) data the previous command would have emitted a message warning about assuming planar coordinates. This is because spatial operations (especially distance and area calculations) cannot be assumed to be accurate in a geographic (longitude/latitude) CRS. In this case one could justify the use of a lon/lat CRS: the data is close to the equator where there is least distortion caused by the curvature of the earth. It is good practice to reproject spatial datasets before performing spatial operations on them.

The spatial subsetting clearly worked: only countries intersecting with the giant circle are returned (Figure @ref(fig:africa-buff)):

plot(africa_buf["pop"])
plot(buff, add = TRUE)

Subset of the africa data selected based on their intersection with a circle 2000 km in radius with a center point at 0 degrees longitude and 0 degrees latitude.

Note that countries that just touch the giant circle are selected such as Chad (northeast of the circle). This is because the default subsetting operator is st_intersects(), which returns any type of spatial relation. Other spatial subsetting operations such as st_within() are more conservative, as shown in section @ref(topological-relations).

buff_agg = aggregate(x = africa[, "pop"], by = buff, FUN = sum)
## Simple feature collection with 1 feature and 1 field
## geometry type:  POLYGON
## dimension:      XY
## bbox:           xmin: -1166021 ymin: -2e+06 xmax: 2833979 ymax: 2e+06
## epsg (SRID):    32630
## proj4string:    +proj=utm +zone=30 +datum=WGS84 +units=m +no_defs
##         pop                       geometry
## 1 487896821 POLYGON ((2833979 0, 283123...
## Simple feature collection with 1 feature and 1 field
## geometry type:  POLYGON
## dimension:      XY
## bbox:           xmin: -1089434 ymin: -2163769 xmax: 4548370 ymax: 3043136
## epsg (SRID):    32630
## proj4string:    +proj=utm +zone=30 +datum=WGS84 +units=m +no_defs
##         pop                           geom
## 1 487896821 POLYGON ((-23422.38 484065....

The result, buff_agg, is a spatial object with the same geometry as by (the circular buffer in this case) but with an additional variable, pop reporting summary statistics for all features in x that intersect with by (the total population of the countries that touch the buffer in this case). Plotting the result (with plot(buff_agg)) shows that the operation does not really make sense: Figure @ref(fig:buff-agg) shows a population of over half a billion people mostly located in a giant circle floating off the west coast of Africa!

Result of spatial aggregation showing the total population of countries that intersect with a large circle whose center lies at 0 degrees longitude and latitude.

Result of spatial aggregation showing the total population of countries that intersect with a large circle whose center lies at 0 degrees longitude and latitude.

The results of the spatial aggregation exercise presented in Figure @ref(fig:buff-agg) are unrealistic for three reasons:

  • People do not live in the sea (the geometry of the aggregating object is not appropriate for the geometry target object).
  • This method would ‘double count’ countries whose borders cross aggregating polygons when multiple, spatially contiguous, features are used as the aggregating object.
  • It is wrong to assume that all the people living in countries that touch the buffer reside within it (the default spatial operator st_intersects() is too ‘greedy’). The most extreme example of this is Algeria, the most northerly country selected: the spatial aggregation operation assumes that all 39 million Algerian citizens reside in the tiny southerly tip that is within the circular buffer.

A number of methods can be used to overcome these issues, and generate a more realistic population attributed to the circular buffer illustrated in Figure @ref(fig:buff-agg). The simplest of these is to convert the country polygons into points representing their geographic centroids before aggregation. This would ensure that any spatially contiguous aggregating object covering the target object (the Earth in this case) would result in the same total: there would be no double counting. The estimated total population residing within the study area would be more realistic if geographic centroids were used. (The centroid of Algeria, for example, is far outside the aggregating buffer.)

Except in cases where the number of target features per aggregating feature is very large, or where the aggregating object is spatially congruent with the target, using centroids can also lead to errors due to boundary effects: imagine a buffer that covers a large area but contains no centroids. These issues can be tackled when aggregating areal target data with areal interpolation.


  1. Recall attribute subsetting can also be done in base R with africa_wgs = world[world$continent == "Africa", ].