Spatial data handling

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Spatial data handling in R

Packages for Spatial Data

Packages:

sp First major spatial data package/format
raster raster (gridded) data
terra raster (gridded) data
sf Spatial Features in the ‘tidyverse’
and a few others…

What is a Spatial Feature (sf)?

Typically a ‘vector-based’ represntation of an object in the real world:

Geometry

Features have a geometry describing where on Earth the feature is located, and they have attributes, which describe other properties.

A Tree:

delineation of its crown
its stem
point indicating its centre

Attributes:

species
height
diameter
date

Spatial Features

What information do we need to store in order to define points, lines, polygons in geographic space?

lat (\(y\))
lon (\(x\))
elevation/altitude (\(z\))
measure (\(m\), rarely used) associated with the point, rather than with the feature as a whole (e.g. coordinate measurement error)
projection
what type (point/line/poly)
if polygon, is it a hole or not
attribute data
… ?

`sp` package

`sp` Package

First to provide classes and methods to create spatial points, lines, polygons, and grids.
~350 spatial analysis packages use sp data types
Important to know how to convert sp to and from sf objects
Recommend using sf methods instead and convert only when necessary.

`sf` Package

Simple feature geometry types

The following seven simple feature types are the most common, and are for instance the only ones used for GeoJSON:

type	description
`POINT`	a single point
`LINESTRING`	sequence of points connected by lines
`POLYGON`	sequence of points form a closed ring
`MULTIPOINT`	set of points
`MULTILINESTRING`	set of linestrings
`MULTIPOLYGON`	set of polygons
`GEOMETRYCOLLECTION`	set of geometries

Uncommon Geometry Types

10 more geometries 10 are rare:

CIRCULARSTRING
COMPOUNDCURVE
CURVEPOLYGON
MULTICURVE
MULTISURFACE
CURVE
SURFACE
POLYHEDRALSURFACE
TIN
TRIANGLE

Coordinate reference system

Coordinates only have meaning on the Earth’s surface when their coordinate reference system (CRS) is known.

Overview of projection systems

Reproject to “Goode Homolosine” projection

data(world) # from spData package
st_crs(world)

## Coordinate Reference System:
##   User input: EPSG:4326 
##   wkt:
## GEOGCRS["WGS 84",
##     DATUM["World Geodetic System 1984",
##         ELLIPSOID["WGS 84",6378137,298.257223563,
##             LENGTHUNIT["metre",1]]],
##     PRIMEM["Greenwich",0,
##         ANGLEUNIT["degree",0.0174532925199433]],
##     CS[ellipsoidal,2],
##         AXIS["geodetic latitude (Lat)",north,
##             ORDER[1],
##             ANGLEUNIT["degree",0.0174532925199433]],
##         AXIS["geodetic longitude (Lon)",east,
##             ORDER[2],
##             ANGLEUNIT["degree",0.0174532925199433]],
##     USAGE[
##         SCOPE["Horizontal component of 3D system."],
##         AREA["World."],
##         BBOX[-90,-180,90,180]],
##     ID["EPSG",4326]]

Reproject to “Goode Homolosine” projection

world_homolosine=world %>% 
  st_transform(crs = "+proj=goode")

p1 <- ggplot(world,aes(fill=gdpPercap),color=NA)+
  geom_sf()
p2 <- ggplot(world_homolosine,aes(fill=gdpPercap))+
  geom_sf()

ggarrange(p1,p2,common.legend = T,legend = "right")

Reproject to “Goode Homolosine” projection

p1 <- ggplot(world,aes(fill=gdpPercap),color=NA)+
  geom_sf()
p2 <- p1+coord_sf(crs="+proj=goode")

ggarrange(p1,p2,common.legend = T,legend = "right")

Defining a projection

EPSG code
- EPSG:4326
Proj4 String
- +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs
WKT (well known text) string

GEOGCS["WGS 84", 
    DATUM["WGS_1984", 
        SPHEROID["WGS 84",6378137,298.257223563,
            AUTHORITY["EPSG","7030"]],  
        AUTHORITY["EPSG","6326"]],  
    PRIMEM["Greenwich",0,  
        AUTHORITY["EPSG","8901"]],  
    UNIT["degree",0.01745329251994328,  
        AUTHORITY["EPSG","9122"]],  
    AUTHORITY["EPSG","4326"]]

spatialreference.org proj.org

How simple features in R are organized

Like PostGIS, all functions in sf prefixed by st_ (spatial and temporal). Easily findable by command-line completion.

Objects stored in data.frame objects (or tbl_df)
Feature geometries in a single data.frame column (as a list).
Each list element holding the simple feature geometry of that feature (e.g. point, polygon)

glimpse(world)

## Rows: 177
## Columns: 11
## $ iso_a2    <chr> "FJ", "TZ", "EH", "CA", "US", "KZ", "UZ", "PG", "ID", "AR", …
## $ name_long <chr> "Fiji", "Tanzania", "Western Sahara", "Canada", "United Stat…
## $ continent <chr> "Oceania", "Africa", "Africa", "North America", "North Ameri…
## $ region_un <chr> "Oceania", "Africa", "Africa", "Americas", "Americas", "Asia…
## $ subregion <chr> "Melanesia", "Eastern Africa", "Northern Africa", "Northern …
## $ type      <chr> "Sovereign country", "Sovereign country", "Indeterminate", "…
## $ area_km2  <dbl> 19289.97, 932745.79, 96270.60, 10036042.98, 9510743.74, 2729…
## $ pop       <dbl> 885806, 52234869, NA, 35535348, 318622525, 17288285, 3075770…
## $ lifeExp   <dbl> 69.96000, 64.16300, NA, 81.95305, 78.84146, 71.62000, 71.039…
## $ gdpPercap <dbl> 8222.2538, 2402.0994, NA, 43079.1425, 51921.9846, 23587.3375…
## $ geom      <MULTIPOLYGON [°]> MULTIPOLYGON (((-180 -16.55..., MULTIPOLYGON ((…

Components

sf, the table (data.frame) with feature attributes and feature geometries, which contains
sfc, the list-column with the geometries for each feature (record), which is composed of
sfg, the feature geometry of an individual simple feature.

If you work with PostGis or GeoJSON you may have come across the WKT (well-known text) format, for example like these:

POINT (30 10)
LINESTRING (30 10, 10 30, 40 40)
POLYGON ((30 10, 40 40, 20 40, 10 20, 30 10))

sf implements this standard natively in R. Data are structured and conceptualized very differently from the sp approach.

sf Highlights

provides fast I/O, particularly relevant for large files
directly reads from and writes to spatial databases such as PostGIS
compatibile with the tidyverse
ggplot compatible with geom_sf()

sp and sf are not only formats for spatial objects. Other spatial packages may use their own class definitions for spatial data (for example spatstat). Usually you can find functions that convert sp and increasingly sf objects to and from these formats.

world_sp = as(world, "Spatial")
world_sf = st_as_sf(world_sp)
str(world_sp)

## Formal class 'SpatialPolygonsDataFrame' [package "sp"] with 5 slots
##   ..@ data       :'data.frame':  177 obs. of  10 variables:
##   .. ..$ iso_a2   : chr [1:177] "FJ" "TZ" "EH" "CA" ...
##   .. ..$ name_long: chr [1:177] "Fiji" "Tanzania" "Western Sahara" "Canada" ...
##   .. ..$ continent: chr [1:177] "Oceania" "Africa" "Africa" "North America" ...
##   .. ..$ region_un: chr [1:177] "Oceania" "Africa" "Africa" "Americas" ...
##   .. ..$ subregion: chr [1:177] "Melanesia" "Eastern Africa" "Northern Africa" "Northern America" ...
##   .. ..$ type     : chr [1:177] "Sovereign country" "Sovereign country" "Indeterminate" "Sovereign country" ...
##   .. ..$ area_km2 : num [1:177] 19290 932746 96271 10036043 9510744 ...
##   .. ..$ pop      : num [1:177] 8.86e+05 5.22e+07 NA 3.55e+07 3.19e+08 ...
##   .. ..$ lifeExp  : num [1:177] 70 64.2 NA 82 78.8 ...
##   .. ..$ gdpPercap: num [1:177] 8222 2402 NA 43079 51922 ...
##   ..@ polygons   :List of 177
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. .. .. ..@ Polygons :List of 3
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -179.9 -16.3
##   .. .. .. .. .. .. ..@ area   : num 0.067
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:5, 1:2] -180 -180 -180 -180 -180 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 178 -17.8
##   .. .. .. .. .. .. ..@ area   : num 0.984
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:9, 1:2] 178 178 179 179 178 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 179.3 -16.6
##   .. .. .. .. .. .. ..@ area   : num 0.589
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:8, 1:2] 180 179 179 179 179 ...
##   .. .. .. ..@ plotOrder: int [1:3] 2 3 1
##   .. .. .. ..@ labpt    : num [1:2] 178 -17.8
##   .. .. .. ..@ ID       : chr "1"
##   .. .. .. ..@ area     : num 1.64
##   .. .. .. ..$ comment: chr "0 0 0"
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. .. .. ..@ Polygons :List of 1
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 34.75 -6.26
##   .. .. .. .. .. .. ..@ area   : num 76.3
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:52, 1:2] 33.9 34.1 37.7 37.8 39.2 ...
##   .. .. .. ..@ plotOrder: int 1
##   .. .. .. ..@ labpt    : num [1:2] 34.75 -6.26
##   .. .. .. ..@ ID       : chr "2"
##   .. .. .. ..@ area     : num 76.3
##   .. .. .. ..$ comment: chr "0"
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. .. .. ..@ Polygons :List of 1
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -12.1 24.3
##   .. .. .. .. .. .. ..@ area   : num 8.6
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:28, 1:2] -8.67 -8.67 -8.68 -8.69 -11.97 ...
##   .. .. .. ..@ plotOrder: int 1
##   .. .. .. ..@ labpt    : num [1:2] -12.1 24.3
##   .. .. .. ..@ ID       : chr "3"
##   .. .. .. ..@ area     : num 8.6
##   .. .. .. ..$ comment: chr "0"
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. .. .. ..@ Polygons :List of 30
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -132.3 53.4
##   .. .. .. .. .. .. ..@ area   : num 1.57
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:11, 1:2] -133 -132 -132 -131 -132 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -126 49.6
##   .. .. .. .. .. .. ..@ area   : num 4.06
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:16, 1:2] -124 -124 -126 -126 -127 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -119.2 76.8
##   .. .. .. .. .. .. ..@ area   : num 6.08
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:12, 1:2] -123 -123 -121 -119 -118 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -101.6 57.7
##   .. .. .. .. .. .. ..@ area   : num 1281
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:274, 1:2] -123 -123 -125 -126 -127 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -121.5 72.9
##   .. .. .. .. .. .. ..@ area   : num 20.1
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:17, 1:2] -122 -120 -118 -117 -116 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -111.7 77.8
##   .. .. .. .. .. .. ..@ area   : num 1.69
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:7, 1:2] -111 -110 -110 -112 -114 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -111.3 78.6
##   .. .. .. .. .. .. ..@ area   : num 0.793
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:7, 1:2] -111 -110 -111 -113 -113 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -111.6 75.5
##   .. .. .. .. .. .. ..@ area   : num 14.3
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:22, 1:2] -108 -107 -106 -106 -106 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -105.6 73.3
##   .. .. .. .. .. .. ..@ area   : num 1.16
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:6, 1:2] -107 -105 -104 -105 -107 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -110.5 70.8
##   .. .. .. .. .. .. ..@ area   : num 54.4
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:45, 1:2] -107 -105 -105 -104 -103 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -102.6 78.6
##   .. .. .. .. .. .. ..@ area   : num 3.98
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:11, 1:2] -105.5 -103.5 -100.8 -100.1 -99.7 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -99.2 72.6
##   .. .. .. .. .. .. ..@ area   : num 9.4
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:15, 1:2] -100.4 -101.5 -100.4 -99.2 -97.4 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -99.8 75.8
##   .. .. .. .. .. .. ..@ area   : num 6.11
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:13, 1:2] -98.5 -97.7 -97.7 -98.2 -99.8 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -97.2 78.4
##   .. .. .. .. .. .. ..@ area   : num 2.14
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:9, 1:2] -96.8 -95.6 -95.8 -97.3 -98.1 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -97.6 69.4
##   .. .. .. .. .. .. ..@ area   : num 2.94
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:11, 1:2] -96.3 -95.6 -96.3 -97.6 -98.4 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -91.6 79.7
##   .. .. .. .. .. .. ..@ area   : num 19.4
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:21, 1:2] -96 -95.3 -94.3 -94.7 -92.4 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -93.8 73.3
##   .. .. .. .. .. .. ..@ area   : num 7.12
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:11, 1:2] -94.5 -92.4 -90.5 -92 -93.2 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -95.1 77.7
##   .. .. .. .. .. .. ..@ area   : num 0.711
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:7, 1:2] -93.8 -94.3 -96.2 -96.4 -94.4 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -95.1 75.1
##   .. .. .. .. .. .. ..@ area   : num 2.18
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:8, 1:2] -93.6 -94.2 -95.6 -96.8 -96.3 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -78.6 80.4
##   .. .. .. .. .. .. ..@ area   : num 105
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:65, 1:2] -91.6 -90.1 -88.9 -87 -85.5 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -88.1 75.4
##   .. .. .. .. .. .. ..@ area   : num 19.2
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:28, 1:2] -88.2 -89.8 -92.4 -92.8 -92.9 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -83 62.6
##   .. .. .. .. .. .. ..@ area   : num 1.04
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:7, 1:2] -84 -83.3 -81.9 -81.9 -83.1 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -84.1 64.3
##   .. .. .. .. .. .. ..@ area   : num 7.97
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:20, 1:2] -83.9 -82.8 -81.6 -81.6 -80.8 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -79.8 62
##   .. .. .. .. .. .. ..@ area   : num 0.532
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:8, 1:2] -80.3 -79.9 -79.5 -79.3 -79.7 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -78.8 73.2
##   .. .. .. .. .. .. ..@ area   : num 3.15
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:11, 1:2] -79.8 -80.9 -80.8 -80.4 -78.1 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -74.9 68.6
##   .. .. .. .. .. .. ..@ area   : num 118
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:73, 1:2] -78.8 -77.8 -75.6 -74.2 -74.1 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -76.2 67.7
##   .. .. .. .. .. .. ..@ area   : num 1.92
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:9, 1:2] -75.2 -75.9 -77 -77.2 -76.8 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -63.1 49.5
##   .. .. .. .. .. .. ..@ area   : num 0.97
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:8, 1:2] -64.5 -64.2 -62.9 -61.8 -61.8 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -63.3 46.4
##   .. .. .. .. .. .. ..@ area   : num 0.873
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
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##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
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##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
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##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
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##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
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##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 106.3 16.7
##   .. .. .. .. .. .. ..@ area   : num 28.6
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:44, 1:2] 104 105 106 106 107 ...
##   .. .. .. ..@ plotOrder: int 1
##   .. .. .. ..@ labpt    : num [1:2] 106.3 16.7
##   .. .. .. ..@ ID       : chr "95"
##   .. .. .. ..@ area     : num 28.6
##   .. .. .. ..$ comment: chr "0"
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. .. .. ..@ Polygons :List of 2
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 127.2 40.1
##   .. .. .. .. .. .. ..@ area   : num 13.3
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:44, 1:2] 131 131 131 130 130 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 130.8 42.2
##   .. .. .. .. .. .. ..@ area   : num 5.06e-12
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:4, 1:2] 130.8 130.8 130.8 130.8 42.2 ...
##   .. .. .. ..@ plotOrder: int [1:2] 1 2
##   .. .. .. ..@ labpt    : num [1:2] 127.2 40.1
##   .. .. .. ..@ ID       : chr "96"
##   .. .. .. ..@ area     : num 13.3
##   .. .. .. ..$ comment: chr "0 0"
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. .. .. ..@ Polygons :List of 1
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 127.8 36.4
##   .. .. .. .. .. .. ..@ area   : num 9.95
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:19, 1:2] 126 126 127 127 128 ...
##   .. .. .. ..@ plotOrder: int 1
##   .. .. .. ..@ labpt    : num [1:2] 127.8 36.4
##   .. .. .. ..@ ID       : chr "97"
##   .. .. .. ..@ area     : num 9.95
##   .. .. .. ..$ comment: chr "0"
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. .. .. ..@ Polygons :List of 1
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 102.9 46.8
##   .. .. .. .. .. .. ..@ area   : num 182
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:75, 1:2] 87.8 88.8 90.7 92.2 93.1 ...
##   .. .. .. ..@ plotOrder: int 1
##   .. .. .. ..@ labpt    : num [1:2] 102.9 46.8
##   .. .. .. ..@ ID       : chr "98"
##   .. .. .. ..@ area     : num 182
##   .. .. .. ..$ comment: chr "0"
##   .. ..$ :Formal class 'Polygons' [package "sp"] with 5 slots
##   .. .. .. ..@ Polygons :List of 1
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] 79.6 22.9
##   .. .. .. .. .. .. ..@ area   : num 278
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:136, 1:2] 97.3 97.4 97.1 97.1 96.4 ...
##   .. .. .. ..@ plotOrder: int 1
##   .. .. .. ..@ labpt    : num [1:2] 79.6 22.9
##   .. .. .. ..@ ID       : chr "99"
##   .. .. .. ..@ area     : num 278
##   .. .. .. ..$ comment: chr "0"
##   .. .. [list output truncated]
##   ..@ plotOrder  : int [1:177] 160 19 4 5 140 30 138 23 6 10 ...
##   ..@ bbox       : num [1:2, 1:2] -180 -89.9 180 83.6
##   .. ..- attr(*, "dimnames")=List of 2
##   .. .. ..$ : chr [1:2] "x" "y"
##   .. .. ..$ : chr [1:2] "min" "max"
##   ..@ proj4string:Formal class 'CRS' [package "sp"] with 1 slot
##   .. .. ..@ projargs: chr "+proj=longlat +datum=WGS84 +no_defs"
##   .. .. ..$ comment: chr "GEOGCRS[\"WGS 84\",\n    DATUM[\"World Geodetic System 1984\",\n        ELLIPSOID[\"WGS 84\",6378137,298.257223"| __truncated__
##   ..$ comment: chr "TRUE"

str(world)

## sf [177 × 11] (S3: sf/tbl_df/tbl/data.frame)
##  $ iso_a2   : chr [1:177] "FJ" "TZ" "EH" "CA" ...
##  $ name_long: chr [1:177] "Fiji" "Tanzania" "Western Sahara" "Canada" ...
##  $ continent: chr [1:177] "Oceania" "Africa" "Africa" "North America" ...
##  $ region_un: chr [1:177] "Oceania" "Africa" "Africa" "Americas" ...
##  $ subregion: chr [1:177] "Melanesia" "Eastern Africa" "Northern Africa" "Northern America" ...
##  $ type     : chr [1:177] "Sovereign country" "Sovereign country" "Indeterminate" "Sovereign country" ...
##  $ area_km2 : num [1:177] 19290 932746 96271 10036043 9510744 ...
##  $ pop      : num [1:177] 8.86e+05 5.22e+07 NA 3.55e+07 3.19e+08 ...
##  $ lifeExp  : num [1:177] 70 64.2 NA 82 78.8 ...
##  $ gdpPercap: num [1:177] 8222 2402 NA 43079 51922 ...
##  $ geom     :sfc_MULTIPOLYGON of length 177; first list element: List of 3
##   ..$ :List of 1
##   .. ..$ : num [1:5, 1:2] -180 -180 -180 -180 -180 ...
##   ..$ :List of 1
##   .. ..$ : num [1:9, 1:2] 178 178 177 177 178 ...
##   ..$ :List of 1
##   .. ..$ : num [1:8, 1:2] 180 180 179 179 179 ...
##   ..- attr(*, "class")= chr [1:3] "XY" "MULTIPOLYGON" "sfg"
##  - attr(*, "sf_column")= chr "geom"
##  - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA NA NA NA NA NA NA NA NA
##   ..- attr(*, "names")= chr [1:10] "iso_a2" "name_long" "continent" "region_un" ...

The structures in the sp packages are more complicated - str(world_sf) vs str(world_sp)
Moreover, many of the sp functions are not “pipeable” (it’s hard to combine them with the tidyverse)

world_sp %>% 
  filter(name_long == "United Kingdom")

Error in UseMethod("filter_") : no applicable method for 'filter_' applied to an object of class "c('SpatialPolygonsDataFrame', 'SpatialPolygons', 'Spatial', 'SpatialPolygonsNULL', 'SpatialVector')"

world %>% 
  filter(name_long == "United Kingdom")%>%
  ggplot()+geom_sf()

Reading and writing spatial data

vector_filepath = system.file("shapes/world.gpkg", package = "spData")
vector_filepath

## [1] "/Users/adamw/Library/R/arm64/4.4/library/spData/shapes/world.gpkg"

world = st_read(vector_filepath)

## Reading layer `world' from data source 
##   `/Users/adamw/Library/R/arm64/4.4/library/spData/shapes/world.gpkg' 
##   using driver `GPKG'
## Simple feature collection with 177 features and 10 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -180 ymin: -89.9 xmax: 180 ymax: 83.64513
## Geodetic CRS:  WGS 84

Counterpart to st_read() is the st_write function, e.g. st_write(world, 'data/new_world.gpkg'). A full list of supported formats could be found using sf::st_drivers().

Structure of the sf objects

world

## Simple feature collection with 177 features and 10 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -180 ymin: -89.9 xmax: 180 ymax: 83.64513
## Geodetic CRS:  WGS 84
## First 3 features:
##   iso_a2      name_long continent region_un       subregion              type
## 1     FJ           Fiji   Oceania   Oceania       Melanesia Sovereign country
## 2     TZ       Tanzania    Africa    Africa  Eastern Africa Sovereign country
## 3     EH Western Sahara    Africa    Africa Northern Africa     Indeterminate
##    area_km2      pop lifeExp gdpPercap                           geom
## 1  19289.97   885806  69.960  8222.254 MULTIPOLYGON (((-180 -16.55...
## 2 932745.79 52234869  64.163  2402.099 MULTIPOLYGON (((33.90371 -0...
## 3  96270.60       NA      NA        NA MULTIPOLYGON (((-8.66559 27...

class(world)

## [1] "sf"         "data.frame"

Structure of the sf objects

world$name_long

## [1] "Fiji"           "Tanzania"       "Western Sahara"

world$geom

## Geometry set for 177 features 
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -180 ymin: -89.9 xmax: 180 ymax: 83.64513
## Geodetic CRS:  WGS 84
## First 3 geometries:

## MULTIPOLYGON (((-180 -16.55522, -179.9174 -16.5...

## MULTIPOLYGON (((33.90371 -0.95, 31.86617 -1.027...

## MULTIPOLYGON (((-8.66559 27.65643, -8.817828 27...

Non-spatial operations on the sf objects

world %>% 
  left_join(worldbank_df, by = "iso_a2") %>%
  dplyr::select(name_long, pop, pop_growth, area_km2) %>%
  mutate(pop_density = pop/area_km2) %>%
  rename(population = pop) %>% 
  arrange(desc(pop_density))%>%
  kable()

name_long	population	pop_growth	area_km2	pop_density	geom
Bangladesh	159405279	1.1571880	133782.141	1191.5288342	MULTIPOLYGON (((92.67272 22…
Palestine	4294682	2.9579950	5037.104	852.6093860	MULTIPOLYGON (((35.39756 31…
Lebanon	5603279	6.0164395	10099.003	554.8348665	MULTIPOLYGON (((35.8211 33….
Republic of Korea	50746659	0.6281499	99044.367	512.3628998	MULTIPOLYGON (((126.1748 37…
Rwanda	11345357	2.5007965	23365.411	485.5620518	MULTIPOLYGON (((30.4191 -1….
Netherlands	16865008	0.3598282	40024.104	421.3712766	MULTIPOLYGON (((6.90514 53….
India	1293859294	1.1893282	3142892.098	411.6779240	MULTIPOLYGON (((97.32711 28…
Puerto Rico	3534874	-1.6331283	9224.663	383.1981652	MULTIPOLYGON (((-66.28243 1…
Burundi	9891790	2.9922647	26238.948	376.9888203	MULTIPOLYGON (((30.46967 -2…
Belgium	11209057	0.2343708	30126.038	372.0720608	MULTIPOLYGON (((6.156658 50…
Haiti	10572466	1.3396542	28540.546	370.4367115	MULTIPOLYGON (((-71.71236 1…
Israel	8215700	1.9195438	22991.166	357.3416011	MULTIPOLYGON (((35.71992 32…
Philippines	100102249	1.6328192	292256.939	342.5145326	MULTIPOLYGON (((118.5046 9….
Sri Lanka	20771000	0.8995128	65370.390	317.7432497	MULTIPOLYGON (((81.78796 7….
Japan	127276000	-0.1326942	404619.933	314.5569204	MULTIPOLYGON (((132.3712 33…
El Salvador	6281189	0.4853518	20893.340	300.6311547	MULTIPOLYGON (((-89.35333 1…
Vietnam	92544915	1.1379986	335990.802	275.4388350	MULTIPOLYGON (((104.3343 10…
United Kingdom	64613160	0.7533495	249986.395	258.4667055	MULTIPOLYGON (((-6.197885 5…
Luxembourg	556319	2.3569787	2416.870	230.1815525	MULTIPOLYGON (((6.043073 50…
Jamaica	2862087	0.3598251	12460.587	229.6911879	MULTIPOLYGON (((-77.5696 18…
Kuwait	3782450	4.9886814	16652.120	227.1452566	MULTIPOLYGON (((47.97452 29…
Germany	80982500	0.4168774	357430.341	226.5686224	MULTIPOLYGON (((14.11969 53…
Dominican Republic	10405844	1.2041249	48157.874	216.0777267	MULTIPOLYGON (((-71.7083 18…
Pakistan	185546257	2.0877924	874119.998	212.2663448	MULTIPOLYGON (((77.83745 35…
Qatar	2374419	5.3612360	11327.855	209.6088863	MULTIPOLYGON (((50.81011 24…
Dem. Rep. Korea	25116363	0.5204839	125679.216	199.8450006	MULTIPOLYGON (((130.64 42.3…
Nigeria	176460502	2.6595507	905071.739	194.9685250	MULTIPOLYGON (((2.691702 6….
Italy	60789140	0.9175041	315104.851	192.9171822	MULTIPOLYGON (((8.709991 40…
Nepal	28323241	1.2002975	150706.871	187.9359630	MULTIPOLYGON (((88.12044 27…
Cyprus	1152309	0.7327776	6207.006	185.6465041	MULTIPOLYGON (((32.73178 35…
Switzerland	8188649	1.2201040	46185.251	177.3000878	MULTIPOLYGON (((9.594226 47…
Trinidad and Tobago	1354493	0.4621243	7737.810	175.0486281	MULTIPOLYGON (((-61.68 10.7…
Kosovo	1821800	NA	11230.262	162.2223999	MULTIPOLYGON (((20.59025 41…
Uganda	38833338	3.3506504	245768.479	158.0078051	MULTIPOLYGON (((33.90371 -0…
Malawi	17068838	2.9229402	111197.018	153.5008605	MULTIPOLYGON (((32.75938 -9…
Guatemala	15923559	2.0771518	109459.049	145.4750354	MULTIPOLYGON (((-92.22775 1…
China	1364270000	0.5063116	9409830.493	144.9834831	MULTIPOLYGON (((80.25999 42…
Indonesia	255131116	1.2220486	1819251.329	140.2396205	MULTIPOLYGON (((104.37 -1.0…
The Gambia	1917852	3.0992829	14031.284	136.6839940	MULTIPOLYGON (((-16.71373 1…
Thailand	68416772	0.4008607	510125.570	134.1175116	MULTIPOLYGON (((105.2188 14…
Denmark	5643475	0.5070533	42759.928	131.9804617	MULTIPOLYGON (((9.921906 54…
Czech Republic	10525347	0.1052776	81207.603	129.6103643	MULTIPOLYGON (((15.017 51.1…
Poland	38011735	-0.0748462	310402.333	122.4595661	MULTIPOLYGON (((23.48413 53…
Togo	7228915	2.6062123	60966.962	118.5710217	MULTIPOLYGON (((0.899563 10…
Slovakia	5418649	0.0970454	47068.082	115.1236415	MULTIPOLYGON (((22.55814 49…
United Arab Emirates	9070867	0.7147625	79880.738	113.5551222	MULTIPOLYGON (((51.57952 24…
Portugal	10401062	-0.5391905	93408.594	111.3501611	MULTIPOLYGON (((-9.034818 4…
Ghana	26962563	2.3123360	243473.120	110.7414361	MULTIPOLYGON (((0.02380252 …
Moldova	3556397	-0.0609701	32320.392	110.0357021	MULTIPOLYGON (((26.61934 48…
Slovenia	2061980	0.0983519	19118.123	107.8547319	MULTIPOLYGON (((13.80648 46…
Hungary	9866468	-0.2693788	92476.460	106.6916701	MULTIPOLYGON (((22.08561 48…
Azerbaijan	9535079	1.2482090	91113.254	104.6508446	MULTIPOLYGON (((46.14362 38…
Syria	19203090	-3.1072294	185004.125	103.7981718	MULTIPOLYGON (((35.71992 32…
Armenia	2906220	0.4383315	28656.601	101.4153781	MULTIPOLYGON (((46.50572 38…
Austria	8546356	0.7308673	85064.895	100.4686597	MULTIPOLYGON (((16.97967 48…
Cuba	11439767	0.2415552	114866.218	99.5920923	MULTIPOLYGON (((-82.26815 2…
Jordan	8809306	4.5975383	89207.137	98.7511348	MULTIPOLYGON (((35.54567 32…
Albania	2889104	-0.2070470	29694.800	97.2932625	MULTIPOLYGON (((21.02004 40…
Turkey	77030628	1.6271941	798849.164	96.4269996	MULTIPOLYGON (((26.11704 41…
Serbia	7130576	-0.4694893	76388.605	93.3460690	MULTIPOLYGON (((18.82982 45…
Sierra Leone	7079162	2.2439381	75980.331	93.1709807	MULTIPOLYGON (((-13.24655 8…
Spain	46480882	-0.2989511	502306.468	92.5349064	MULTIPOLYGON (((-7.453726 3…
Egypt	91812566	2.2081428	996311.623	92.1524590	MULTIPOLYGON (((36.86623 22…
Malaysia	30228017	1.7395792	338226.487	89.3721166	MULTIPOLYGON (((100.0858 6….
Costa Rica	4757575	1.0814588	53832.136	88.3779723	MULTIPOLYGON (((-82.5462 9….
Benin	10286712	2.7822871	116998.713	87.9215828	MULTIPOLYGON (((2.691702 6….
Ethiopia	97366774	2.5790683	1132393.167	85.9831875	MULTIPOLYGON (((47.78942 8….
Cambodia	15270790	1.6379995	182235.978	83.7967902	MULTIPOLYGON (((102.5849 12…
Romania	19908979	-0.3745755	238356.297	83.5261298	MULTIPOLYGON (((28.23355 45…
Macedonia	2077495	0.0845606	25062.255	82.8933780	MULTIPOLYGON (((22.38053 42…
Greece	10892413	-0.6661133	131964.647	82.5403870	MULTIPOLYGON (((22.95238 41…
Timor-Leste	1212814	2.3735669	14714.931	82.4206361	MULTIPOLYGON (((124.9687 -8…
Iraq	35006080	3.2604068	436965.034	80.1118562	MULTIPOLYGON (((39.19547 32…
Ireland	4657740	0.4108510	58457.513	79.6773542	MULTIPOLYGON (((-6.197885 5…
Ukraine	45271947	-0.4796159	572548.984	79.0708713	MULTIPOLYGON (((35.01266 45…
Lesotho	2145785	1.3334951	27505.655	78.0125033	MULTIPOLYGON (((28.97826 -2…
Kenya	46024250	2.6361164	590836.914	77.8967070	MULTIPOLYGON (((39.20222 -4…
Honduras	8809216	1.7339530	113789.775	77.4165870	MULTIPOLYGON (((-83.14722 1…
Myanmar	51924182	0.9209218	679573.994	76.4069585	MULTIPOLYGON (((100.116 20….
Senegal	14546111	2.9708778	194390.439	74.8293542	MULTIPOLYGON (((-16.71373 1…
Croatia	4238389	-0.4073432	57530.852	73.6715844	MULTIPOLYGON (((16.56481 46…
eSwatini	1295097	1.8422895	18118.634	71.4787324	MULTIPOLYGON (((32.07167 -2…
Tunisia	11143908	1.1675129	156237.322	71.3267988	MULTIPOLYGON (((9.48214 30….
Bosnia and Herzegovina	3566002	-1.0876413	50605.075	70.4672804	MULTIPOLYGON (((18.56 42.65…
Côte d’Ivoire	22531350	2.5397666	329825.951	68.3128477	MULTIPOLYGON (((-8.029944 1…
Uzbekistan	30757700	1.6869004	461410.258	66.6601998	MULTIPOLYGON (((55.96819 41…
Bulgaria	7223938	-0.5683893	110216.875	65.5429397	MULTIPOLYGON (((22.65715 44…
Burkina Faso	17585977	2.9619779	271593.672	64.7510558	MULTIPOLYGON (((-5.404342 1…
Ecuador	15903112	1.5306341	250747.110	63.4229125	MULTIPOLYGON (((-75.37322 -…
Mexico	124221600	1.3662456	1969480.307	63.0732887	MULTIPOLYGON (((-117.1278 3…
Tajikistan	8362745	2.2362456	138111.759	60.5505646	MULTIPOLYGON (((67.83 37.14…
Morocco	34318082	1.4479043	591718.989	57.9972632	MULTIPOLYGON (((-2.169914 3…
Yemen	26246327	2.5859054	455915.007	57.5684647	MULTIPOLYGON (((52.00001 19…
Tanzania	52234869	3.1075724	932745.792	56.0011843	MULTIPOLYGON (((33.90371 -0…
Georgia	3727000	-1.3061628	69048.161	53.9768181	MULTIPOLYGON (((39.95501 43…
Panama	3903986	1.6926317	75265.449	51.8695637	MULTIPOLYGON (((-77.35336 8…
Afghanistan	32758020	3.1832015	652270.070	50.2215593	MULTIPOLYGON (((66.51861 37…
Guinea	11805509	2.3040396	239565.079	49.2789226	MULTIPOLYGON (((-13.70048 1…
Iran	78411092	1.2521563	1617559.040	48.4749490	MULTIPOLYGON (((48.56797 29…
Cameroon	22239904	2.6618761	460324.702	48.3135142	MULTIPOLYGON (((14.49579 12…
Guinea-Bissau	1725744	2.5974983	36191.886	47.6831745	MULTIPOLYGON (((-16.67745 1…
Nicaragua	6013997	1.1413412	129540.212	46.4257154	MULTIPOLYGON (((-83.65561 1…
Montenegro	621810	0.0970220	13443.678	46.2529672	MULTIPOLYGON (((20.0707 42….
Lithuania	2932367	-0.8598273	63831.091	45.9394776	MULTIPOLYGON (((26.49433 55…
Fiji	885806	0.6899974	19289.971	45.9205466	MULTIPOLYGON (((-180 -16.55…
Belarus	9474511	0.0899026	208969.830	45.3391335	MULTIPOLYGON (((28.17671 56…
South Africa	54539571	1.4259250	1216400.831	44.8368413	MULTIPOLYGON (((16.34498 -2…
Liberia	4390737	2.4075304	98206.783	44.7091012	MULTIPOLYGON (((-8.439298 7…
Djibouti	912164	1.7111823	21880.251	41.6889194	MULTIPOLYGON (((42.35156 12…
Equatorial Guinea	1129424	4.1284210	27120.575	41.6445451	MULTIPOLYGON (((9.649158 2….
Colombia	47791911	0.9437827	1151882.926	41.4902504	MULTIPOLYGON (((-66.87633 1…
Zimbabwe	15411675	2.3447991	376328.489	40.9527194	MULTIPOLYGON (((31.19141 -2…
Madagascar	23589801	2.7010975	589382.827	40.0245815	MULTIPOLYGON (((49.54352 -1…
Brunei Darussalam	411704	1.4651237	10700.334	38.4758074	MULTIPOLYGON (((115.4507 5….
Vanuatu	258850	2.2298147	7490.040	34.5592273	MULTIPOLYGON (((166.7932 -1…
Venezuela	30738378	1.3775390	908499.070	33.8342427	MULTIPOLYGON (((-60.73357 5…
Mozambique	27212382	2.9006957	810994.757	33.5543254	MULTIPOLYGON (((34.55999 -1…
United States	318622525	0.7431243	9510743.745	33.5013258	MULTIPOLYGON (((-171.7317 6…
Democratic Republic of the Congo	73722860	3.3191759	2323492.477	31.7293302	MULTIPOLYGON (((29.34 -4.49…
Latvia	1993782	-0.9417434	63923.533	31.1901096	MULTIPOLYGON (((27.28818 57…
Kyrgyzstan	5835500	2.0061079	195874.658	29.7920111	MULTIPOLYGON (((70.96231 42…
Estonia	1314545	-0.2622562	44678.197	29.4225169	MULTIPOLYGON (((27.98113 59…
Lao PDR	6576397	1.2522585	229080.422	28.7078090	MULTIPOLYGON (((107.3827 14…
Somalia	13513125	2.8582860	484332.793	27.9004957	MULTIPOLYGON (((41.58513 -1…
Bahamas	382169	1.2981329	15584.791	24.5219204	MULTIPOLYGON (((-78.98 26.7…
Brazil	204213133	0.8875633	8508557.092	24.0009124	MULTIPOLYGON (((-53.37366 -…
Peru	30973354	1.3248298	1309699.636	23.6492041	MULTIPOLYGON (((-69.89364 -…
Solomon Islands	575504	2.1055775	24728.114	23.2732668	MULTIPOLYGON (((157.14 -7.0…
Chile	17613798	0.8599246	814844.220	21.6161538	MULTIPOLYGON (((-69.59042 -…
Angola	26920466	3.4854125	1245463.748	21.6148130	MULTIPOLYGON (((12.32243 -6…
Sweden	9696110	0.9922197	450581.582	21.5190997	MULTIPOLYGON (((11.02737 58…
Zambia	15620974	3.0402108	751921.215	20.7747483	MULTIPOLYGON (((30.74001 -8…
Sudan	37737913	2.3811846	1850885.565	20.3891120	MULTIPOLYGON (((23.88711 8….
Bhutan	776448	1.4904821	39377.402	19.7181114	MULTIPOLYGON (((91.69666 27…
Uruguay	3419546	0.3380718	176853.636	19.3354577	MULTIPOLYGON (((-57.62513 -…
South Sudan	11530971	3.1134611	624909.099	18.4522373	MULTIPOLYGON (((30.83385 3….
Algeria	39113313	2.0006665	2315916.658	16.8889122	MULTIPOLYGON (((-8.6844 27….
Papua New Guinea	7755785	2.1230026	464520.072	16.6963399	MULTIPOLYGON (((141.0002 -2…
Paraguay	6552584	1.3342008	401335.916	16.3269315	MULTIPOLYGON (((-58.16639 -…
New Zealand	4509700	1.5103395	277627.605	16.2437017	MULTIPOLYGON (((169.6678 -4…
Niger	19148219	3.8426809	1182269.648	16.1961521	MULTIPOLYGON (((14.8513 22….
Saudi Arabia	30776722	2.7413758	1920324.146	16.0268370	MULTIPOLYGON (((34.95604 29…
Finland	5461512	0.4135602	341242.339	16.0047901	MULTIPOLYGON (((28.59193 69…
Belize	351694	2.1593798	22045.451	15.9531326	MULTIPOLYGON (((-89.14308 1…
Argentina	42981515	1.0327093	2784468.589	15.4361644	MULTIPOLYGON (((-68.63401 -…
Republic of the Congo	4871101	2.4882151	339681.855	14.3401860	MULTIPOLYGON (((18.45307 3….
Mali	16962846	2.9010310	1235561.373	13.7288575	MULTIPOLYGON (((-11.51394 1…
Oman	3960925	6.5046596	309302.034	12.8060102	MULTIPOLYGON (((55.20834 22…
New Caledonia	268050	1.8832948	23219.012	11.5444190	MULTIPOLYGON (((165.78 -21….
Turkmenistan	5466241	1.8456805	480809.522	11.3688285	MULTIPOLYGON (((52.50246 41…
Chad	13569438	3.2647064	1271694.598	10.6703591	MULTIPOLYGON (((23.83766 19…
Bolivia	10562159	1.5446518	1085269.596	9.7322905	MULTIPOLYGON (((-69.52968 -…
Russian Federation	143819666	0.2177001	17018507.409	8.4507802	MULTIPOLYGON (((180 70.8322…
Central African Republic	4515392	0.3491722	621860.349	7.2611029	MULTIPOLYGON (((27.37423 5….
Gabon	1875713	3.1652929	269475.798	6.9605991	MULTIPOLYGON (((11.27645 2….
Kazakhstan	17288285	1.4797223	2729810.513	6.3331447	MULTIPOLYGON (((87.35997 49…
Mauritania	4063920	2.9402537	1054107.194	3.8553195	MULTIPOLYGON (((-17.06342 2…
Suriname	547928	0.9882076	144268.723	3.7979681	MULTIPOLYGON (((-54.52475 2…
Libya	6204108	0.1312573	1633720.717	3.7975328	MULTIPOLYGON (((25 22, 25 2…
Botswana	2168573	1.8648553	591912.017	3.6636746	MULTIPOLYGON (((29.43219 -2…
Guyana	763393	0.6982731	209801.857	3.6386380	MULTIPOLYGON (((-56.53939 1…
Canada	35535348	1.0835878	10036042.977	3.5407728	MULTIPOLYGON (((-132.71 54….
Australia	23504138	1.5358789	7687613.843	3.0574036	MULTIPOLYGON (((126.1487 -3…
Iceland	327386	1.1125048	107735.721	3.0387878	MULTIPOLYGON (((-14.5087 66…
Namibia	2370992	2.3242373	824886.561	2.8743249	MULTIPOLYGON (((19.89577 -2…
Mongolia	2923896	1.8916142	1544322.150	1.8933200	MULTIPOLYGON (((87.75126 49…
Greenland	56295	-0.3333987	2206644.440	0.0255116	MULTIPOLYGON (((-46.76379 8…
Western Sahara	NA	NA	96270.601	NA	MULTIPOLYGON (((-8.66559 27…
Falkland Islands	NA	NA	16363.799	NA	MULTIPOLYGON (((-61.2 -51.8…
Norway	NA	1.1277367	397994.629	NA	MULTIPOLYGON (((15.14282 79…
French Southern and Antarctic Lands	NA	NA	11602.572	NA	MULTIPOLYGON (((68.935 -48….
France	NA	0.5038689	644847.882	NA	MULTIPOLYGON (((-51.6578 4….
Taiwan	NA	NA	34345.701	NA	MULTIPOLYGON (((121.7778 24…
Eritrea	NA	NA	119319.585	NA	MULTIPOLYGON (((36.42951 14…
Antarctica	NA	NA	12335956.076	NA	MULTIPOLYGON (((-180 -89.9,…
Northern Cyprus	NA	NA	3786.365	NA	MULTIPOLYGON (((32.73178 35…
Northern Cyprus	NA	NA	3786.365	NA	MULTIPOLYGON (((32.73178 35…
Northern Cyprus	NA	NA	3786.365	NA	MULTIPOLYGON (((32.73178 35…
Somaliland	NA	NA	167349.613	NA	MULTIPOLYGON (((48.9482 11….
Somaliland	NA	NA	167349.613	NA	MULTIPOLYGON (((48.9482 11….
Somaliland	NA	NA	167349.613	NA	MULTIPOLYGON (((48.9482 11….

Summarize/Aggregate using column

world

## Simple feature collection with 177 features and 10 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -180 ymin: -89.9 xmax: 180 ymax: 83.64513
## Geodetic CRS:  WGS 84
## First 10 features:
##    iso_a2        name_long     continent region_un          subregion
## 1      FJ             Fiji       Oceania   Oceania          Melanesia
## 2      TZ         Tanzania        Africa    Africa     Eastern Africa
## 3      EH   Western Sahara        Africa    Africa    Northern Africa
## 4      CA           Canada North America  Americas   Northern America
## 5      US    United States North America  Americas   Northern America
## 6      KZ       Kazakhstan          Asia      Asia       Central Asia
## 7      UZ       Uzbekistan          Asia      Asia       Central Asia
## 8      PG Papua New Guinea       Oceania   Oceania          Melanesia
## 9      ID        Indonesia          Asia      Asia South-Eastern Asia
## 10     AR        Argentina South America  Americas      South America
##                 type    area_km2       pop  lifeExp gdpPercap
## 1  Sovereign country    19289.97    885806 69.96000  8222.254
## 2  Sovereign country   932745.79  52234869 64.16300  2402.099
## 3      Indeterminate    96270.60        NA       NA        NA
## 4  Sovereign country 10036042.98  35535348 81.95305 43079.143
## 5            Country  9510743.74 318622525 78.84146 51921.985
## 6  Sovereign country  2729810.51  17288285 71.62000 23587.338
## 7  Sovereign country   461410.26  30757700 71.03900  5370.866
## 8  Sovereign country   464520.07   7755785 65.23000  3709.082
## 9  Sovereign country  1819251.33 255131116 68.85600 10003.089
## 10 Sovereign country  2784468.59  42981515 76.25200 18797.548
##                              geom
## 1  MULTIPOLYGON (((-180 -16.55...
## 2  MULTIPOLYGON (((33.90371 -0...
## 3  MULTIPOLYGON (((-8.66559 27...
## 4  MULTIPOLYGON (((-132.71 54....
## 5  MULTIPOLYGON (((-171.7317 6...
## 6  MULTIPOLYGON (((87.35997 49...
## 7  MULTIPOLYGON (((55.96819 41...
## 8  MULTIPOLYGON (((141.0002 -2...
## 9  MULTIPOLYGON (((104.37 -1.0...
## 10 MULTIPOLYGON (((-68.63401 -...

world_cont = world %>% 
        group_by(continent) %>% 
        summarize(pop_sum = sum(pop, na.rm = TRUE))
world_cont

## Simple feature collection with 8 features and 2 fields
## Geometry type: GEOMETRY
## Dimension:     XY
## Bounding box:  xmin: -180 ymin: -89.9 xmax: 180 ymax: 83.64513
## Geodetic CRS:  WGS 84
## # A tibble: 8 × 3
##   continent                  pop_sum                                        geom
##   <chr>                        <dbl>                              <GEOMETRY [°]>
## 1 Africa                  1154946633 MULTIPOLYGON (((36.86623 22, 36.69069 22.2…
## 2 Antarctica                       0 MULTIPOLYGON (((-180 -89.9, 180 -89.9, 180…
## 3 Asia                    4311408059 MULTIPOLYGON (((36.14976 35.82153, 35.9050…
## 4 Europe                   669036256 MULTIPOLYGON (((26.29 35.29999, 25.74502 3…
## 5 North America            565028684 MULTIPOLYGON (((-82.26815 23.18861, -82.51…
## 6 Oceania                   37757833 MULTIPOLYGON (((166.7932 -15.66881, 167.00…
## 7 Seven seas (open ocean)          0 POLYGON ((68.935 -48.625, 68.8675 -48.83, …
## 8 South America            412060811 MULTIPOLYGON (((-66.95992 -54.89681, -66.4…

ggplot(world_cont,aes(fill=pop_sum))+
  geom_sf()

The st_set_geometry function can be used to remove the geometry column:

world_df =st_set_geometry(world_cont, NULL)
class(world_df)

## [1] "tbl_df"     "tbl"        "data.frame"

Spatial operations

It’s a big topic which includes:

Spatial subsetting
Spatial joining/aggregation
Topological relations
Distances
Spatial geometry modification
Raster operations (map algebra)

See Chapter 4 of Geocomputation with R

CRS

Transform (warp) to a different projection:

na_2163 = world %>%
  filter(continent == "North America") %>% 
  st_transform(2163) #US National Atlas Equal Area
st_crs(na_2163)

## Coordinate Reference System:
##   User input: EPSG:2163 
##   wkt:
## PROJCRS["NAD27 / US National Atlas Equal Area",
##     BASEGEOGCRS["NAD27",
##         DATUM["North American Datum 1927",
##             ELLIPSOID["Clarke 1866",6378206.4,294.978698213898,
##                 LENGTHUNIT["metre",1]]],
##         PRIMEM["Greenwich",0,
##             ANGLEUNIT["degree",0.0174532925199433]],
##         ID["EPSG",4267]],
##     CONVERSION["US National Atlas Equal Area",
##         METHOD["Lambert Azimuthal Equal Area (Spherical)",
##             ID["EPSG",1027]],
##         PARAMETER["Latitude of natural origin",45,
##             ANGLEUNIT["degree",0.0174532925199433],
##             ID["EPSG",8801]],
##         PARAMETER["Longitude of natural origin",-100,
##             ANGLEUNIT["degree",0.0174532925199433],
##             ID["EPSG",8802]],
##         PARAMETER["False easting",0,
##             LENGTHUNIT["metre",1],
##             ID["EPSG",8806]],
##         PARAMETER["False northing",0,
##             LENGTHUNIT["metre",1],
##             ID["EPSG",8807]]],
##     CS[Cartesian,2],
##         AXIS["easting (X)",east,
##             ORDER[1],
##             LENGTHUNIT["metre",1]],
##         AXIS["northing (Y)",north,
##             ORDER[2],
##             LENGTHUNIT["metre",1]],
##     USAGE[
##         SCOPE["Statistical analysis."],
##         AREA["United States (USA) - onshore and offshore."],
##         BBOX[15.56,167.65,74.71,-65.69]],
##     ID["EPSG",9311]]

Compare projections

na = world %>%
  filter(continent == "North America") 
p1=ggplot(na)+geom_sf()
p2=ggplot(na_2163)+geom_sf()
ggarrange(p1,p2)

The `world` dataset

plot(na_2163)

## Warning: plotting the first 9 out of 10 attributes; use max.plot = 10 to plot
## all

Spatial operations

canada = na_2163 %>% 
  filter(name_long=="Canada")

canada_buffer=canada%>%
  st_buffer(500000) %>%
  filter()

ggplot()+
  geom_sf(data=canada)+
  geom_sf(data=canada_buffer,col="red",fill=NA)

Basic maps

Basic maps of sf objects can be quickly created using the plot() function:

plot(world[0])

Basic maps

plot(world["pop"])

leaflet

library(leaflet)
library(widgetframe)

## Loading required package: htmlwidgets

leaflet(world) %>%
        addTiles() %>%
        addPolygons(color = "#444444", weight = 1, fillOpacity = 0.5,
                    fillColor = ~colorQuantile("YlOrRd", lifeExp)(lifeExp),
                    popup = paste(round(world$lifeExp, 2)))

l = leaflet(world) %>%
  addTiles() %>%
  addPolygons(color = "#444444", 
              weight = 1, fillOpacity = 0.5, 
              fillColor = ~colorQuantile("YlOrRd", lifeExp)(lifeExp),
              popup = paste(round(world$lifeExp, 2)))
saveWidget(l, file = "leaflet.html",selfcontained = T)

Raster data in the tidyverse

Raster data is not yet closely connected to the tidyverse, however:

Some functions from the raster and terra packages work well in pipes
You can convert vector data to the Spatial* form using as(my_vector, "Spatial")before working on raster-vector interactions
There are some initial efforts to bring raster data closer to the tidyverse, such as tabularaster, sfraster, or fasterize
The stars, package focuses on multidimensional, large datasets.

stars example

library(stars)

## Loading required package: abind

tif = system.file("tif/L7_ETMs.tif", package = "stars")
read_stars(tif) |>
  slice(index = 1, along = "band") |>
  plot()

stars example 2

prec_file = system.file("nc/test_stageiv_xyt.nc", package = "stars")
prec = read_stars(gdal_subdatasets(prec_file)[[1]])

prec %>% 
  slice(index = 1:12, along = "time") |>
  plot()

stars example 3

sf::read_sf(system.file("gpkg/nc.gpkg", package = "sf"), "nc.gpkg") %>%  
  st_transform(st_crs(prec)) %>% # transform from NAD27 to WGS84
  st_geometry() %>% 
  st_union() ->
  nc_outline

plot_hook = function() plot(nc_outline, border = 'red', add = TRUE)

prec %>% 
  slice(index = 1:12, along = "time") |>
  plot(downsample = c(3, 3, 1), hook = plot_hook)

Sources

Slides adapted from:
- “Robin Lovelace and Jakub Nowosad” draft book Geocomputation with R (to be published in 2018). Source code at https://github.com/robinlovelace/geocompr.
- Claudia Engel’s spatial analysis workshop

Spatial data handling

Course Schedule

Resource Presentations

Case Study Presentations - Let’s pick a winner!

Next Week’s Case Study

Spatial data handling in R

Packages for Spatial Data

What is a Spatial Feature (sf)?

Geometry

Spatial Features

sp package

sp Package

sf Package

Simple feature geometry types

Uncommon Geometry Types

Coordinate reference system

Reproject to “Goode Homolosine” projection

Reproject to “Goode Homolosine” projection

Reproject to “Goode Homolosine” projection

Defining a projection

How simple features in R are organized

Components

sf Highlights

Reading and writing spatial data

Structure of the sf objects

Structure of the sf objects

Non-spatial operations on the sf objects

Summarize/Aggregate using column

Spatial operations

CRS

Compare projections

The world dataset

Spatial operations

Basic maps

Basic maps

leaflet

Raster data in the tidyverse

stars example

stars example 2

stars example 3

Sources

`sp` package

`sp` Package

`sf` Package

The `world` dataset