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

• 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.

Simple feature geometry types

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

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()

Reproject to “Goode Homolosine” projection

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

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
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##   .. .. .. .. ..$ :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
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##   .. .. .. .. ..$ :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
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##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -88.1 75.4
##   .. .. .. .. .. .. ..@ area   : num 19.2
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
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##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -83 62.6
##   .. .. .. .. .. .. ..@ area   : num 1.04
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
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##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -84.1 64.3
##   .. .. .. .. .. .. ..@ area   : num 7.97
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
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##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -79.8 62
##   .. .. .. .. .. .. ..@ area   : num 0.532
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
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##   .. .. .. .. ..$ :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
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##   .. .. .. .. ..$ :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
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##   .. .. .. .. ..$ :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
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##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -63.3 46.4
##   .. .. .. .. .. .. ..@ area   : num 0.873
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
##   .. .. .. .. .. .. ..@ coords : num [1:9, 1:2] -64 -63.7 -62.9 -62 -62.5 ...
##   .. .. .. .. ..$ :Formal class 'Polygon' [package "sp"] with 5 slots
##   .. .. .. .. .. .. ..@ labpt  : num [1:2] -56 48.7
##   .. .. .. .. .. .. ..@ area   : num 15.2
##   .. .. .. .. .. .. ..@ hole   : logi FALSE
##   .. .. .. .. .. .. ..@ ringDir: int 1
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##   .. .. .. ..@ 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')"

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()

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…

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