The geotargets package extends targets to
work with geospatial data formats, such as rasters and vectors (e.g.,
shape files). In particular, geotargets aims to support use
of the terra package, which tend to cause problems if used
in targets created with tar_target() . If you are new to
targets, you should start by looking at the targets manual to get a
handle on the basics.
The design of geotargets is to specify target factories
like so: tar_<pkg>_<type>.
In this vignette we will demonstrate the use of the
terra R package, and we will demonstrate how to build
raster (rast), vector (vect), raster
collection (sprc), and raster dataset (sds)
targets with:
tar_terra_rast(): targets with terra
rasters
# contents of _targets.R:
library(targets)
library(geotargets)
tar_option_set(packages = "terra")
geotargets_option_set(gdal_raster_driver = "COG")
list(
tar_target(
tif_file,
system.file("ex/elev.tif", package = "terra"),
format = "file"
),
tar_terra_rast(
r,
{
rast <- rast(tif_file)
units(rast) <- "m"
rast
}
),
tar_terra_rast(
r_agg,
aggregate(r, 2)
)
)Above is a basic example showing the use of
tar_terra_rast() in a targets pipeline. The command for
tar_terra_rast() can be any function that returns a
SpatRaster object. In this example, we’ve set the output to
a cloud optimized geotiff (“COG”), but any GDAL driver that works with
terra::writeRaster() should also work here. You can also
set this option on a target-by-target basis with the
filetype argument to tar_terra_rast().
Running the pipeline:
tar_make()
#> ▶ dispatched target tif_file
#> ● completed target tif_file [0.009 seconds, 7.994 kilobytes]
#> ▶ dispatched target r
#> ● completed target r [0.01 seconds, 10.433 kilobytes]
#> ▶ dispatched target r_agg
#> ● completed target r_agg [0.002 seconds, 6.303 kilobytes]
#> ▶ ended pipeline [0.135 seconds]
#>
tar_read(r)
#> class : SpatRaster
#> dimensions : 90, 95, 1 (nrow, ncol, nlyr)
#> resolution : 0.008333333, 0.008333333 (x, y)
#> extent : 5.741667, 6.533333, 49.44167, 50.19167 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> source : r
#> name : elevation
#> min value : 141
#> max value : 547
tar_read(r_agg)
#> class : SpatRaster
#> dimensions : 45, 48, 1 (nrow, ncol, nlyr)
#> resolution : 0.01666667, 0.01666667 (x, y)
#> extent : 5.741667, 6.541667, 49.44167, 50.19167 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> source : r_agg
#> name : elevation
#> min value : 166.75
#> max value : 529.50Raster metadata
You may have noticed that the units for the r target
above have gone missing. This is due to limitations of
terra and targets—terra saves
some metadata in “sidecar” aux.json files and targets
enforces a strict one file per target rule. You can get around this by
setting preserve_metadata = "zip" in
tar_terra_rast() to save the output files, including the
metadata, as a minimally compressed zip archive. You can also set this
for all raster targets with
geotargets_option_set(terra_preserve_metadata = "zip").
Note: there are likely performance costs associated with this
option.
As an alternative, you can encode information in the layer names by
setting names(r) <- which are retained even with the
default preserve_metadata = "drop".
# contents of _targets.R:
library(targets)
library(geotargets)
tar_option_set(packages = "terra")
geotargets_option_set(gdal_raster_driver = "COG")
list(
tar_target(
tif_file,
system.file("ex/elev.tif", package = "terra"),
format = "file"
),
tar_terra_rast(
r,
{
rast <- rast(tif_file)
units(rast) <- "m"
rast
},
preserve_metadata = "zip"
)
)
tar_terra_vect(): targets with terra
vectors
For terra SpatVector objects, use
tar_terra_vect() in the pipeline. You can set vector
specific options with geotargets_option_set() or with the
filetype and gdal arguments to individual
tar_terra_vect() calls.
# contents of _targets.R:
library(targets)
library(geotargets)
geotargets_option_set(gdal_vector_driver = "GeoJSON")
list(
tar_target(
vect_file,
system.file("ex", "lux.shp", package = "terra"),
format = "file"
),
tar_terra_vect(
v,
terra::vect(vect_file)
),
tar_terra_vect(
v_proj,
terra::project(v, "EPSG:2196")
)
)
tar_make()
#> ▶ dispatched target vect_file
#> ● completed target vect_file [0.001 seconds, 64.692 kilobytes]
#> ▶ dispatched target v
#> ● completed target v [0.007 seconds, 117.605 kilobytes]
#> ▶ dispatched target v_proj
#> ● completed target v_proj [0.015 seconds, 213.51 kilobytes]
#> ▶ ended pipeline [0.133 seconds]
#>
tar_read(v)
#> class : SpatVector
#> geometry : polygons
#> dimensions : 12, 6 (geometries, attributes)
#> extent : 5.74414, 6.528252, 49.44781, 50.18162 (xmin, xmax, ymin, ymax)
#> source : v
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> names : ID_1 NAME_1 ID_2 NAME_2 AREA POP
#> type : <num> <chr> <num> <chr> <num> <int>
#> values : 1 Diekirch 1 Clervaux 312 18081
#> 1 Diekirch 2 Diekirch 218 32543
#> 1 Diekirch 3 Redange 259 18664
tar_read(v_proj)
#> class : SpatVector
#> geometry : polygons
#> dimensions : 12, 6 (geometries, attributes)
#> extent : -69990.51, -13879.85, 5484907, 5566555 (xmin, xmax, ymin, ymax)
#> source : v_proj
#> coord. ref. : ETRS89 / Kp2000 Jutland (EPSG:2196)
#> names : ID_1 NAME_1 ID_2 NAME_2 AREA POP
#> type : <num> <chr> <num> <chr> <num> <int>
#> values : 1 Diekirch 1 Clervaux 312 18081
#> 1 Diekirch 2 Diekirch 218 32543
#> 1 Diekirch 3 Redange 259 18664
tar_terra_sprc(): targets with terra
raster collections
Targets that produce a SpatRasterCollection can be
created with tar_terra_sprc(). The various rasters in the
collection are saved as subdatasets to adhere to targets
one file per target rule.
# contents of _targets.R:
library(targets)
library(geotargets)
elev_scale <- function(raster, z = 1, projection = "EPSG:4326") {
terra::project(
raster * z,
projection
)
}
tar_option_set(packages = "terra")
geotargets_option_set(gdal_raster_driver = "GTiff")
list(
tar_target(
elev_file,
system.file("ex", "elev.tif", package = "terra"),
format = "file"
),
tar_target(
r,
rast(elev_file)
),
tar_terra_sprc(
raster_elevs,
# two rasters, one unaltered, one scaled by factor of 2 and
# reprojected to interrupted Goode homolosine
terra::sprc(list(
elev_scale(r, 1),
elev_scale(r, 2, "+proj=igh")
))
)
)
tar_make()
#> ▶ dispatched target elev_file
#> ● completed target elev_file [0.009 seconds, 7.994 kilobytes]
#> ▶ dispatched target r
#> ● completed target r [0.01 seconds, 959.578 kilobytes]
#> ▶ dispatched target raster_elevs
#> ● completed target raster_elevs [0.048 seconds, 36.423 kilobytes]
#> ▶ ended pipeline [1.109 seconds]
#>
tar_read(raster_elevs)
#> class : SpatRasterCollection
#> length : 2
#> nrow : 90, 115
#> ncol : 95, 114
#> nlyr : 1, 1
#> extent : 5.741667, 1558890, 49.44167, 5556741 (xmin, xmax, ymin, ymax)
#> crs (first) : lon/lat WGS 84 (EPSG:4326)
#> names : raster_elevs, raster_elevs
tar_terra_sds(): targets with terra raster
datasets
A terra SpatRasterDataset is very similar
to a SpatRasterCollection except that all sub-datasets must
have the same projection and extent
# contents of _targets.R:
library(targets)
library(geotargets)
tar_option_set(packages = "terra")
list(
tar_target(
logo_file,
system.file("ex/logo.tif", package="terra"),
format = "file"
),
tar_terra_sds(
raster_dataset,
{
x <- sds(rast(logo_file), rast(logo_file)/2)
names(x) <- c("first", "second")
x
}
)
)
tar_make()
#> ▶ dispatched target logo_file
#> ● completed target logo_file [0.01 seconds, 22.458 kilobytes]
#> ▶ dispatched target raster_dataset
#> ● completed target raster_dataset [0.051 seconds, 53.667 kilobytes]
#> ▶ ended pipeline [0.162 seconds]
#>
tar_read(raster_dataset)
#> class : SpatRasterDataset
#> subdatasets : 2
#> dimensions : 77, 101 (nrow, ncol)
#> nlyr : 3, 3
#> resolution : 1, 1 (x, y)
#> extent : 0, 101, 0, 77 (xmin, xmax, ymin, ymax)
#> coord. ref. : Cartesian (Meter)
#> source(s) : raster_dataset
#> names : raster_dataset, raster_dataset