gpkg - Utilities for the OGC ‘GeoPackage’ Format
High-level wrapper functions to build Open Geospatial Consortium (OGC) ‘GeoPackage’ files. GDAL utilities for read and write of spatial data (vector and gridded) are provided via the {terra} package. Additional ‘GeoPackage’ and ‘SQLite’ specific functions manipulate attributes and tabular data via the {RSQLite} package.
Installation
Install the latest release from CRAN:
install.packages("gpkg")The development package can be installed from GitHub with {remotes}
if (!requireNamespace("remotes"))
install.packages("remotes")
remotes::install_github("brownag/gpkg")Background
What is a GeoPackage?
GeoPackage is an open, standards-based, platform-independent, portable, self-describing, compact format for transferring geospatial information. The GeoPackage Encoding Standard describes a set of conventions for storing the following within an SQLite database:
vector features
tile matrix sets of imagery and raster maps at various scales
attributes (non-spatial data)
extensions
Create a Geopackage
gpkg_write() can handle a variety of different input types. Here we start by adding two DEM (GeoTIFF) files.
library(gpkg)
library(terra)
#> terra 1.7.73
dem <- system.file("extdata", "dem.tif", package = "gpkg")
stopifnot(nchar(dem) > 0)
gpkg_tmp <- tempfile(fileext = ".gpkg")
if (file.exists(gpkg_tmp))
file.remove(gpkg_tmp)
# write a gpkg with two DEMs in it
gpkg_write(
dem,
destfile = gpkg_tmp,
RASTER_TABLE = "DEM1",
FIELD_NAME = "Elevation"
)
gpkg_write(
dem,
destfile = gpkg_tmp,
append = TRUE,
RASTER_TABLE = "DEM2",
FIELD_NAME = "Elevation",
NoData = -9999
)Insert Vector Layers
We can also write vector data to GeoPackage. Here we use gpkg_write() to add a bounding box polygon layer derived from extent of "DEM1".
# add bounding polygon vector layer via named list
r <- gpkg_tables(geopackage(gpkg_tmp))[['DEM1']]
v <- terra::as.polygons(r, ext = TRUE)
gpkg_write(list(bbox = v), destfile = gpkg_tmp, append = TRUE)Insert Attribute Table
Similarly, data.frame-like objects (non-spatial “attributes”) can be written to GeoPackage.
z <- data.frame(a = 1:10, b = LETTERS[1:10])
gpkg_write(list(myattr = z), destfile = gpkg_tmp, append = TRUE)Read a GeoPackage
geopackage() is a constructor that can create a simple container for working with geopackages from several types of inputs. Often you will have a character file path to a GeoPackage (.gpkg) file.
g <- geopackage(gpkg_tmp, connect = TRUE)
g
#> <geopackage>
#> --------------------------------------------------------------------------------
#> # of Tables: 20
#>
#> DEM1, DEM2, bbox, gpkg_2d_gridded_coverage_ancillary,
#> gpkg_2d_gridded_tile_ancillary, gpkg_contents, gpkg_extensions,
#> gpkg_geometry_columns, gpkg_metadata, gpkg_metadata_reference,
#> gpkg_ogr_contents, gpkg_spatial_ref_sys, gpkg_tile_matrix,
#> gpkg_tile_matrix_set, myattr, rtree_bbox_geom, rtree_bbox_geom_node,
#> rtree_bbox_geom_parent, rtree_bbox_geom_rowid, sqlite_sequence
#> --------------------------------------------------------------------------------
#> <SQLiteConnection>
#> Path: /tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg
#> Extensions: TRUE
class(g)
#> [1] "geopackage"Other times you may have a list of tables and layers you want to be in a GeoPackage that does not exist yet.
g2 <- geopackage(list(dem = r, bbox = v))
g2
#> <geopackage>
#> --------------------------------------------------------------------------------
#> # of Tables: 18
#>
#> bbox, dem, gpkg_2d_gridded_coverage_ancillary,
#> gpkg_2d_gridded_tile_ancillary, gpkg_contents, gpkg_extensions,
#> gpkg_geometry_columns, gpkg_metadata, gpkg_metadata_reference,
#> gpkg_ogr_contents, gpkg_spatial_ref_sys, gpkg_tile_matrix,
#> gpkg_tile_matrix_set, rtree_bbox_geom, rtree_bbox_geom_node,
#> rtree_bbox_geom_parent, rtree_bbox_geom_rowid, sqlite_sequence
#> --------------------------------------------------------------------------------
#> <SQLiteConnection>
#> Path: /tmp/Rtmp3fzTbi/Rgpkg4aeef68782c44.gpkg
#> Extensions: TRUE
class(g2)
#> [1] "geopackage"Note that a temporary GeoPackage (/tmp/Rtmp3fzTbi/Rgpkg4aeef68782c44.gpkg) is automatically created when using the geopackage(<list>) constructor.
You also may have a DBIConnection to a GeoPackage database already opened that you want to use. In any case (character, list, SQLiteConnection) there is an S3 method to facilitate creating the basic geopackage class provided by {gpkg}. All other methods are designed to be able to work smoothly with geopackage class input.
Inspect Contents of GeoPackage
We can list the table names in a GeoPackage with gpkg_list_tables() and fetch pointers (SpatRaster, SpatVectorProxy, and lazy data.frame) to the data in them with gpkg_table(). We can check the status of the internal geopackage class SQLiteConnection with gpkg_is_connected() and disconnect it with gpkg_disconnect().
# enumerate tables
gpkg_list_tables(g)
#> [1] "DEM1" "DEM2"
#> [3] "bbox" "gpkg_2d_gridded_coverage_ancillary"
#> [5] "gpkg_2d_gridded_tile_ancillary" "gpkg_contents"
#> [7] "gpkg_extensions" "gpkg_geometry_columns"
#> [9] "gpkg_metadata" "gpkg_metadata_reference"
#> [11] "gpkg_ogr_contents" "gpkg_spatial_ref_sys"
#> [13] "gpkg_tile_matrix" "gpkg_tile_matrix_set"
#> [15] "myattr" "rtree_bbox_geom"
#> [17] "rtree_bbox_geom_node" "rtree_bbox_geom_parent"
#> [19] "rtree_bbox_geom_rowid" "sqlite_sequence"
# inspect tables
gpkg_tables(g)
#> $DEM1
#> class : SpatRaster
#> dimensions : 30, 31, 1 (nrow, ncol, nlyr)
#> resolution : 0.008333333, 0.008333333 (x, y)
#> extent : 6.008333, 6.266667, 49.69167, 49.94167 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> source : file4aeef285aa462.gpkg:DEM1
#> varname : file4aeef285aa462
#> name : DEM1
#> min value : 195
#> max value : 500
#>
#> $DEM2
#> class : SpatRaster
#> dimensions : 30, 31, 1 (nrow, ncol, nlyr)
#> resolution : 0.008333333, 0.008333333 (x, y)
#> extent : 6.008333, 6.266667, 49.69167, 49.94167 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> source : file4aeef285aa462.gpkg:DEM2
#> varname : file4aeef285aa462
#> name : DEM2
#> min value : 195
#> max value : 500
#>
#> $myattr
#> # Source: table<myattr> [10 x 2]
#> # Database: sqlite 3.45.0 [/tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg]
#> a b
#> <int> <chr>
#> 1 1 A
#> 2 2 B
#> 3 3 C
#> 4 4 D
#> 5 5 E
#> 6 6 F
#> 7 7 G
#> 8 8 H
#> 9 9 I
#> 10 10 J
#>
#> $bbox
#> class : SpatVectorProxy
#> geometry : polygons
#> dimensions : 1, 0 (geometries, attributes)
#> extent : 6.008333, 6.266667, 49.69167, 49.94167 (xmin, xmax, ymin, ymax)
#> source : file4aeef285aa462.gpkg (bbox)
#> layer : bbox
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
# inspect a specific table
gpkg_table(g, "myattr", collect = TRUE)
#> a b
#> 1 1 A
#> 2 2 B
#> 3 3 C
#> 4 4 D
#> 5 5 E
#> 6 6 F
#> 7 7 G
#> 8 8 H
#> 9 9 I
#> 10 10 JNote that the collect = TRUE forces data be loaded into R memory for vector and attribute data; this is the difference in result object class of SpatVectorProxy/SpatVector and tbl_SQLiteConnection/data.frame for vector and attribute data, respectively.
gpkg_collect() is a helper method to call gpkg_table(..., collect = TRUE) for in-memory loading of specific tables.
gpkg_collect(g, "DEM1")
#> id zoom_level tile_column tile_row tile_data
#> 1 1 0 0 0 blob[3.98 kB]Note that with grid data returned from gpkg_collect() you get a table result with the tile contents in a blob column of a data.frame instead of SpatRaster object.
The inverse function of gpkg_collect() is gpkg_tbl() which always returns a tbl_SQLiteConnection.
gpkg_tbl(g, "gpkg_contents")
#> # Source: table<gpkg_contents> [4 x 10]
#> # Database: sqlite 3.45.0 [/tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg]
#> table_name data_type identifier description last_change min_x min_y max_x
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 DEM1 2d-gridded… DEM1 "" 2024-02-23… 6.01 49.7 6.27
#> 2 DEM2 2d-gridded… DEM2 "" 2024-02-23… 6.01 49.7 6.27
#> 3 bbox features bbox "" 2024-02-23… 6.01 49.7 6.27
#> 4 myattr attributes myattr "" 2024-02-22… -180 -90 180
#> # ℹ 2 more variables: max_y <dbl>, srs_id <int>More on how to use this type of result next.
Lazy Data Access
There are several other methods that can be used for working with tabular data in a GeoPackage in a “lazy” fashion.
Method 1: gpkg_table_pragma()
gpkg_table_pragma() is a low-frills data.frame result containing important table information, but not values. The PRAGMA table_info() is stored as a nested data.frame table_info. This representation has no dependencies beyond {RSQLite} and is efficient for inspection of table structure and attributes, though it is less useful for data analysis.
head(gpkg_table_pragma(g))
#> dsn table_name nrow table_info.cid
#> 1 /tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg DEM1 1 0
#> 2 /tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg DEM1 1 1
#> 3 /tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg DEM1 1 2
#> 4 /tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg DEM1 1 3
#> 5 /tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg DEM1 1 4
#> 6 /tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg DEM2 1 0
#> table_info.name table_info.type table_info.notnull table_info.dflt_value
#> 1 id INTEGER 0 <NA>
#> 2 zoom_level INTEGER 1 <NA>
#> 3 tile_column INTEGER 1 <NA>
#> 4 tile_row INTEGER 1 <NA>
#> 5 tile_data BLOB 1 <NA>
#> 6 id INTEGER 0 <NA>
#> table_info.pk
#> 1 1
#> 2 0
#> 3 0
#> 4 0
#> 5 0
#> 6 1Method 2: gpkg_vect() and gpkg_query()
gpkg_vect() is a wrapper around terra::vect() you can use to create ‘terra’ SpatVector objects from the tables found in a GeoPackage.
gpkg_vect(g, 'bbox')
#> class : SpatVector
#> geometry : polygons
#> dimensions : 1, 0 (geometries, attributes)
#> extent : 6.008333, 6.266667, 49.69167, 49.94167 (xmin, xmax, ymin, ymax)
#> source : file4aeef285aa462.gpkg (bbox)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)The table of interest need not have a geometry column, but this method does not work on GeoPackage that contain only gridded data, and some layer in the GeoPackage must have some geometry.
gpkg_vect(g, 'gpkg_ogr_contents')
#> class : SpatVector
#> geometry : none
#> dimensions : 0, 2 (geometries, attributes)
#> extent : 0, 0, 0, 0 (xmin, xmax, ymin, ymax)
#> source : file4aeef285aa462.gpkg (SELECT)
#> coord. ref. :
#> names : table_name feature_count
#> type : <chr> <int>The SpatVectorProxy is used for “lazy” references to of vector and attribute contents of a GeoPackage; this object for vector data is analogous to the SpatRaster for gridded data. The ‘terra’ package provides “GDAL plumbing” for filter and query utilities.
gpkg_query() by default uses the ‘RSQLite’ driver, but the richer capabilities of OGR data sources can be harnessed with SQLite SQL dialect. These additional features can be utilized with the ogr=TRUE argument to gpkg_query(), or gpkg_ogr_query() for short. This assumes that GDAL is built with support for SQLite (and ideally also with support for Spatialite).
For example, we use built-in functions such as ST_MinX() to calculate summaries for "bbox" table, geometry column "geom". In this case we expect the calculated quantities to match the coordinates/boundaries of the bounding box:
res <- gpkg_ogr_query(g, "SELECT
ST_MinX(geom) AS xmin,
ST_MinY(geom) AS ymin,
ST_MaxX(geom) AS xmax,
ST_MaxY(geom) AS ymax
FROM bbox")
as.data.frame(res)
#> xmin ymin xmax ymax
#> 1 6.008333 49.69167 6.266667 49.94167Method 3: gpkg_rast()
Using gpkg_rast() you can quickly access references to all tile/gridded datasets in a GeoPackage.
For example:
gpkg_rast(g)
#> class : SpatRaster
#> dimensions : 30, 31, 2 (nrow, ncol, nlyr)
#> resolution : 0.008333333, 0.008333333 (x, y)
#> extent : 6.008333, 6.266667, 49.69167, 49.94167 (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326)
#> sources : file4aeef285aa462.gpkg:DEM1
#> file4aeef285aa462.gpkg:DEM2
#> varnames : file4aeef285aa462
#> file4aeef285aa462
#> names : DEM1, DEM2
#> min values : 195, 195
#> max values : 500, 500Method 4: gpkg_table()
With the gpkg_table() method you access a specific table (by name) and get a “lazy” tibble object referencing that table.
This is achieved via {dplyr} and the {dbplyr} database connection to the GeoPackage via the {RSQLite} driver. The resulting object’s data can be used in more complex analyses by using other {dbplyr}/{tidyverse} functions.
For example, we inspect the contents of the gpkg_contents table that contains critical information on the data contained in a GeoPackage.
gpkg_table(g, "gpkg_contents")
#> # Source: table<gpkg_contents> [4 x 10]
#> # Database: sqlite 3.45.0 [/tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg]
#> table_name data_type identifier description last_change min_x min_y max_x
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl>
#> 1 DEM1 2d-gridded… DEM1 "" 2024-02-23… 6.01 49.7 6.27
#> 2 DEM2 2d-gridded… DEM2 "" 2024-02-23… 6.01 49.7 6.27
#> 3 bbox features bbox "" 2024-02-23… 6.01 49.7 6.27
#> 4 myattr attributes myattr "" 2024-02-22… -180 -90 180
#> # ℹ 2 more variables: max_y <dbl>, srs_id <int>As a more complicated example we access the gpkg_2d_gridded_tile_ancillary table, and perform some data processing.
We dplyr::select() mean and std_dev columns from the dplyr::filter()ed rows where tpudt_name == "DEM2". Finally we materialize a tibble with dplyr::collect():
library(dplyr, warn.conflicts = FALSE)
gpkg_table(g, "gpkg_2d_gridded_tile_ancillary") %>%
filter(tpudt_name == "DEM2") %>%
select(mean, std_dev) %>%
collect()
#> # A tibble: 1 × 2
#> mean std_dev
#> <dbl> <dbl>
#> 1 324. 58.5Managing Connections
Several helper methods are available for checking GeoPackage SQLiteConnection status, as well as connecting and disconnecting an existing geopackage object (g).
# still connected
gpkg_is_connected(g)
#> [1] TRUE
# disconnect geopackage
gpkg_disconnect(g)
# reconnect
gpkg_connect(g)
#> <geopackage>
#> --------------------------------------------------------------------------------
#> # of Tables: 21
#>
#> DEM1, DEM2, bbox, dummy_feature, gpkg_2d_gridded_coverage_ancillary,
#> gpkg_2d_gridded_tile_ancillary, gpkg_contents, gpkg_extensions,
#> gpkg_geometry_columns, gpkg_metadata, gpkg_metadata_reference,
#> gpkg_ogr_contents, gpkg_spatial_ref_sys, gpkg_tile_matrix,
#> gpkg_tile_matrix_set, myattr, rtree_bbox_geom, rtree_bbox_geom_node,
#> rtree_bbox_geom_parent, rtree_bbox_geom_rowid, sqlite_sequence
#> --------------------------------------------------------------------------------
#> <SQLiteConnection>
#> Path: /tmp/Rtmp3fzTbi/file4aeef285aa462.gpkg
#> Extensions: TRUE
# disconnect
gpkg_disconnect(g)