Using the Geopackage Format with R14 Jul 2016
Many (most?) people involved in vector geospatial data analysis work exlusively with shapefiles. However, the shapefile format has a number of drawbacks including the fact that spatial attributes, metadata, and projection information are stored in seperate files. For instance, it can take as much as 45 lines of code to ensure a complete “shapefile” download.
Barry Rowlingson b.rowlingson at lancaster.ac.uk Wed Jul 13 19:44:28 CEST 2016 [...] the agency from which I got the data has been enlightened enough not to use the clunky, outdated, and limited "shapefile" format and has released the data as a modern, OGC-standard GeoPackage. My variables have long names, my metadata is stored with my data, and its all in one file instead of six. [...] Shapefiles are an awful, awful format which Esri didn't think people would actually use. They should not be encouraged. [...] Barry
The interested but time-limited geospatial analyst might wonder; Can I easily switch from a shapefile workflow to a GeoPackage workflow? Will my colleagues be able to open and interact with GeoPackage files? Fortunately, the answer is yes because the
R package supports reading and writing of vector geospatial data to GeoPackage files.
First, lets load some geospatial data into a
library(rgdal) cities <- readOGR(system.file("vectors", package = "rgdal"), "cities") class(cities)
>  "SpatialPointsDataFrame" > attr(,"package") >  "sp"
Now lets write the data to disk using the GeoPackage format:
# outname <- file.path(tempdir(), "cities.gpkg") outname <- "cities.gpkg" writeOGR(cities, dsn = outname, layer = "cities", driver = "GPKG")
This file can then be read back into R:
cities_gpkg <- readOGR("cities.gpkg", "cities") identical(cities, cities_gpkg)
>  TRUE
The file can also be opened in your standalone GIS program of choice such as GRASS, QGIS, or even ArcGIS.
Sometimes you may want to directly access the metadata for your spatial data without loading the object geometry. Because GeoPackage files are formatted as SQLite databases you can use the existing
R tools for SQLite files. One option is to use the slick
library(dplyr) cities_sqlite <- tbl(src_sqlite("cities.gpkg"), "cities") print(cities_sqlite, n = 5)
> Source: sqlite 3.8.6 [cities.gpkg] > From: cities [606 x 6] > fid geom NAME COUNTRY POPULATION CAPITAL > (int) (chr) (chr) (chr) (dbl) (chr) > 1 1 <raw> Murmansk Russia 468000 N > 2 2 <raw> Arkhangelsk Russia 416000 N > 3 3 <raw> Saint Petersburg Russia 5825000 N > 4 4 <raw> Magadan Russia 152000 N > 5 5 <raw> Perm' Russia 1160000 N > .. ... ... ... ... ... ...
Another option is to use the more primitive
library(RSQLite) con <- dbConnect(RSQLite::SQLite(), dbname = "cities.gpkg") dbListTables(con) cities_rsqlite <- dbGetQuery(con, 'select * from cities') head(cities_rsqlite[, -which(names(cities_rsqlite) == "geom")]) dbGetQuery(con, 'select * from gpkg_spatial_ref_sys')[3,"description"]
> fid NAME COUNTRY POPULATION CAPITAL > 1 1 Murmansk Russia 468000 N > 2 2 Arkhangelsk Russia 416000 N > 3 3 Saint Petersburg Russia 5825000 N > 4 4 Magadan Russia 152000 N > 5 5 Perm' Russia 1160000 N > 6 6 Yekaterinburg Russia 1620000 N >  "longitude/latitude coordinates in decimal degrees on the WGS 84 spheroid"