Merge pull request #7 from b-cubed-eu/geopackage

Geopackage

Author: wlangera

README.Rmd

@@ -88,7 +88,7 @@ library(frictionless)
 The content of the data package can be consulted using `read_package()`.
 
 ```{r}
-b3data_package <- read_package("https://zenodo.org/records/15181098/files/datapackage.json")
+b3data_package <- read_package("https://zenodo.org/records/15211029/files/datapackage.json")
 b3data_package
 ```
 
@@ -105,7 +105,7 @@ For non-tabular resources (e.g. spatial or raster data), use packages like `sf`
 
 ```{r}
 mgrs10_belgium <- sf::st_read(
-  "https://zenodo.org/records/15181098/files/mgrs10_refgrid_belgium.geojson",
+  "https://zenodo.org/records/15211029/files/mgrs10_refgrid_belgium.gpkg",
   quiet = TRUE)
 head(mgrs10_belgium)
 ```

README.md

@@ -109,7 +109,7 @@ like `sf` or `terra` directly.
 
 ``` r
 mgrs10_belgium <- sf::st_read(
-  "https://zenodo.org/records/15181098/files/mgrs10_refgrid_belgium.geojson",
+  "https://zenodo.org/records/15181098/files/mgrs10_refgrid_belgium.gpkg",
   quiet = TRUE)
 head(mgrs10_belgium)
 #> Simple feature collection with 6 features and 1 field

data/b3data_package/datapackage.json

@@ -1,7 +1,7 @@
 {
   "name": "b3data",
-  "id": "https://doi.org/10.5281/zenodo.15181098",
-  "version": "0.1.0",
+  "id": "https://doi.org/10.5281/zenodo.15211029",
+  "version": "0.1.2",
   "resources": [
     {
       "name": "bird_cube_belgium_mgrs10",
@@ -11,7 +11,7 @@
       "mediatype": "text/csv",
       "encoding": "utf-8",
       "title": "Occurrence cube for birds in Belgium (MGRS 10 km)",
-      "description": "Occurrence cube for birds in Belgium between 2000 en 2024. The taxonomical resolution is 'species' and the temporal resolution is 'year' Spatial aggregation is done using the MGRS grid at 10 km scale. Only grid cells that fall within the 10 km MGRS reference grid for mainland Belgium (see b3data: `mgrs10_refgrid_belgium.geojson`) are included.",
+      "description": "Occurrence cube for birds in Belgium between 2000 en 2024. The taxonomical resolution is 'species' and the temporal resolution is 'year' Spatial aggregation is done using the MGRS grid at 10 km scale. Only grid cells that fall within the 10 km MGRS reference grid for mainland Belgium (see b3data: `mgrs10_refgrid_belgium.gpkg`) are included.",
       "sources": [
         {
           "title": "GBIF Occurrence Download",
@@ -64,10 +64,10 @@
     },
     {
       "name": "mgrs10_refgrid_belgium",
-      "path": "mgrs10_refgrid_belgium.geojson",
-      "format": "geojson",
+      "path": "mgrs10_refgrid_belgium.gpkg",
+      "format": "gpkg",
       "title": "MGRS 10 km reference grid Belgium",
-      "description": "MGRS 10 km reference grid for the mainland of Belgium.",
+      "description": "MGRS 10 km reference grid for the mainland of Belgium. EPSG:32631 (WGS 84 / UTM zone 31N).",
       "licenses": [
         {
           "name": "CC0-1.0",

inst/en_gb.dic

@@ -1,12 +1,14 @@
 Daele
 EEA
 GeoJSON
+GeoPackage
 Havenlaan
 Langeraert
 MGRS
 NC
 Rproj
 Teirlinckgebouw
+WGS
 cff
 dic
 gb

source/R/download_occ_cube.R

@@ -6,8 +6,10 @@ download_occ_cube <- function(sql_query, file, path, overwrite = FALSE) {
   # Stop if overwrite = FALSE and file does not exist
   file_path <- file.path(path, file)
   if (file.exists(file_path) && !overwrite) {
-    message(paste("File already exists. Reading existing file.",
-            "Set `overwrite = TRUE` to overwrite file.", sep = "\n"))
+    message(
+      paste("File already exists. Reading existing file.",
+            "Set `overwrite = TRUE` to overwrite file.", sep = "\n")
+    )
 
     occ_cube <- readr::read_csv(file = file_path, show_col_types = FALSE)
 
@@ -34,7 +36,8 @@ download_occ_cube <- function(sql_query, file, path, overwrite = FALSE) {
   readr::write_csv(
     x = occ_cube,
     file = file_path,
-    append = FALSE)
+    append = FALSE
+  )
 
   # Return tibble
   return(occ_cube)

source/add_spatial_resources.Rmd

@@ -39,7 +39,7 @@ Add spatial data resources to b3data frictionless data package.
 
 # Methods
 
-This report focuses on adding spatial resources (e.g. GeoJSON, raster) to the **b3data** frictionless data package.
+This report focuses on adding spatial resources (e.g. GeoPackage, raster) to the **b3data** frictionless data package.
 
 ## Source Data
 
@@ -57,7 +57,7 @@ Example:
 
 Each dataset includes the following metadata (see: [Frictionless resource spec](https://docs.ropensci.org/frictionless/articles/data-resource.html#properties-implementation)):
 
-- **format**: e.g. `geojson`
+- **format**: e.g. `gpkg`
 - **title**: e.g. `"MGRS 10 km reference grid for Belgium"`
 - **description**: concise explanation of content
 - **sources**: source if applicable
@@ -77,20 +77,22 @@ ggplot() + geom_sf(data = utm10_bel)
 ```
 
 Clean data and transform cell codes to MGRS.
+Convert to EPSG:32631 (WGS 84 / UTM zone 31N).
 
 ```{r}
 mgrs10_refgrid_belgium <- utm10_bel %>%
   select(utm_tag = TAG, geometry) %>%
   mutate(mgrscode = ifelse(grepl("^[A-G]", utm_tag), paste0("31U", utm_tag),
                            paste0("32U", utm_tag))) %>%
-  select(mgrscode, geometry)
+  select(mgrscode, geometry) %>%
+  st_transform(32631)
 ```
 
 Write to data package and add metadata.
 
 ```{r}
 st_write(mgrs10_refgrid_belgium,
-         file.path(package_path, "mgrs10_refgrid_belgium.geojson"),
+         file.path(package_path, "mgrs10_refgrid_belgium.gpkg"),
          delete_dsn = TRUE)
 ```
 
@@ -101,25 +103,28 @@ b3data_package <- read_package(file.path(package_path, "datapackage.json"))
 # Add resource to data package
 mgrs10_resource <- list(
   name = "mgrs10_refgrid_belgium",
-  path = "mgrs10_refgrid_belgium.geojson",
-  format = "geojson",
+  path = "mgrs10_refgrid_belgium.gpkg",
+  format = "gpkg",
   title = "MGRS 10 km reference grid Belgium",
-  description = "MGRS 10 km reference grid for the mainland of Belgium.",
+  description = paste("MGRS 10 km reference grid for the mainland of Belgium.",
+                      "EPSG:32631 (WGS 84 / UTM zone 31N)."),
   licenses = list(list(
     name = "CC0-1.0",
     path = "https://creativecommons.org/publicdomain/zero/1.0/",
     title = "Creative Commons Zero v1.0 Universal"
-    ))
-  )
+  ))
+)
 
 b3data_package <- add_manual_resource(
-  b3data_package, mgrs10_resource, replace = TRUE)
+  b3data_package, mgrs10_resource, replace = TRUE
+)
 
 # Write package to directory
 write_package(
   package = b3data_package,
   directory = package_path,
-  compress = TRUE)
+  compress = TRUE
+)
 ```
 
 ## EEA 100 km reference grid Europe

source/create_b3data_package.Rmd

@@ -38,7 +38,7 @@ Create [frictionless](https://docs.ropensci.org/frictionless/) data package with
 # Methods
 
 This report focuses on creating the **b3data** frictionless data package for tabular datasets.  
-A separate report adds spatial resources (e.g. GeoJSON, raster) to the same data package.
+A separate report adds spatial resources (e.g. GeoPackage, raster) to the same data package.
 
 ## Data Package Overview
 
@@ -134,7 +134,7 @@ bird_cube_belgium_mgrs10_full <- download_occ_cube(
 )
 ```
 
-We only select the grid cells that belong to the MGRS 10 km reference grid for the mainland of Belgium (see b3data `mgrs10_refgrid_belgium.geojson`).
+We only select the grid cells that belong to the MGRS 10 km reference grid for the mainland of Belgium (see b3data `mgrs10_refgrid_belgium.gpkg`).
 
 ```{r}
 # Read reference grid
@@ -166,8 +166,9 @@ b3data_package <- create_package() %>%
       "the temporal resolution is 'year'",
       "Spatial aggregation is done using the MGRS grid at 10 km scale.",
       "Only grid cells that fall within the 10 km MGRS reference grid for",
-      "mainland Belgium (see b3data: `mgrs10_refgrid_belgium.geojson`) are",
-      "included."),
+      "mainland Belgium (see b3data: `mgrs10_refgrid_belgium.gpkg`) are",
+      "included."
+    ),
     sources = list(list(
       title = "GBIF Occurrence Download",
       path = "https://doi.org/10.15468/dl.y3wpwk"
@@ -176,7 +177,7 @@ b3data_package <- create_package() %>%
       name = "CC0-1.0",
       path = "https://creativecommons.org/publicdomain/zero/1.0/",
       title = "Creative Commons Zero v1.0 Universal"
-      ))
+    ))
   )
 ```
 
@@ -193,10 +194,10 @@ b3data_package <- append(b3data_package,
                          c(name = "b3data"),
                          after = 0)
 b3data_package <- append(b3data_package,
-                         c(id = "https://doi.org/10.5281/zenodo.15181098"),
+                         c(id = "https://doi.org/10.5281/zenodo.15211029"),
                          after = 1)
 b3data_package <- append(b3data_package,
-                         c(version = "0.1.0"),
+                         c(version = "0.1.2"),
                          after = 2)
 
 # Warning: append() drops the custom datapackage class.
@@ -215,5 +216,6 @@ dir.create(package_path, showWarnings = FALSE, recursive = TRUE)
 write_package(
   package = b3data_package,
   directory = package_path,
-  compress = TRUE)
+  compress = TRUE
+)
 ```