Add spatial data

.gitignore

@@ -16,10 +16,10 @@
 *.shx
 *.xls*
 *_files
-*.csv
 *.gz
-*.zip
+*.geojson
 docs
 libs
 output
 renv/library
+data/raw

README.Rmd

@@ -46,6 +46,22 @@ This repository contains scripts to create the b3data [frictionless](https://doc
 
 This code is developed in context of **T5.5** of the [B-Cubed project](https://b-cubed.eu/).
 
+## Order of execution
+
+Follow the steps below to run the scripts in a logical order.
+
+**1.** `create_b3data_package.Rmd`
+
+- creates the data package
+- adds tabular resources
+- writes data package
+
+**2.** `add_spatial_resources.Rmd`
+
+- loads data package
+- adds spatial resources
+- writes data package
+
 ## 📦 The `b3data` data package
 
 - **Name**: `b3data`

README.md

@@ -33,6 +33,22 @@ on [Zenodo](https://zenodo.org/). <!-- description: end -->
 This code is developed in context of **T5.5** of the [B-Cubed
 project](https://b-cubed.eu/).
 
+## Order of execution
+
+Follow the steps below to run the scripts in a logical order.
+
+**1.** `create_b3data_package.Rmd`
+
+- creates the data package
+- adds tabular resources
+- writes data package
+
+**2.** `add_spatial_resources.Rmd`
+
+- loads data package
+- adds spatial resources
+- writes data package
+
 ## 📦 The `b3data` data package
 
 - **Name**: `b3data`

data/b3data_package/datapackage.json

@@ -10,9 +10,16 @@
       "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.",
-      "sources": ["GBIF Occurrence Download", "https://doi.org/10.15468/dl.y3wpwk"],
-      "licenses": [" CC BY-NC 4.0", "https://creativecommons.org/licenses/by-nc/4.0/", "Creative Commons Attribution-NonCommercial 4.0 International"],
+      "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.",
+      "sources": {
+        "title": "GBIF Occurrence Download",
+        "path": "https://doi.org/10.15468/dl.y3wpwk"
+      },
+      "licenses": {
+        "name": "CC BY-NC 4.0",
+        "path": "https://creativecommons.org/licenses/by-nc/4.0/",
+        "title": "Creative Commons Attribution-NonCommercial 4.0 International"
+      },
       "schema": {
         "fields": [
           {
@@ -49,27 +56,47 @@
           }
         ]
       }
+    },
+    {
+      "name": "mgrs10_refgrid_belgium",
+      "path": "mgrs10_refgrid_belgium.geojson",
+      "profile": "spatial-data-resource",
+      "format": "geojson",
+      "title": "MGRS 10 Km reference grid Belgium",
+      "description": "MGRS 10 Km reference grid for the mainland of Belgium.",
+      "licenses": {
+        "name": "CC0 1.0",
+        "path": "https://creativecommons.org/publicdomain/zero/1.0/",
+        "title": "Creative Commons Zero v1.0 Universal"
+      }
     }
   ],
   "title": "b3data: Data resources for the b3verse",
   "description": "This data package contains data resources to be used across the b3verse (https://docs.b-cubed.eu/guides/b3verse/). This includes example datasets (occurrence cubes) as well as spatial resources like reference grids or raster data.",
-  "keywords1": "data cubes",
-  "licenses.name": " CC BY-NC 4.0",
+  "keywords": ["data cubes", "b3verse", "frictionless", "biodiversity"],
+  "licenses": {
+    "name": "CC BY-NC 4.0",
+    "path": "https://creativecommons.org/licenses/by-nc/4.0/",
+    "title": "Creative Commons Attribution-NonCommercial 4.0 International"
+  },
   "version": "0.1.0",
-  "sources.title": "b3data-scripts",
-  "contributors.title": "Ward Langeraert",
-  "contributors.path": "https://orcid.org/0000-0002-5900-8109",
-  "contributors.email": "[email protected]",
-  "contributors.role": "author",
-  "contributors.organization": "Research Institute for Nature and Forest (INBO)",
-  "contributors.title.1": "Toon Van Daele",
-  "contributors.path.1": "https://orcid.org/0000-0002-1362-853X",
-  "contributors.role.1": "contributor",
-  "contributors.organization.1": "Research Institute for Nature and Forest (INBO)",
-  "sources.path": "https://github.com/b-cubed-eu/b3data-scripts",
-  "licenses.path": "https://creativecommons.org/licenses/by-nc/4.0/",
-  "licenses.title": "Creative Commons Attribution-NonCommercial 4.0 International",
-  "keywords2": "b3verse",
-  "keywords3": "frictionless",
-  "keywords4": "biodiversity"
+  "sources": {
+    "title": "b3data-scripts",
+    "path": "https://github.com/b-cubed-eu/b3data-scripts"
+  },
+  "contributors": [
+    {
+      "title": "Ward Langeraert",
+      "path": "https://orcid.org/0000-0002-5900-8109",
+      "email": "[email protected]",
+      "role": "author",
+      "organization": "Research Institute for Nature and Forest (INBO)"
+    },
+    {
+      "title": "Toon Van Daele",
+      "path": "https://orcid.org/0000-0002-1362-853X",
+      "role": "contributor",
+      "organization": "Research Institute for Nature and Forest (INBO)"
+    }
+  ]
 }

source/R/add_manual_resource.R

@@ -0,0 +1,23 @@
+add_manual_resource <- function(package, new_resource, replace = TRUE) {
+  if (replace) {
+    # Filter out any resource with same name or path
+    package$resources <- Filter(function(res) {
+      !(res$name == new_resource$name && res$path == new_resource$path)
+    }, package$resources)
+  } else {
+    # If not overwriting, check for duplicates and warn
+    conflict <- any(vapply(package$resources, function(res) {
+      res$name == new_resource$name && res$path == new_resource$path
+    }, logical(1)))
+
+    if (conflict) {
+      warning(paste("Resource with same name and path already exists and",
+                    "`replace = FALSE`. Skipping."))
+      return(package)
+    }
+  }
+
+  # Append new resource
+  package$resources <- append(package$resources, list(new_resource))
+  return(package)
+}

source/add_spatial_resources.Rmd

@@ -0,0 +1,129 @@
+---
+title: "Add spatial resources to b3data data package"
+author: "Ward Langeraert"
+date: "`r Sys.Date()`"
+output:
+  html_document:
+    code_folding: hide
+    toc: true
+    toc_float: true
+    toc_collapsed: true
+editor_options: 
+  chunk_output_type: console
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+```{r, warning=FALSE, message=FALSE}
+# Load packages
+library(tidyverse)     # Data wrangling and visualisation
+library(frictionless)  # Create frictionless data package
+library(sf)            # Spatial objects
+
+# Source functions
+source(here::here("source", "R", "add_manual_resource.R"))
+
+# Data path and create directory if necessary
+data_path <- here::here("data", "raw")
+dir.create(data_path, showWarnings = FALSE, recursive = TRUE)
+
+package_path <- here::here("data", "b3data_package")
+dir.create(package_path, showWarnings = FALSE, recursive = TRUE)
+```
+
+# Goal
+
+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.
+
+## Source Data
+
+Spatial data need to be saved locally in the data package directory and then added manually to the descriptor file using `append()`.
+We provide the reference grids for the occurrence cubes in the data package following this naming convention:
+
+```
+resource_name = "<grid><resolution>refgrid<region>"
+```
+
+Example:  
+`mgrs10_refgrid_belgium` → MGRS 10 km reference grid Belgium
+
+## Resource-level Metadata
+
+Each dataset includes the following metadata (see: [Frictionless resource spec](https://docs.ropensci.org/frictionless/articles/data-resource.html#properties-implementation)):
+
+- **profile**: `spatial-data-resource`
+- **format**: e.g. `geojson`
+- **title**: e.g. `"MGRS 10 km reference grid for Belgium"`
+- **description**: concise explanation of content
+- **sources**: source if applicable
+- **licenses**: [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/)
+
+# Datasets
+## MGRS 10 Km reference grid Belgium
+
+Load the data.
+
+```{r}
+# Read reference grid
+utm10_bel <- st_read(file.path(data_path, "utm10_bel.shp"))
+
+# Visualise
+ggplot() + geom_sf(data = utm10_bel)
+```
+
+Clean data and transform cell codes to MGRS.
+
+```{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)
+```
+
+Write to data package and add metadata.
+
+```{r}
+st_write(mgrs10_refgrid_belgium,
+         file.path(package_path, "mgrs10_refgrid_belgium.geojson"),
+         delete_dsn = TRUE)
+```
+
+```{r}
+# Read package
+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",
+  profile = "spatial-data-resource",
+  format = "geojson",
+  title = "MGRS 10 Km reference grid Belgium",
+  description = "MGRS 10 Km reference grid for the mainland of Belgium.",
+  licenses = 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)
+
+# Write package to directory
+write_package(
+  package = b3data_package,
+  directory = package_path,
+  compress = TRUE)
+```
+
+## EEA 100 km reference grid Europe
+
+> Coming soon