Scripts used to create the b3data frictionless data package

Langeraert, Ward¹²³ Van Daele, Toon⁴⁵ Research Institute for Nature and Forest (INBO)⁶ European Union’s Horizon Europe Research and Innovation Programme (ID No 101059592)⁷

keywords: data package; b3verse; frictionless; data cubes

This repository contains scripts to create the b3data frictionless data package. This data package includes data resources used across the b3verse and is published on Zenodo.

This code is developed in context of T5.5 of the B-Cubed project.

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
• Published at:
• Used in: b3verse
• Importable in R via: frictionless R package

Resources can be imported in R like this:

Step 1 — Load the frictionless R package

# install.packages("frictionless")
library(frictionless)

Step 2 — Read the package descriptor from Zenodo

The content of the data package can be consulted using read_package().

b3data_package <- read_package("https://zenodo.org/records/15211029/files/datapackage.json")
b3data_package
#> A Data Package with 2 resources:
#> • bird_cube_belgium_mgrs10
#> • mgrs10_refgrid_belgium
#> For more information, see <https://doi.org/10.5281/zenodo.15211029>.
#> Use `unclass()` to print the Data Package as a list.

Step 3 — Import a resource (dataset)

Tabular datasets can be loaded using read_resource().

bird_cube_belgium <- read_resource(b3data_package, "bird_cube_belgium_mgrs10")
head(bird_cube_belgium)
#> # A tibble: 6 × 8
#>    year mgrscode specieskey species          family     n mincoordinateuncerta…¹
#>   <dbl> <chr>         <dbl> <chr>            <chr>  <dbl>                  <dbl>
#> 1  2000 31UDS65     2473958 Perdix perdix    Phasi…     1                   3536
#> 2  2000 31UDS65     2474156 Coturnix coturn… Phasi…     1                   3536
#> 3  2000 31UDS65     2474377 Fulica atra      Ralli…     5                   1000
#> 4  2000 31UDS65     2475443 Merops apiaster  Merop…     6                   1000
#> 5  2000 31UDS65     2480242 Vanellus vanell… Chara…     1                   3536
#> 6  2000 31UDS65     2480637 Accipiter nisus  Accip…     1                   3536
#> # ℹ abbreviated name: ¹​mincoordinateuncertaintyinmeters
#> # ℹ 1 more variable: familycount <dbl>

For non-tabular resources (e.g. spatial or raster data), use packages like sf or terra directly.

mgrs10_belgium <- sf::st_read(
  "https://zenodo.org/records/15211029/files/mgrs10_refgrid_belgium.gpkg",
  quiet = TRUE)
head(mgrs10_belgium)
#> Simple feature collection with 6 features and 1 field
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: 460000.1 ymin: 5620000 xmax: 480000.1 ymax: 5670000
#> Projected CRS: WGS 84 / UTM zone 31N
#>   mgrscode                           geom
#> 1  31UDS65 POLYGON ((470000.1 5651000,...
#> 2  31UDS66 POLYGON ((470000.1 5661000,...
#> 3  31UDS72 POLYGON ((480000 5621000, 4...
#> 4  31UDS73 POLYGON ((480000.1 5631000,...
#> 5  31UDS74 POLYGON ((480000.1 5641000,...
#> 6  31UDS75 POLYGON ((480000.1 5651000,...

📁 Repository structure

├── source                         ├ R markdown files
│   └── R                          ├ R scripts
├── data
│   ├── raw                        ├ create this folder and store raw data
│   ├── processed                  ├ store processed data
│   └── b3data_package             ├ b3data frictionless data package
├── checklist.yml                  ├ options checklist package (https://github.com/inbo/checklist)
├── organisation.yml               ├ organisation info (https://inbo.github.io/checklist/articles/organisation.html)
├── inst
│   └── en_gb.dic                  ├ dictionary with words that should not be checked by the checklist package
├── .github                        │ 
│   ├── workflows                  │ 
│   │   └── checklist_project.yml  ├ GitHub action settings
│   ├── CODE_OF_CONDUCT.md         │ 
│   └── CONTRIBUTING.md            │
├── b3data-scripts.Rproj           ├ R project
├── README.md                      ├ project description
├── LICENSE.md                     ├ license
├── CITATION.cff                   ├ citation info
├── .zenodo.json                   ├ zenodo metadata
└── .gitignore                     ├ files to ignore

Footnotes

1. author ↩

2. contact person ↩

3. Research Institute for Nature and Forest (INBO), Herman Teirlinckgebouw, Havenlaan 88 PO Box 73, B-1000 Brussels, Belgium ↩

4. author ↩

5. Research Institute for Nature and Forest (INBO), Herman Teirlinckgebouw, Havenlaan 88 PO Box 73, B-1000 Brussels, Belgium ↩

6. copyright holder ↩

7. funder ↩