Compare unstructured data

Langeraert, Ward¹²³ Cartuyvels, Emma¹³ Van Daele, Toon¹³ Research Institute for Nature and Forest (INBO)⁴ European Union's Horizon Europe Research and Innovation Programme (ID No 101059592)⁵

keywords: structured data; data quality; unstructured data; data cubes; biodiversity informatics

Scripts to explore the conditions that determine the reliability of models, trends and status by comparing aggregated cubes with structured monitoring schemes.

This code is developed in context of T4.5 of the B-Cubed project.

Analyses workflow

To download the latest version of each of the data sets run prepare_abv_data.Rmd and Prepare_data_10km.Rmd. Alternatively, you can download the exact same data we used by following the GBIF links in these same Rmd's. These data sets are saved under data/raw, the Rmd's further clean the data and add geometric properties. The cleaned data is stored in both .csv and .gpkg format under data/interim.

To get the list of ABV birds used to filter the data in both pipelines run the get_abv_species.R after sourcing the functions in taxon_mapping.R.

To run the targets pipelines, run run_pipeline.R in the folder of the pipeline you want to run. Afterwards, you can run the associated Rmd found under reports.

Repo structure

├── source                         ├ 
│   ├── pipelines                  ├ target pipelines https://books.ropensci.org/targets/
│   ├── R                          ├ R scripts and R markdown files
│   └── reports                    ├ reports based on output from target pipelines
├── data
│   ├── raw                        ├ create this folder and store raw data, see prepare_abv_data.Rmd
│   ├── intermediate               ├ store intermediate data
│   └── processed                  ├ store processed data
├── 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 repo settings
│   ├── CODE_OF_CONDUCT.md         │ 
│   └── CONTRIBUTING.md            │
├── comp-unstructured-data.Rproj   ├ R project
├── README.md                      ├ project description
├── LICENSE.md                     ├ licence
├── LICENSE                        │
├── CITATION.cff                   ├ citation info
├── .zenodo.json                   ├ zenodo metadata
└── .gitignore                     ├ files to ignore

Footnotes

1. author ↩ ↩² ↩³

2. contact person ↩

3. Research Institute for Nature and Forest (INBO), Herman Teirlinckgebouw, Havenlaan 88 PO Box 73, B-1000 Brussels, Belgium ↩ ↩² ↩³

4. copyright holder ↩

5. funder ↩