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Compare unstructured data

Langeraert, Ward[^aut][^cre][^INBO] Cartuyvels, Emma[^aut][^INBO] Van Daele, Toon[^aut][^INBO] Research Institute for Nature and Forest (INBO)[^cph] European Union's Horizon Europe Research and Innovation Programme (ID No 101059592)^fnd

[^cph]: copyright holder

[^cre]: contact person [^INBO]: Research Institute for Nature and Forest (INBO), Herman Teirlinckgebouw, Havenlaan 88 PO Box 73, B-1000 Brussels, Belgium

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. <!-- description: end -->

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