Data and code for "Report on the criteria for data quality and species characteristics for estimating species status and trends" (Flanders case study)

Description This archive contains the complete reproducible research compendium used in the accompanying report "Report on the criteria for data quality and species characteristics for estimating species status and trends", developed in the context of Task 4.5 of the B-Cubed project (Horizon Europe, Grant No. 101059592). The objective of this work is to explore the conditions under which models, trends, and biodiversity indicators derived from aggregated unstructured biodiversity data are reliable, by systematically comparing them to structured monitoring schemes. The archive includes: All R scripts and {targets} pipelines required to reproduce the analyses The exact data versions used in the study Processed datasets used for modelling and cube aggregation Rendered HTML reports generated from R Markdown Output figures and derived results The workflow follows a fully reproducible, pipeline-based structure built around the {targets} R package, ensuring transparent dependency management and incremental execution. Workflow structure The analysis proceeds in four stages: Data acquisition and preprocessing Species list preparation Cube aggregation, modelling, and indicator computation via {targets} pipelines Reporting and visualisation through R Markdown All intermediate and final outputs are included in this archive to ensure long-term reproducibility independent of external services. Data sources The archive contains biodiversity data retrieved primarily via GBIF. The exact download DOIs corresponding to the data versions used are included and cited to guarantee traceability and version control.