D5.5 R Package and Documentation (Vignettes) for the Calculation of the Indicators

This report outlines the design, implementation, and public release of the complete R package ecosystem, the b3verse, developed under Work Package 5 of the B3 project. The b3verse consists of eleven software packages and one dedicated data package (b3data). Together, these packages consolidate biodiversity indicator calculation into a single coherent and reproducible open-source framework, covering general biodiversity indicators, phylogenetic diversity indicators, alien species impact indicators, and bootstrap-based uncertainty estimation.

The ecosystem includes core indicator packages (b3gbi, pdindicatoR, impIndicator, and dubicube), as well as modelling-oriented cube packages (dissmapr for compositional turnover modelling, and invasimapr for invasion risk assessment based on occurrence and trait-derived invasion fitness and community invasibility). Supporting packages provide data access, simulation utilities, workflow infrastructure, and documentation, complemented by the example dataset package b3data to enable reproducible demonstrations and testing.

Quality and sustainability are core principles of current and future development. The software adheres to B3 development guidelines, utilizes automated integration workflows via a dedicated R-universe platform for continuous distribution, and employs automated unit tests to guarantee the efficiency and stability of results against a variety of data inputs. Furthermore, the entire suite is permanently archived on Zenodo to ensure long-term reproducibility and stable citation.

The b3verse delivers comprehensive documentation, including detailed R package documentation, vignettes, and tutorials, maximizing user accessibility. The robust automation capabilities lay the necessary groundwork for generating simple dashboards in Work Package 6 to facilitate cloud computing and direct accessibility for policymakers. Future efforts will focus on finalizing formal code reviews, expanding unit test coverage, and ensuring the continued maintenance and evolution of the packages.