NEWS.md
In bioregion: Comparison of Bioregionalisation Methods

bioregion 1.2.0.9000

This is a list of changes made in the development/GitHub version of the package between bioregion 1.2.0 (CRAN release 2025-01-31) and the next CRAN release.

bioregion 1.2.0

This is a list of changes made between bioregion 1.1.1 (CRAN release 2024-04-19) and bioregion 1.2.0 (CRAN release 2025-01-31).

Added affinity propagation algorithm (nhclu_affprop()).
Added a new method in hclu_hierarclust() to construct a consensus tree called Iterative Hierarchical Consensus Tree (IHCT). This resolves issues related to the order of sites in the distance matrix and builds a consensus hierarchical tree with meaningful topology.
Made many changes to functions related to hclu_hierarclust() due to this major update.
Updated generic functions to provide plot and print methods for hclu_diana().
Added site_species_metrics() to the package and workflow.
Added bioregion_metrics() to the package and workflow.
Renamed subset_node() to site_species_subset().
Added indices Cz to site_species_metrics().
Updated install_binaries():
Archive bin.zip now stored on GitHub and backed up on NextCloud.
Added Infomap version 2.8.0.
Added argument download_only to execute only the download step.
Added check_install argument to netclu_infomap(), netclu_louvain(), and netclu_oslom().
Added betapart_to_bioregion() to the package.
Added compare_bioregionalizations() to the package.
Added bioregionalization_metrics() to the package.
Updated documentation, vignettes, and tests.
Modified the way seeds are generated for nhclu_clara() and nhclu_clarans().

bioregion 1.1.1

This is a list of changes made between bioregion 1.1.0 (CRAN release 2024-03-19) and bioregion 1.1.1 (CRAN release 2024-04-19).

Added hierarchy support for Louvain (C++).
Added seed argument to stochastic algorithms (except Louvain C++).
Added cut_weight argument to netclu_* functions.
Changed value for sites without clusters from 0 to NA.
Updated automated tests (code coverage > 60%).
Standardized controls, inputs, and outputs.
Fixed a bug in find_optimal_n() for cases where partition metrics did not vary.

bioregion 1.1.0

This is a list of changes made between bioregion 1.0.0 (CRAN release 2023-04-15) and bioregion 1.1.0 (CRAN release 2024-03-19).

Added the resolution parameter to the igraph Louvain implementation.
Added options to mat_to_net() to exclude diagonal and lower triangular matrices using include_diag and include_lower.
Added a function to extract a subset of nodes (sites or species) from bioregion.clusters objects containing both types.
Added a generic function to maintain attributes of bioregion.pairwise.metric objects and track the number of sites and species.
Added new functions: nhclu_clara() and nhclu_clarans().
Edited vignettes to document new functions.
Modified controls for bioregion.pairwise.metric objects.
Added the include_formula argument to similarity_dissimilarity_conversion() to (not) select formula metrics.
Allowed negative values in similarity() with the Euclidean metric.