Changelog • bioregion

bioregion 1.5.0.9000

This is a list of changes made in the development/GitHub version of the package between bioregion 1.5.0 (CRAN release 2026-10-10) and the next CRAN release.

Multiple bug fixes following recent name changes in bioregionalization_metrics(): fixed print() outputs of find_optimal_n(), fixed the cluster_info of hclu_diana(), re-implemented the inclusion of the output of find_optimal_n() into n_clust argument of cut_tree(), hclu_hierarclust() and hclu_diana() (documented but broke in recent updates), fixed print() and str() on the output of site_species_metrics(), which did not list the silhouette metric and, for str(), the prop_endemics metric), fixed print() on the output of hclu_hierarclust().
New plot() for the outputs of hclu_hierarclust(), hclu_diana() and cut_tree(). The clusters are now shown as coloured bars under the tree (one bar per partition) instead of rectangles. The colours are those of bioregion_colors(), so that trees and maps share the same colours. Trees can now be mirrored (tree_flip = TRUE) or drawn horizontally (tree_horizontal = TRUE), and site names can be removed (tree_labels = FALSE). The plot method has its own help page (?plot.bioregion.clusters).
Breaking change: in map_bioregions(), a numeric partition_index now gives the number of the partition (1 for the first partition) instead of its column in bioregionalization$clusters (where the first partition was 2). Code using numbers must subtract 1 from them; names are not affected. A message recalls this change the first time numbers are used in a session.
map_bioregions() now uses the default colors of bioregion_colors() when the bioregionalization has no colors (instead of the default colors of sf), so that colors match among the package visualization functions when default parameters are used.

bioregion 1.5.0

This is a list of changes made in the development/GitHub version of the package between bioregion 1.4.0 (CRAN release 2026-03-29) and bioregion 1.5.0 (CRAN release 2026-10-10).

The tree evaluation function is now implemented in C++ to be faster across all methods in hclu_hierarclust().
The iterative hierarchical consensus tree is now available on its own with the new function ihct(). In hclu_hierarclust(), the default of optimal_tree_method is now called "ihct“” which now runs 5 to 7 times faster. The former name "iterative_consensus_tree" is still accepted and gives the same result (PR #38).
Integrated fixes for the upcoming release of dbscan 1.2.7 (PR #37).
Minor fix to the map_bioregions() documentation (#35).
Improved get_pairwise_membership efficiency (PR #32).
Metric names have been changed to snake_case in site_species_metrics(), bioregion_metrics() and bioregionalization_metrics(). The package is being progressively standardized on snake_case metric names. Old metric names are still accepted as inputs but are converted to snake_case in outputs.
find_optimal_n() has been updated. bioregionalizationsargument changed to evaluation_df.
bioregionalization_metrics() has been updated. The anosim metric (along with the associated p-value) is now computed with vegan. The eval_metric argument changed to eval_metrics and net to comat. col_sites, andcol_species arguments are now deprecated.
Relaxed matching controls in site_species_metrics() and bioregion_metrics().

bioregion 1.4.0

This is a list of changes made between bioregion 1.3.0 (CRAN release 2026-01-23) and bioregion 1.4.0 (CRAN release 2026-03-29).

bioregion_metrics() has been updated. It now supports multiple bioregionpartitions and spatial coherence can be computed using either the size orthe area of the largest contiguous component. The col_bioregion argumentis now deprecated.
map_bioregion() has been reformatted: bioregionalization argument changed to partition_index, clusters to bioregionalization, geometry to map and write_clusters to map_as_output.
map_bioregion() can now handle terra inputs (terra added in Suggests).
clusters argument changed to bioregionalization in site_species_subset().
Added seed argument to hclu_hierarclust() (issue #10).
Fixed invalid input, control and output in nhclu_affprop() (issue #14).

bioregion 1.3.0

This is a list of changes made between bioregion 1.2.0 (CRAN release 2025-01-31) and bioregion 1.3.0 (CRAN release 2026-01-23).

Function changes

Added the inputs$data_type field to all clustering outputs to explicitly track whether original co-occurrence data were occurrence-based or abundance-based. This field is automatically determined based on the algorithm type and the similarity/dissimilarity metric used.
Added the inputs$node_type field to all clustering outputs to explicitly indicate whether the clustering includes only sites or both sites and species. This changes include the hidden node_type attributes.
site_species_metrics() has been thoroughly reformatted and now provides: species-per-bioregions metrics, species-in-bioregionalization metrics, site-per-chorotypes metrics, site-in-chorological classification metrics, site-per-bioregions metrics, and site-in-bioregionalization metrics, all of which are rigorously defined in the corresponding vignette.
site_species_subset() has been simplified taking advantage on inputs$node_type.
Renamed the class bioregion.pairwise.metric to bioregion.pairwise.
Added a verbose argument to all talkative functions allowing users to control the display of progress messages.
bioregionalization_metrics() now returns a data.frame (columns partition, n_bioregions, then one column per metric) instead of a list with an evaluation_df element. Code that used x$evaluation_df should now use x directly.

New features

Added export of the function exportGDF() with documentation and tests.
Added bioregion_colors() to provide consistent bioregion color palettes for use across multiple visualizations (maps, networks, graphs, etc.).
Updated map_bioregions() to handle bioregion colors.
Added a generic function summary() for a clearer display of results.
Added bind_pairwise() to combine pairwise (dis)similarity objects.
Added as_bioregion_pairwise() to replace and improve upon betapart_to_bioregion(), which is now deprecated.
Added a comparison with other R packages for computing dissimilarity metrics in tutorial 3 (Pairwise similarity/dissimilarity metrics).

Bug fixes

Fixed an tibble input problem with net_to_mat() (issue #11).
Fixed a problem in inputs$pairwise_metric when numeric index in all clustering outputs.
Modified the keep_trials argument in hclu_hierarclust() and fixed a potential issue with randomized matrix storage.

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 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 objects.
Added the include_formula argument to similarity_dissimilarity_conversion() to (not) select formula metrics.
Allowed negative values in similarity() with the Euclidean metric.

bioregion 1.0.0

First release on CRAN