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 the next CRAN release.
site_species_metrics() and bioregion_metrics().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 bioregion
partitions and spatial coherence can be computed using either the size or
the area of the largest contiguous component. The col_bioregion argument
is 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).
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$node_type.
Renamed the class bioregion.pairwise.metric to bioregion.pairwise.
Added a verbose argument to all talkative functions allowing users to
control the display of progress messages.
New features
Added export of the function exportGDF() with documentation and tests.
Added bioregion_colors() to provide consistent bioregion color palettes for
use across multiple visualizations (maps, networks, graphs, etc.).
Updated map_bioregions() to handle bioregion colors.
Added a generic function summary() for a clearer display of results.
Added bind_pairwise() to combine pairwise (dis)similarity objects.
Added as_bioregion_pairwise() to replace and improve upon
betapart_to_bioregion(), which is now deprecated.
Added a comparison with other R packages for computing dissimilarity metrics in tutorial 3 (Pairwise similarity/dissimilarity metrics).
Bug fixes
Fixed an tibble input problem with net_to_mat() (issue #11).
Fixed a problem in inputs$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.
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():
bin.zip now stored on GitHub and backed up on NextCloud.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().
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.
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.
First release on CRAN