This is a list of changes made in the development/GitHub version ofthe package between bioregion 1.2.0 (CRAN release 2025-01-31) and thenext CRAN release.
This is a list of changes made betweenbioregion1.1.1 (CRAN release 2024-04-19) andbioregion1.2.0 (CRAN release 2025-01-31).
Added affinity propagation algorithm(nhclu_affprop()).
Added a new method inhclu_hierarclust() toconstruct a consensus tree called Iterative Hierarchical Consensus Tree(IHCT). This resolves issues related to the order of sites in thedistance matrix and builds a consensus hierarchical tree with meaningfultopology.
Made many changes to functions related tohclu_hierarclust() due to this major update.
Updated generic functions to provideplot andprint methods forhclu_diana().
Addedsite_species_metrics() to the package andworkflow.
Addedbioregion_metrics() to the package andworkflow.
Renamedsubset_node() tosite_species_subset().
Added indicesCz tosite_species_metrics().
Updatedinstall_binaries():
bin.zip now stored on GitHub and backed up onNextCloud.download_only to execute only thedownload step.Addedcheck_install argument tonetclu_infomap(),netclu_louvain(), andnetclu_oslom().
Addedbetapart_to_bioregion() to thepackage.
Addedcompare_bioregionalizations() to thepackage.
Addedbioregionalization_metrics() to thepackage.
Updated documentation, vignettes, and tests.
Modified the way seeds are generated fornhclu_clara() andnhclu_clarans().
This is a list of changes made betweenbioregion1.1.0 (CRAN release 2024-03-19) andbioregion1.1.1 (CRAN release 2024-04-19).
Added hierarchy support for Louvain (C++).
Addedseed argument to stochastic algorithms (exceptLouvain C++).
Addedcut_weight argument tonetclu_*functions.
Changed value for sites without clusters from0 toNA.
Updated automated tests (code coverage > 60%).
Standardized controls, inputs, and outputs.
Fixed a bug infind_optimal_n() for cases wherepartition metrics did not vary.
This is a list of changes made betweenbioregion1.0.0 (CRAN release 2023-04-15) andbioregion1.1.0 (CRAN release 2024-03-19).
Added theresolution parameter to the igraph Louvainimplementation.
Added options tomat_to_net() to exclude diagonaland lower triangular matrices usinginclude_diag andinclude_lower.
Added a function to extract a subset of nodes (sites or species)frombioregion.clusters objects containing bothtypes.
Added a generic function to maintain attributes ofbioregion.pairwise.metric objects and track the number ofsites and species.
Added new functions:nhclu_clara() andnhclu_clarans().
Edited vignettes to document new functions.
Modified controls forbioregion.pairwise.metricobjects.
Added theinclude_formula argument tosimilarity_dissimilarity_conversion() to (not) selectformula metrics.
Allowed negative values insimilarity() with theEuclidean metric.
First release on CRAN