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bioregion 1.1.1.9000

This is a list of changes made in the development/GitHub version of the package between bioregion 1.1.1 (CRAN release 2024-04-19) and the next CRAN release.

  • 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.

bioregion 1.0.0

First release on CRAN