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Changelog

Source: NEWS.md

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.

  • Affinity propagation algorithm added (function nhclu_affprop).

  • Added a new method to construct a consensus tree in hclu_hierarclust. This method is called Iterative Hierarchical Consensus Tree (IHCT). It conclusively solves issues related to the order of sites in the distance matrix and building a consensus hierarchical tree with a meaningful topology.

  • Many changes to functions related to hclu_hierarclust due to this major change.

  • Updated generic functions to provide plot and print for diana.

  • Function site_species_metrics() added to the package and the workflow.

  • Function bioregion_metrics() added to the package and the workflow.

  • Function subset_node() renamed site_species_subset().

  • Indices Cz added 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 only execute the download step
       

  • Added argument check_install in netclu_infomap, netclu_louvain, and netclu_oslom.

  • Function betapart_to_bioregion() added to the package.

  • Function compare_bioregionalizations() added to the package.

  • Function bioregionalization_metrics() added to the package.

  • Function bioregion_metrics() added to the package.

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 for Louvain cpp.

  • Added seed argument to stochastic algorithms (except Louvain cpp).

  • Added argument cut_weight in netclu_ fonctions.

  • Changed value for sites without cluster (0 -> NA).

  • Updated automated tests (code coverage > 60%).

  • Controls and outputs/inputs standardization.

  • Fixed a bug in find_optimal_n() in the special case 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 in the igraph Louvain version.

  • Added possibility to remove diagonal and lower triangular matrix in mat_to_net() for squared matrix with argument include_diag and include_lower.

  • Added a function to extract a subset of node according to its type (sites or species) from a bioregion.clusters object containing both types of nodes (sites and species).

  • Added a generic function to maintain attributes of bioregion.pairwise.metric objects + keep track of number of sites and species.

  • Functions added: nhclu_clara(), nhclu_clarans().

  • The corresponding vignettes are edited to document the new functions.

  • Modification of the way ‘bioregion.pairwise.metric’ object are controlled.

  • Allow to (not) select ‘formula metrics’ in similarity_dissimilarity_conversion() with the new argument “include_formula”.

  • Allow negative values in similarity() with the Euclidean metric.

bioregion 1.0.0

First release on CRAN