The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

bioregion 1.2.0.9000

This is a list of changes made in the development/GitHub version of the package between bioregion 1.2.0 (CRAN release 2025-01-31) and the next CRAN release.

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.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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.