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.
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.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.
First release on CRAN