This is a list of changes made between bioregion 1.1.2 (CRAN unreleased) and bioregion 1.1.3 (CRAN unreleased).
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
Indices Cz added to contribution()
This is a list of changes made between bioregion 1.1.1 (CRAN release 2024-04-19) and bioregion 1.1.2 (CRAN unreleased).
Affinity propagation algorithm added (function nhclu_affprop)
Function contribution() added to the package and the workflow.
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.
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.
First release on CRAN