Comparison of Bioregionalization Methods
Convert dissimilarity metrics to similarity metrics
Compute dissimilarity metrics (beta-diversity) between sites based on ...
Export a network to GDF format for Gephi visualization
Search for an optimal number of clusters in a list of bioregionalizati...
Divisive hierarchical clustering based on dissimilarity or beta-divers...
Hierarchical clustering based on dissimilarity or beta-diversity
OPTICS hierarchical clustering algorithm
Extract a subset of sites or species from a bioregion.clusters objec...
Calculate metrics for one or several bioregionalizations
Compare cluster memberships among multiple bioregionalizations
Cut a hierarchical tree
Infomap community finding
Finding communities based on propagating labels
Finding communities based on the leading eigenvector of the community ...
Finding communities using the Leiden algorithm
Louvain community finding
OSLOM community finding
Community structure detection via short random walks
Non-hierarchical clustering: Affinity Propagation
Non-hierarchical clustering: CLARA
Non-hierarchical clustering: CLARANS
Non-hierarchical clustering: DBSCAN
Non-hierarchical clustering: K-means analysis
Non-hierarchical clustering: Partitioning Around Medoids
Convert similarity metrics to dissimilarity metrics
Compute similarity metrics between sites based on species composition
Calculate metrics for sites and species relative to bioregions and cho...
Convert a matrix or list of matrices to a bioregion (dis)similarity ob...
Convert betapart dissimilarity to bioregion dissimilarity (DEPRECATED)
Combine and enrich bioregion (dis)similarity object(s)
Add color palettes to bioregion cluster objects
Calculate contribution metrics for bioregions
Download, unzip, check permissions, and test the bioregion's binary fi...
Create a map of bioregions
Create a data.frame from a contingency table
Create a contingency table from a data.frame
Community structure detection in weighted bipartite networks via modul...
Community structure detection via greedy optimization of modularity
The main purpose of this package is to propose a transparent methodological framework to compare bioregionalization methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).
Useful links