Comparison of Bioregionalization Methods

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Documentation for package ‘bioregion’ version 1.3.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

as_bioregion_pairwise	Convert a matrix or list of matrices to a bioregion (dis)similarity object
betapart_to_bioregion	Convert betapart dissimilarity to bioregion dissimilarity (DEPRECATED)
bind_pairwise	Combine and enrich bioregion (dis)similarity object(s)
bioregionalization_metrics	Calculate metrics for one or several bioregionalizations
bioregion_colors	Add color palettes to bioregion cluster objects
bioregion_metrics	Calculate contribution metrics for bioregions
compare_bioregionalizations	Compare cluster memberships among multiple bioregionalizations
cut_tree	Cut a hierarchical tree
dissimilarity	Compute dissimilarity metrics (beta-diversity) between sites based on species composition
dissimilarity_to_similarity	Convert dissimilarity metrics to similarity metrics
exportGDF	Export a network to GDF format for Gephi visualization
find_optimal_n	Search for an optimal number of clusters in a list of bioregionalizations
fishdf	Spatial distribution of fish in Europe (data.frame)
fishmat	Spatial distribution of fish in Europe (co-occurrence matrix)
fishsf	Spatial distribution of fish in Europe
hclu_diana	Divisive hierarchical clustering based on dissimilarity or beta-diversity
hclu_hierarclust	Hierarchical clustering based on dissimilarity or beta-diversity
hclu_optics	OPTICS hierarchical clustering algorithm
install_binaries	Download, unzip, check permissions, and test the bioregion's binary files
map_bioregions	Create a map of bioregions
mat_to_net	Create a data.frame from a contingency table
netclu_beckett	Community structure detection in weighted bipartite networks via modularity optimization
netclu_greedy	Community structure detection via greedy optimization of modularity
netclu_infomap	Infomap community finding
netclu_labelprop	Finding communities based on propagating labels
netclu_leadingeigen	Finding communities based on the leading eigenvector of the community matrix
netclu_leiden	Finding communities using the Leiden algorithm
netclu_louvain	Louvain community finding
netclu_oslom	OSLOM community finding
netclu_walktrap	Community structure detection via short random walks
net_to_mat	Create a contingency table from a data.frame
nhclu_affprop	Non-hierarchical clustering: Affinity Propagation
nhclu_clara	Non-hierarchical clustering: CLARA
nhclu_clarans	Non-hierarchical clustering: CLARANS
nhclu_dbscan	Non-hierarchical clustering: DBSCAN
nhclu_kmeans	Non-hierarchical clustering: K-means analysis
nhclu_pam	Non-hierarchical clustering: Partitioning Around Medoids
similarity	Compute similarity metrics between sites based on species composition
similarity_to_dissimilarity	Convert similarity metrics to dissimilarity metrics
site_species_metrics	Calculate metrics for sites and species relative to bioregions and chorotypes
site_species_subset	Extract a subset of sites or species from a 'bioregion.clusters' object
vegedf	Spatial distribution of Mediterranean vegetation (data.frame)
vegemat	Spatial distribution of Mediterranean vegetation (co-occurrence matrix)
vegesf	Spatial distribution of Mediterranean vegetation (spatial grid)