Function reference

install_binaries()
 Download, unzip, check permission and test the bioregion's binary files

mat_to_net()
 Create a data.frame from a contingency table

net_to_mat()
 Create a contingency table from a data.frame

subset_node()
 Extract a subset of node from a bioregion.clusters object

similarity()
 Compute similarity metrics between sites based on species composition

dissimilarity()
 Compute dissimilarity metrics (betadiversity) between sites based on species composition

similarity_to_dissimilarity()
 Convert similarity metrics to dissimilarity metrics

dissimilarity_to_similarity()
 Convert dissimilarity metrics to similarity metrics

hclu_hierarclust()
 Hierarchical clustering based on dissimilarity or betadiversity

hclu_diana()
 Divisive hierarchical clustering based on dissimilarity or betadiversity

cut_tree()
 Cut a hierarchical tree

hclu_optics()
 OPTICS hierarchical clustering algorithm

nhclu_dbscan()
 dbscan clustering

nhclu_kmeans()
 Non hierarchical clustering: kmeans analysis

nhclu_pam()
 Non hierarchical clustering: partitioning around medoids

nhclu_clara()
 Non hierarchical clustering: CLARA

nhclu_clarans()
 Non hierarchical clustering: CLARANS

netclu_beckett()
 Community structure detection in weighted bipartite network via modularity optimization

netclu_infomap()
 Infomap community finding

netclu_greedy()
 Community structure detection via greedy optimization of modularity

netclu_labelprop()
 Finding communities based on propagating labels

netclu_leadingeigen()
 Finding communities based on leading eigen vector of the community matrix

netclu_louvain()
 Louvain community finding

netclu_oslom()
 OSLOM community finding

netclu_walktrap()
 Community structure detection via short random walks

netclu_leiden()
 Finding communities using the Leiden algorithm

partition_metrics()
 Calculate metrics for one or several partitions

find_optimal_n()
 Search for an optimal number of clusters in a list of partitions

compare_partitions()
 Compare cluster memberships among multiple partitions

map_clusters()
 Create a map of bioregions

vegedf
 Spatial distribution of Mediterranean vegetation (data.frame)

vegemat
 Spatial distribution of Mediterranean vegetation (cooccurrence matrix)

vegesf
 Spatial distribution of Mediterranean vegetation (spatial grid)

fishdf
 Spatial distribution of fish in Europe (data.frame)

fishmat
 Spatial distribution of fish in Europe (cooccurrence matrix)

fishsf
 Spatial distribution of fish in Europe