Function reference

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

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

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

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 indices to dissimilarity metrics

dissimilarity_to_similarity()
 Convert dissimilarity indices to similarity indices

hclu_hierarclust()
 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

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

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 eigenvector of the community matrix

netclu_louvain()
 Louvain community finding

netclu_oslom()
 OSLOM community finding

netclu_walktrap()
 Community structure detection via short random walks

partition_metrics()
 Calculate metrics for one or several partitions

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

map_clusters()
 Create a map of bioregions