Comparison of Bioregionalisation Methods

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Documentation for package ‘bioregion’ version 1.0.0

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compare_partitions Compare cluster memberships among multiple partitions
cut_tree Cut a hierarchical tree
dissimilarity Compute dissimilarity metrics (beta-diversity) between sites based on species composition
dissimilarity_to_similarity Convert dissimilarity indices to similarity indices
find_optimal_n Search for an optimal number of clusters in a list of partitions
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_hierarclust Hierarchical clustering based on dissimilarity or beta-diversity
hclu_optics OPTICS hierarchical clustering algorithm
install_binaries Download, unzip, check permission and test the bioregion's binary files
map_clusters Create a map of bioregions
mat_to_net Create a data.frame from a contingency table
netclu_beckett Community structure detection in weighted bipartite network 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 leading eigen vector 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_dbscan dbscan clustering
nhclu_kmeans Non hierarchical clustering: k-means analysis
nhclu_pam Non hierarchical clustering: partitioning around medoids
partition_metrics Calculate metrics for one or several partitions
similarity Compute similarity metrics between sites based on species composition
similarity_to_dissimilarity Convert similarity indices to dissimilarity metrics
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)