# Comparison of Bioregionalisation Methods

## Documentation for package ‘bioregion’ version 1.0.0

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

## Help Pages

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)