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Utils

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

Pairwise similarity and distance metrics

similarity()
Compute similarity metrics between sites based on species composition
dissimilarity()
Compute dissimilarity metrics (beta-diversity) between sites based on species composition
similarity_to_dissimilarity()
Convert similarity indices to dissimilarity metrics
dissimilarity_to_similarity()
Convert dissimilarity indices to similarity indices

Clustering

Hierarchical clustering

hclu_hierarclust()
Hierarchical clustering based on dissimilarity or beta-diversity
cut_tree()
Cut a hierarchical tree
hclu_optics()
OPTICS hierarchical clustering algorithm

Non-hierarchical clustering

nhclu_dbscan()
dbscan clustering
nhclu_kmeans()
Non hierarchical clustering: k-means analysis
nhclu_pam()
Non hierarchical clustering: partitioning around medoids

Network clustering

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

Clustering analysis

partition_metrics()
Calculate metrics for one or several partitions
find_optimal_n()
Search for an optimal number of clusters in a list of partitions

Visualisation

map_clusters()
Create a map of bioregions

Data

vegedf
Spatial distribution of Mediterranean vegetation (data.frame)
vegemat
Spatial distribution of Mediterranean vegetation (co-occurrence matrix)
vegesp
Spatial distribution of Mediterranean vegetation (spatial grid)