Function reference • phyloregion

All functions
`EDGE()`	Evolutionary Distinctiveness and Global Endangerment
`PD()` `RPD()`	Phylogenetic diversity
`PD_ses()`	Phylogenetic diversity standardized for species richness
`africa`	Plants of southern Africa
`arc_labels()`	Add arc labels to plotted phylogeny
`backg()` `randpoints()`	Sample background points
`beta_core()` `beta_diss()`	Taxonomic (non-phylogenetic) beta diversity
`choropleth()`	Bin values
`coldspots()` `hotspots()` `rast_hotspot()`	Computes biodiversity coldspots and hotspots
`collapse_range()`	Collapse nodes and ranges based on divergence times
`counts()`	Phyloregions for functional traits and phylogeny
`dirpath()`	Get current directory
`evol_distinct()`	Species' evolutionary distinctiveness
`fishnet()`	Create fishnet of regular grids
`fitgom()`	Fits Grade of membership models for biogeographic regionalization
`functional_beta()`	Functional beta diversity for mixed-type functional traits
`get_clades()`	Get descendant nodes of phylogeny at a given time depth
`hexcols()`	Generate diverging colors in HCL colour space.
`indicators()`	Top driving species in phyloregions
`long2sparse()` `sparse2long()` `dense2sparse()` `sparse2dense()` `long2dense()` `dense2long()`	Conversion of community data
`map_trait()`	Map species' trait values in geographic space
`match_phylo_comm()`	Match taxa and in phylogeny and community matrix
`mean_dist()`	Mean distance matrix from a set of distance matrices
`nodepie()`	Label phylogenetic nodes using pie
`optimal_phyloregion()`	Determine optimal number of clusters
`phylo_endemism()`	Phylogenetic Endemism
`phylobeta_core()` `phylobeta()`	Phylogenetic beta diversity
`phylobeta_ses()`	Phylogenetic beta diversity standardized for species beta diversity
`phylobuilder()`	Create a subtree with largest overlap from a species list.
`phyloregion-package`	Biogeographic regionalization and macroecology
`phyloregion()` `infomap()`	Compute phylogenetic regionalization and evolutionary distinctiveness of phyloregions
`plot(<phyloregion>)` `plot_NMDS()` `text_NMDS()`	Visualize biogeographic patterns
`plot(<sparse>)`	Create illustrative sparse matrix
`plot_pie()`	Visualize biogeographic patterns using pie charts
`random_species()`	Generate random species distributions in space
`rast2comm()` `polys2comm()` `points2comm()`	Convert raw input distribution data to community
`rast_quantile()`	Standardizes raster values for mapping
`read.community()`	Read in sparse community matrices
`sdm()`	Fast species distribution model
`select_linkage()`	Cluster algorithm selection and validation
`selectbylocation()`	Select polygon features from another layer and adds polygon attributes to layer
`timeslice()`	Slice phylogenetic tree at various time depths
`tree_sampler()`	Subset trees from posterior distribution of trees.
`unifrac()`	UniFrac distance
`weighted_endemism()`	Measure the distribution of narrow-ranged or endemic species.

Reference

All functions