All functions

EDGE()

Evolutionary Distinctiveness and Global Endangerment

PD()

Phylogenetic diversity

africa

Plants of southern Africa

arc_labels()

Add arc labels to plotted phylogeny

beta_core() beta_diss()

Taxonomic (non-phylogenetic) beta diversity

choropleth()

Bin values

coldspots() hotspots()

Computes biodiversity coldspots and hotspots

collapse_range()

Collapse nodes and ranges based on divergence times

counts()

Phyloregions for functional traits and phylogeny

evol_distinct()

Species' evolutionary distinctiveness

fishnet()

Create a fishnet of regular grids

fitgom()

Fits Grade of membership models for biogeographic regionalization

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

phylobuilder()

Create a subtree with largest overlap from a species list.

phyloregion-package

Biogeographic regionalization and spatial conservation

phyloregion() infomap()

Calculate evolutionary distinctiveness of phyloregions

plot(<phyloregion>) plot_NMDS() text_NMDS()

Visualize biogeographic patterns

plot_pie()

Visualize biogeographic patterns using pie charts

plot_structure()

Visualize biogeographic patterns using structure plots

plot_swatch()

Plot shapefile polygons based on slot values

random_species()

Generate random species distributions in space

raster2comm() polys2comm() points2comm()

Convert raw input distribution data to community

read.community()

Read in sparse community matrices

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

weighted_endemism()

Measure the distribution of narrow-ranged or endemic species.