# Biogeographic Regionalization and Macroecology

## Documentation for package ‘phyloregion’ version 1.0.9

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

africa | Plants of southern Africa
arc_labels | Add arc labels to plotted phylogeny
arc_labels.default | Add arc labels to plotted phylogeny
backg | Sample background points
beta_core | Taxonomic (non-phylogenetic) beta diversity
beta_diss | Taxonomic (non-phylogenetic) beta diversity
choropleth | Bin values
coldspots | Computes biodiversity coldspots and hotspots
collapse_range | Collapse nodes and ranges based on divergence times
counts | Phyloregions for functional traits and phylogeny
dense2long | Conversion of community data
dense2sparse | Conversion of community data
dirpath | Get current directory
EDGE | Evolutionary Distinctiveness and Global Endangerment
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.
hotspots | Computes biodiversity coldspots and hotspots
indicators | Top driving species in phyloregions
infomap | Compute phylogenetic regionalization and evolutionary distinctiveness of phyloregions
long2dense | Conversion of community data
long2sparse | 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
PD | Phylogenetic diversity
PD_ses | Phylogenetic diversity standardized for species richness
phylobeta | Phylogenetic beta diversity
phylobeta_core | 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 | Compute phylogenetic regionalization and evolutionary distinctiveness of phyloregions
phylo_endemism | Phylogenetic Endemism
plot.phyloregion | Visualize biogeographic patterns
plot.sparse | Create illustrative sparse matrix
plot_NMDS | Visualize biogeographic patterns
plot_spatial_membership | Visualize spatial memberships
points2comm | Convert raw input distribution data to community
polys2comm | Convert raw input distribution data to community
random_species | Generate random species distributions in space
randpoints | Sample background points
rast2comm | Convert raw input distribution data to community
rast_hotspot | Computes biodiversity coldspots and hotspots
rast_quantile | Standardizes raster values for mapping
read.community | Read in sparse community matrices
RPD | Phylogenetic diversity
sdm | Fast species distribution model
selectbylocation | Select polygon features from another layer and adds polygon attributes to layer
select_linkage | Cluster algorithm selection and validation
sparse2dense | Conversion of community data
sparse2long | Conversion of community data
text_NMDS | Visualize biogeographic patterns
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.