Biogeographic Regionalization and Macroecology

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Documentation for package ‘phyloregion’ version 1.0.8

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

phyloregion-package	Biogeographic regionalization and macroecology
africa	Plants of southern Africa
arc_labels	Add arc labels to plotted phylogeny
arc_labels.default	Add arc labels to plotted phylogeny
beta_core	Taxonomic (non-phylogenetic) beta diversity
beta_diss	Taxonomic (non-phylogenetic) beta diversity
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
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_pie	Visualize biogeographic patterns using pie charts
points2comm	Convert raw input distribution data to community
polys2comm	Convert raw input distribution data to community
random_species	Generate random species distributions in space
rast2comm	Convert raw input distribution data to community
read.community	Read in sparse community matrices
sdm	Species distribution models
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
unifrac	UniFrac distance
weighted_endemism	Measure the distribution of narrow-ranged or endemic species.