Biogeographic Regionalization and Macroecology


[Up] [Top]

Documentation for package ‘phyloregion’ version 1.0.4

Help Pages

phyloregion-package Biogeographic regionalization and spatial conservation
africa Plants of southern Africa
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
dense2long Conversion of community data
dense2sparse Conversion of community data
EDGE Evolutionary Distinctiveness and Global Endangerment
evol_distinct Species' evolutionary distinctiveness
fishnet Create a fishnet of regular grids
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 Calculate 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
optimal_phyloregion Determine optimal number of clusters
PD Phylogenetic diversity
phylobeta Phylogenetic beta diversity
phylobeta_core Phylogenetic beta diversity
phylobuilder Create a subtree with largest overlap from a species list.
phyloregion Calculate evolutionary distinctiveness of phyloregions
phylo_endemism Phylogenetic Endemism
plot.phyloregion Visualize biogeographic patterns
plot_NMDS Visualize biogeographic patterns
plot_swatch Plot shapefile polygons based on slot values
points2comm Convert raw input distribution data to community
polys2comm Convert raw input distribution data to community
random_species Generate random species distributions in space
raster2comm Convert raw input distribution data to community
read.community Read in sparse community matrices
selectbylocation Select features within polygon from another 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
weighted_endemism Measure the distribution of narrow-ranged or endemic species.