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. |