Function reference

All functions

AU_adj

Adjacency matrix for focal and adjacent assemblages

AU_grid

Australia grid map

CpB()

Calculates the rate of accumulation of phylogenetic B-diversity (CpB) over time slices

CpB_RW()

Calculates the range weighted rate of accumulation of phylogenetic B-diversity (CpB_RW) over time slices

CpD()

Calculates the rate of accumulation of phylogenetic diversity (CpD) over time slices

CpE()

Calculates the rate of accumulation of phylogenetic endemism (CpE) over time slices

CpR_graph()

Make a line graph or a grid map of estimated rates of accumulation of a given phylogenetic index.

CpR_sensitivity()

Runs a sensitivity analysis for rates of accumulation of a given phylogenetic index

CpR_sensitivity_plot()

Make a plot of the sensitivity analysis evaluated under cumulative phylogenetic rate functions

DR()

Calculate the tip diversification rates (DR) for a phylogenetic tree

nodes_config()

Capture general branching information for an inputted phylogenetic tree

pass_mat

Presence-absence matrix of Australian passeriformes

pass_trees

Phylogenetic tree of passerines from Australia

phylo_pieces()

Slices a phylogenetic tree into multiple temporal slices

prune_tips()

Collapse the tips of a phylogenetic tree based on a temporal threshold

r_phylo()

Calculates the relative value of a phylogenetic index in a temporal sequence of phylogenetic slices.

squeeze_int()

Slices a temporal interval within a phylogenetic tree

squeeze_root()

Slices a phylogenetic tree following a 'rootward' orientation

squeeze_tips()

Slices a phylogenetic tree following a 'tipward' orientation