To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time

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Documentation for package ‘treesliceR’ version 1.0.1

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

Help Pages

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