# To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time

## Documentation for package ‘treesliceR’ version 1.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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
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