rase (version 0.2-2)

tree.slice: Identify Tree Branches That Intersect With a Given Time Slice.

Description

Identifies the branches in a phylogenetic tree that the slice intersects with. It is used by rase.slice.

Usage

tree.slice(tree, slice)

Arguments

tree

phylogenetic tree of class "phylo".

slice

the time at which to slice. It should be in the same units of the phylogenetic tree.

Value

• returns a matrix where each row is an intersecting branch with the following columns: two integers associating the branch (i.e., ancestor, descendant), the age of the ancestral node, and the age of the descendant node.

Details

The tree must be fully dichotomous and all the tips should be extant lineages (time = 0).

References

Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology. doi: 10.1093/sysbio/syv057

See Also

rase.slice

Examples

#load data
data(rase_data, package = 'rase')	
	
# a phylogenetic tree used in the rase run
psophia_tree
		
# define the slice of time;
# say, 1 Million years ago (Ma)
slice <- 1
	
# slice the tree
slice_results <- tree.slice(psophia_tree, slice = slice)
	
#check results
slice_results