tree.slice: Identify Tree Branches That Intersect With a Given Time...
In ignacioq/rase: Range Ancestral State Estimation for Phylogeography and Comparative Analyses

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1	tree.slice(tree, slice)

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

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

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.

Ignacio Quintero

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

rase.slice

#load data
data(rase_data, package = 'rase')	
	
## Not run: 
	
# 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

## End(Not run)