AvoBind {avotrex}

AvoBind - Bind extinct species to the tree

Description

Binds an extinct species at either (1) a randomly selected point along a branch, after truncating either end, (2) a specific fraction along a branch, or (3) a specific time point along a branch.

Usage

AvoBind(tree, node, per, per_fixed = FALSE, sp_name,
 time_graft = FALSE, terminal = FALSE, mindist = 0.1)

Arguments

tree

Tree object (i.e., phylogeny)

node

Target node

per

The fraction (0-1) of total branch length to truncate at either end of the branch for grafting (e.g. 0.2 cuts of 20% of the total branch length from either end) if per_fixed == FALSE. If per_fixed == TRUE, then the point along the branch where the grafting occurs: value between 0-1, with a larger number meaning the grafting occurs closer to the rootward end of the branch. If time_graft = TRUE, the specific point (in millions of years, if BirdTree trees are used) for the grafting to occur.

per_fixed

Logical argument: whether to graft a species on at an exact point (as a fraction) along a branch (TRUE), which is chosen using the per argument, rather than random (FALSE; default). Is ignored if time_graft = TRUE.

sp_name

Name of the grafted species.

time_graft

Should the grafting occur at a particular time point (in millions of years if BirdTree trees provided) along a given branch, using avotrex:::AgeBind(). The specific point is provided using the per argument.

terminal

Logical value: if time_graft = TRUE, is the species being grafted to a terminal branch.

mindist

If time_graft = TRUE, but the provided grafting time point (per) is too old (i.e., older than the parent node) or too young (i.e., younger than the child node) relative to the focal branch, grafting will occur mindist below the parent node or above the child node.

Value

Returns a tree of class "phylo", with the extinct species grafted on.

Author(s)

Joe Wayman, Tom Matthews and Pedro Cardoso (AgeBind)