Add tip to a tree

Returns a tree with a new tip ID added

Usage

addTip(
  tree,
  tid,
  sid,
  strt_age = NULL,
  end_age = 0,
  tree_age = NULL,
  pid = paste0("p_", tid)
)

Arguments

tree

TreeMan object

tid

tip ID

sid

ID of node that will become new tip sisters

strt_age

timepoint at which new tips first appear in the tree

end_age

timepoint at which new tips end appear in the tree, default 0.

tree_age

age of tree

pid

parent ID (default is 'p_' + tid)

Details

User must provide new tip ID, the ID of the node which will become the new tip's sister, and new branch lengths. The tip ID must only contain letters numbers and underscores. Optionally, user can specify the IDs for the new parental internal nodes. Ensure that the strt_age is greater than the end_age, and that the strt_age falls within the age span of the sister ID. Otherwise, negative spns may be produced leading to an error. Note, returned tree will not have a node matrix. Note, providing negative end ages will increase the age of the tree.

See also

rmTips, https://github.com/DomBennett/treeman/wiki/manip-methods

Examples

tree <- randTree(10)
tree_age <- getAge(tree)
possible_ages <- getSpnAge(tree, "t1", tree_age)
start_age <- runif(1, possible_ages[["end"]], possible_ages[["start"]])
end_age <- possible_ages[["end"]]
tree <- addTip(tree,
  tid = "t11", sid = "t1", strt_age = start_age,
  end_age = end_age, tree_age = tree_age
)
summary(tree)
#> Tree (TreeMan Object):
#>   + 11 tips
#>   + 10 internal nodes
#>   + Binary
#>   + PD 8.72
#>   + Root node is "n1"