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Bind a tip to a phylogeny (data frame version)

bind_tip_df.Rd

Graft a tip to a phylogeny at location specified.

Usage

bind_tip_df(
  tree = NULL,
  where,
  tip_label,
  frac = 0.5,
  new_node_above = FALSE,
  node_label = NULL,
  return_tree = TRUE,
  tree_tbl = NULL,
  node_heights = NULL,
  use_castor = FALSE
)

Arguments

tree

A phylogeny, with class of "phylo".

where

Location where to insert the tip. It can be either tip label or node label, but must be characters. If the location does not have a name, assign it first.

tip_label

Name of the new tip inserted.

frac

The fraction of branch length, must be between 0 and 1. This only applies when location is a tip or new_node_above = TRUE. The distance from the new inserted node to the location (a node or a tip) is the branch length of the location * (1 - frac).

new_node_above

Whether to insert the new node above when the location is a node? Default is FALSE, which will attach the new tip to the location node.

node_label

Name of the new node created. This only applies when location is a tip or new_node_above = TRUE.

return_tree

Whether to return a phylogeny with class "phylo?" Default is TRUE. Otherwise, it will return a data frame.

tree_tbl

A tibble version of the tree, optional.

node_heights

A named numeric vector of node hieghts of the tree, generated by ape::branching.times(). It is also optional if tree is specified; but required if tree_tbl is specified.

use_castor

Whether to use package castor to get the phylogeny at a node; it is faster than tidytree::offspring to figure out what are the tip offsprings at a node.

Value

Either a phylogeny or a data frame, which can be then converted to a phylogeny later.

Examples

tr <- ape::read.tree(text = "((A:1,B:1):1,C:2);")
tr$node.label <- c("root", "N1")
bind_tip_df(tr, where = "N1", tip_label = "D")
#> 
#> Phylogenetic tree with 4 tips and 2 internal nodes.
#> 
#> Tip labels:
#>   A, B, D, C
#> Node labels:
#>   root, N1
#> 
#> Rooted; includes branch length(s).
tr_tbl <- tidytree::as_tibble(tr)
node_hts <- ape::branching.times(tr)
bind_tip_df(tree_tbl = tr_tbl, where = "N1",
            tip_label = "D", node_heights = node_hts)
#> 
#> Phylogenetic tree with 4 tips and 2 internal nodes.
#> 
#> Tip labels:
#>   A, B, D, C
#> Node labels:
#>   root, N1
#> 
#> Rooted; includes branch length(s).