bind_tip_df: Bind a tip to a phylogeny (data frame version)

In daijiang/rtrees: Deriving Phylogenies from Synthesis Trees

Bind a tip to a phylogeny (data frame version)

Description

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

## Not run: 
library(rtrees)
bind_tip(tree_plant_otl, "N70407", tip_label = "test_sp")
tree_plant_otl_df = tidytree::as_tibble(tree_plant_otl)
node_heights = ape::branching.times(tree_plant_otl)
bind_tip(tree_tbl = tree_plant_otl_df, where = "N70407", 
         tip_label = "test_sp", node_heights = node_heights)

## End(Not run)

daijiang/rtrees documentation built on June 24, 2024, 12:35 a.m.