rtrees: Deriving Phylogenies from Synthesis Trees

add_root_info

R Documentation

Add genus and family basal/root node information to a phylogeny

Description

Based on the classification of tips, find where is the basal and root node for each genus and each family. Such information can be later used to graft new tips onto the phylogeny. This function can be used to process a user provided tree.

Usage

add_root_info(
  tree,
  classification,
  process_all_tips = TRUE,
  genus_list = NULL,
  family_list = NULL,
  show_warning = FALSE
)

Arguments

`tree`	A phylogeny with class "phylo".
`classification`	A data frame of 2 columns: genus, family. It should include all genus the tips of the tree belong to.
`process_all_tips`	Whether to find basal nodes for all tips? Default is `TRUE`.
`genus_list`	An optinoal subset list of genus to find root information.
`family_list`	An optinoal subset list of family to find root information. This should be for species that do not have co-genus in the tree.
`show_warning`	Whether to print warning information about non-monophyletic clades or not.