tax2tree: tax2tree

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

tax2tree

Description

tax2tree

Usage

tax2tree(
  x,
  ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species"),
  depth = NULL,
  summarise = FALSE,
  output = "phylo",
  replace_bads = FALSE,
  append_sum = TRUE
)

Arguments

x	a DNAbin object or an object coercible to DNAbin
ranks	The taxonomic ranks currently assigned to the names
depth	The depth within the tree to return. Default NULL to return lowest input rank
summarise	Select a taxonomic rank to summarise below. Default is FALSE to return a tree of the same size as input
output	The output to return, options are: "phylo" to return an ape phylo object. If summarise is set to a rank, the number of distinct taxa at that rank numbers are appended to the tip labels if append_sum is TRUE, or returned as an attribute and can be accessed with attr(tree, "sum") "data.tree" to return a data.tree node object "treedf" to return a simplified tree with taxon summaries in a data frame "newick" to return a newick file for visualisation in other software. If summarise is set to a rank, the number of distinct taxa at that rank numbers are returned as an attribute and can be accessed with attr(tree, "sum")
replace_bads	An option to automatically replace invalid newick characters with '-'
append_sum	An option to append the summary number to the output trees tip labels when summarise is a rank and output is 'phylo'. If FALSE, summary numbers are returned as an attribute and can be accessed with attr(tree, "sum")

Value

a phylo, data.tree, newick, or treedf object

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.