addSingleTip: Add Tips to a Phylogenetic Tree

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Add tips (species) to a phylogenetic tree according to their taxonomic classification.

Usage

addSingleTip(
  phy,
  tip,
  sister,
  tax,
  insert = "crown",
  ignore.monophyly,
  stem.edge = 0.5,
  quiet = FALSE
)

Arguments

phy	An object of class phylo.
tip	A character string giving the name of the species to be added.
sister	A character string giving the name of the species or genus to which tip shuold be added as sister; this argument overrides tax.
tax	A data frame containing the taxonomic classification.
insert	A character string indicating the positions where the species is to be inserted: "crown", "stem", "randomly", or any unambigous abbreviation of these. This option will only have an effect if phy contains more than one congeneric of tip.
ignore.monophyly	Logical, indicating if monophyly should be considered when selecting the anchor point for tips.
stem.edge	A real number greater than 0 and smaller than 1, which gives the fraction of the terminal branch length that will be assigned to the branch subtending the newly created MRCA of tip and its single congeneric species in phy. Will have no effect if phy contains more than one congeneric of tip.
quiet	Logical, indicating if screen output should be suppressed.

Value

An object of class phylo.

See Also

dbReadTaxonomy for reading a taxonomy table from the postgreSQL database.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.