get_clade: Function to extract clades from the backbone phylogeny.

In iramosgutierrez/randtip: A generalized framework to expand incomplete phylogenies with taxonomic information

Function to extract clades from the backbone phylogeny.

Description

This function serves to extract the clade in the backbone phylogeny that includes all the species in the specified group (as defined in the info data frame).

Usage

get_clade(info, tree, group)

Arguments

info	An 'info' (or 'input') data frame.
tree	The backbone tree to be subsetted.
group	Taxonomic group of species that defines the clade to extract.

Value

A list with four objects that will be used for automatic plotting with the plot_clade function. 'Tree' is the subtree; 'info' is the handed info data frame; 'rank' is the taxonomic rank of the specified group, and 'clade' is the name of the clade. ## SAME AS ABOVE, SHOULD BE 'group'

Author(s)

Ignacio Ramos-Gutierrez, Rafael Molina-Venegas, Herlander Lima

Examples

catspecies <- c("Lynx_lynx", "Panthera_uncia",
"Panthera_onca", "Felis_catus", "Puma_concolor",
"Lynx_canadensis", "Panthera_tigris", "Panthera_leo",
"Felis_silvestris")

cats.info <- build_info(species=catspecies, tree= cats,
     find.ranks=TRUE, db="ncbi", mode="backbone")

felinae.clade <- get_clade(info=cats.info,
tree=cats, group="Felinae")

iramosgutierrez/randtip documentation built on March 19, 2024, 6:35 p.m.