phylobuilder: Create a subtree with largest overlap from a species list.

In darunabas/phyloregion: Biogeographic Regionalization and Macroecology

Create a subtree with largest overlap from a species list.

Description

phylobuilder creates a subtree with largest overlap from a species list. If species in the species list are not already in the tip label, species will be added at the most recent common ancestor at the genus or family level when possible.

Usage

phylobuilder(species, tree, extract = TRUE)

Arguments

species	A vector or matrix containing a species list
tree	a phylogenetic tree (object of class phylo)
extract	extract the species in the list after trying to add missing labels to the tree. If FALSE phylobuilder adds only the taxa in the list.

Value

phylobuilder returns a phylogenetic tree, i.e. an object of class phylo.

See Also

add.tips, label2table, stripLabel

Examples

library(ape)
txt <- "(((((Panthera_leo,Panthera_pardus), Panthera_onca),(Panthera_uncia,
  (Panthera_tigris_altaica, Panthera_tigris_amoyensis)))Panthera)Felidae,
  (((((((Canis_lupus,Canis_lupus_familiaris),Canis_latrans),Canis_anthus),
  Canis_aureus),Lycaon_pictus),(Canis_adustus,Canis_mesomelas))Canis)
  Canidae)Carnivora;"
txt <- gsub("[[:space:]]", "", txt)
cats_and_dogs <- read.tree(text=txt)
plot(cats_and_dogs, node.depth=2, direction="downwards")
nodelabels(cats_and_dogs$node.label, frame="none", adj = c(0.5, 0))

tree <- drop.tip(cats_and_dogs, c("Panthera_uncia", "Lycaon_pictus"),
  collapse.singles=FALSE)

dogs <- c("Canis_lupus", "Canis_lupus_familiaris", "Canis_latrans",
  "Canis_anthus", "Canis_aureus", "Lycaon_pictus", "Canis_adustus",
  "Canis_mesomelas")

# try to extract tree with all 'dogs'
t1 <- phylobuilder(dogs, tree)
plot(t1, direction="downwards")
attr(t1, "species_list")

# providing extra information ("Family", "Order", ...) can help
sp <- data.frame(Order = c("Carnivora", "Carnivora", "Carnivora"),
  Family = c("Felidae", "Canidae", "Canidae"),
  Genus = c("Panthera", "Lycaon", "Vulpes"),
  Species = c("uncia", "pictus", "vulpes"),
  Common_name = c("Snow leopard", "Africa wild dog", "Red fox"))
sp
# Now we just add some species
t2 <- phylobuilder(sp, tree, extract=FALSE)
plot(t2, direction="downwards")
attr(t2, "species_list")

darunabas/phyloregion documentation built on Feb. 3, 2024, 8:59 p.m.