phylobuilder function

Create a subtree with largest overlap from a species list.

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.

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.

Returns

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

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")

See Also

add.tips, label2table, stripLabel