Create a subtree with largest overlap from a species list.

Source: R/phylo_builder.R

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.

Value

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")
#>      species                  added    
#> [1,] "Canis_lupus"            "tree"   
#> [2,] "Canis_lupus_familiaris" "tree"   
#> [3,] "Canis_latrans"          "tree"   
#> [4,] "Canis_anthus"           "tree"   
#> [5,] "Canis_aureus"           "tree"   
#> [6,] "Lycaon_pictus"          "missing"
#> [7,] "Canis_adustus"          "tree"   
#> [8,] "Canis_mesomelas"        "tree"   

# 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
#>       Order  Family    Genus Species     Common_name
#> 1 Carnivora Felidae Panthera   uncia    Snow leopard
#> 2 Carnivora Canidae   Lycaon  pictus Africa wild dog
#> 3 Carnivora Canidae   Vulpes  vulpes         Red fox
# Now we just add some species
t2 <- phylobuilder(sp, tree, extract=FALSE)
plot(t2, direction="downwards")

attr(t2, "species_list")
#>      species          added   
#> [1,] "Panthera_uncia" "genus" 
#> [2,] "Lycaon_pictus"  "family"
#> [3,] "Vulpes_vulpes"  "family"