Derive a phylogeny from a mega-tree — get_one

For a list of species, generate a phylogeny from a provided mega-tree. If a species is not in the mega-tree, it will be grafted to the mega-tree with three scenarioes.

Usage

get_one_tree(
  sp_list,
  tree,
  taxon,
  scenario = c("at_basal_node", "random_below_basal"),
  show_grafted = FALSE,
  tree_by_user = FALSE,
  .progress = "text",
  dt = TRUE
)

Arguments

sp_list

A character vector or a data frame with at least three columns: species, genus, family. Species column holds the species for which we want to have a phylogeny. It can also have two optional columns: close_sp and close_genus. We can specify the closest species/genus of the species based on expert knowledge. If specified, the new species will be grafted to that particular location.

It can also be a string vector if taxon is specified. Though it probably is a better idea to prepare your data frame with sp_list_df(). The string vector can also have the same format as that required by Phylomatic (i.e., family/genus/genus_sp).

tree

A mega-tree with class phylo or a list of mega-trees with class multiPhylo. Optional if taxon is specified, in which case, a default mega-phylogeny (or a set of 100 randomly selected posterior phylogenies) will be used (see their own documentations from the megatrees package).

For amphibian, the mega-trees are megatrees::tree_amphibian_n100.
For bee, the mega-tree is megatrees::tree_bee, with megatrees::tree_bee_n100 be the other option.
For bird, the mega-trees are megatrees::tree_bird_n100.
For fish, the mega-tree is megatrees::tree_fish_12k, with megatrees::tree_fish_32k_n50 be the other option.
For mammal, the default mega-trees are megatrees::tree_mammal_n100_vertlife, with megatrees::tree_mammal_n100_phylacine be the other option.
For plant, the mega-tree is megatrees::tree_plant_otl.
For reptile, the mega-trees are megatrees::tree_reptile_n100.
For shark, ray, and chimaeras, the mega-trees are megatrees::tree_shark_ray_n100.

taxon

The taxon of species in the sp_list. Currently, can be amphibian, bird, fish, mammal, plant, reptile, or shark_ray.

scenario

How to insert a species into the mega-tree?

In both scenarioes, if there is only 1 species in the genus or family, a new node will be inserted to the middle point of this only species' branch length and the new species will be attached to this new node.
If scenario = "at_basal_node", a species is attached to the basal node of the same genus or the same family if the mega-tree does not have any species of this genus.
If scenario = "random_below_basal", a species is attached to a randomly selected node that is at or below the basal node of the same genus of the same family if the mega-tree does not have any species in this genus. The probability of node been selected is proportional to its branch length. Because of the random sampling involved, you may want to run several times to get a collection of derived phylogenies.

show_grafted

Whether to indicate which species was grafted onto the mega-tree. If TRUE, a * will be appended to the species name on the tip if it was grafted within the same genus; ** will be appended if it was grafted within the same family.

tree_by_user

Is the mega-tree provided by user? Default is FALSE but it will be automatically set to TRUE when the class of tree is multiPhylo since we don't provide any such mega-trees here.

.progress

Form of progress bar, default to be text.

dt

Whether to use data.table version to bind tips bind_tip. The default is TRUE as it maybe slightly faster.

Value

A phylogeny for the species required, with class phylo.