get_tree: Get one or multiple trees from megatree(s)

In daijiang/rtrees: Deriving Phylogenies from Synthesis Trees

Get one or multiple trees from megatree(s)

Description

For some taxa groups, there are multiple posterior megatrees. It is a common task to derive a phylogeny from each of these (or a random subset of) megatrees.

Usage

get_tree(
  sp_list,
  tree,
  taxon = NULL,
  scenario = c("at_basal_node", "random_below_basal"),
  show_grafted = FALSE,
  tree_by_user = FALSE,
  mc_cores = future::availableCores() - 2,
  .progress = "text",
  fish_tree = c("timetree", "all-taxon"),
  mammal_tree = c("vertlife", "phylacine"),
  bee_tree = c("maximum-likelihood", "bootstrap"),
  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 butterfly, the mega-tee is megatrees::tree_butterfly. 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.
mc_cores	Number of cores to parallel processing when tree is a list of large number of trees. The default is the number of available cores minus 2.
.progress	Form of progress bar, default to be text.
fish_tree	Which fish tree do you want to use? If it is "timetree" (default), it will be the smaller time tree with 11638 species that all have sequence data; if it is "all-taxon", then it will be the 100 larger posterior phylogenies with 31516 soecues.
mammal_tree	Which set of mammal trees to use? If it is "vertlife" (default), then 100 randomly selected posterior phylogenies provided by Vertlife will be used; if it is "phylacine", then 100 randomly selected posterior phylogenies provided by PHYLACINE will be used.
bee_tree	Which bee tree to use? If it is "maximum-likelihood" (default), the a single maximum likelihood tree will be used. If it is "bootstrap", then a set of 100 randomly selected posterior phylogenies will be used. All trees are provided by the Bee Tree of Life.
dt	Whether to use data.table version to bind tips bind_tip. The default is TRUE as it maybe slightly faster.

Details

Derive a phylogeny from a mega-tree

For a list of species, generate a phylogeny or multiple phylogenies from a provided mega-tree or mega-trees. If a species is not in the mega-tree, it will be grafted to the mega-tree with two scenarios.

Value

A phylogeny for the species required, with class phylo; or a list of phylogenies with class multiPhylo depends on the input tree. Within each phylogeny, the grafted status of all species was saved as a data frame named as "graft_status".

Examples

test_sp = c("Serrasalmus_geryi", "Careproctus_reinhardti", "Gobiomorphus_coxii", 
"Periophthalmus_barbarus", "Prognichthys_glaphyrae", "Barathronus_bicolor", 
"Knipowitschia_croatica", "Rhamphochromis_lucius", "Neolissochilus_tweediei", 
"Haplochromis_nyanzae", "Astronesthes_micropogon", "Sanopus_reticulatus")
test_tree = get_tree(sp_list = test_sp,
                     taxon = "fish",
                     show_grafted = TRUE)

daijiang/rtrees documentation built on June 24, 2024, 12:35 a.m.