get_one_tree | R Documentation |
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.
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
)
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 |
tree |
A mega-tree with class
|
taxon |
The taxon of species in the |
scenario |
How to insert a species into the mega-tree?
|
show_grafted |
Whether to indicate which species was grafted onto the mega-tree.
If |
tree_by_user |
Is the mega-tree provided by user? Default is |
.progress |
Form of progress bar, default to be text. |
dt |
Whether to use data.table version to bind tips bind_tip. The default is |
A phylogeny for the species required, with class phylo
.
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