make_datelife_query: Go from taxon names to a 'datelifeQuery' object

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Go from taxon names to a datelifeQuery object

Description

Go from taxon names to a datelifeQuery object

Usage

make_datelife_query(
  input = c("Rhea americana", "Pterocnemia pennata", "Struthio camelus"),
  use_tnrs = TRUE,
  get_spp_from_taxon = FALSE,
  reference_taxonomy = "ott"
)

Arguments

input	Taxon names as one of the following: A character vector of taxon names With taxon names as a single comma separated starting or concatenated with c(). A phylogenetic tree with taxon names as tip labels As a phylo or multiPhylo object, OR as a newick character string.
use_tnrs	Whether to use Open Tree of Life's Taxonomic Name Resolution Service (TNRS) to process input taxon names. Default to TRUE, it corrects misspellings and taxonomic name variations with tnrs_match(), a wrapper of rotl::tnrs_match_names().
get_spp_from_taxon	Whether to search ages for all species belonging to a given taxon or not. Default to FALSE. If TRUE, it must have same length as input. If input is a newick string with some clades it will be converted to a phylo object, and the order of get_spp_from_taxon will match phy$tip.label.
reference_taxonomy	A character vector specifying the reference taxonomy to use for TNRS. Options are "ott", "ncbi", "gbif" or "irmng". The function defaults to "ott".

Details

It processes phylo objects and newick character string inputs with input_process(). If input is a multiPhylo object, only the first phylo element will be used. Similarly, if an input newick character string has multiple trees, only the first one will be used.

Value

A datelifeQuery object, which is a list of three elements:

$phy

A phylo object or NA, if input is not a tree.

$cleaned_names

A character vector of cleaned taxon names.

$ott_ids

A numeric vector of OTT ids if use_tnrs = TRUE, or NULL if use_tnrs = FALSE.

phylotastic/datelife documentation built on Jan. 17, 2024, 11:10 p.m.