get_bold_data: Get genetic data from the Barcode of Life Database (BOLD) for...

View source: R/bold_data.R

get_bold_dataR Documentation

Get genetic data from the Barcode of Life Database (BOLD) for a set of taxon names.

Description

get_bold_data uses taxon names from a tree topology, a character vector of names or a datelifeQuery object, to search for genetic markers in the Barcode of Life Database (BOLD).

Usage

get_bold_data(
  input = c("Rhea americana", "Struthio camelus", "Gallus gallus"),
  marker = "COI",
  ...
)

Arguments

input

One of the following:

A character vector

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.

A datelifeQuery object

An output from make_datelife_query().

marker

A character vector indicating the gene from BOLD system to be used for branch length estimation. It searches "COI" marker by default.

...

Arguments passed on to get_otol_synthetic_tree

otol_version

Version of Open Tree of Life to use

resolve

Defaults to TRUE. Whether to resolve the tree at random or not.

ott_ids

If not NULL, it takes this argument and ignores input. A numeric vector of ott ids obtained with rotl::taxonomy_taxon_info() or rotl::tnrs_match_names() or tnrs_match().

Details

If input is a phylo object or a newick string, it is used as backbone topology. If input is a character vector of taxon names, an induced synthetic OpenTree subtree is used as backbone.

Value

A phylo object. If there are enough BOLD sequences available for the input taxon names, the function returns a tree with branch lengths proportional to relative substitution rate. If not enough BOLD sequences are available for the input taxon names, the function returns the topology given as input, or a synthetic Open Tree of Life for the taxon names given in input, obtained with get_otol_synthetic_tree().


datelife documentation built on July 10, 2023, 2:02 a.m.