make_bold_otol_tree: Use Barcode of Life data to get branch lengths on the OToL...

Description Usage Arguments Value

View source: R/all_calibrations.R

Description

Use Barcode of Life data to get branch lengths on the OToL tree of a set of taxa.

Usage

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make_bold_otol_tree(input = c("Rhea americana", "Struthio camelus",
  "Gallus gallus"), use_tnrs = FALSE, approximate_match = TRUE,
  marker = "COI", otol_version = "v3", chronogram = TRUE,
  doML = FALSE, get_spp_from_taxon = FALSE, verbose = FALSE)

Arguments

input

Target taxa names as a character vector, a newick character string, or a phylo object.

use_tnrs

If TRUE, use OpenTree's services to resolve names. This can dramatically improve the chance of matches, but also take much longer.

approximate_match

If TRUE, use a slower TNRS to correct mispellings, increasing the chance of matches (including false matches).

marker

A character vector with the name of the gene from Barcode of Life Data Systems (BOLD) to be used for branch length estimation.

otol_version

Version of OToL to use

chronogram

Boolean; default to TRUE: branch lengths represent time estimated with ape::chronoMPL. If FALSE, branch lengths represent relative substitution rates estimated with phangorn::acctran.

doML

Boolean; if TRUE, does ML branch length optimization with phangorn::optim.pml

get_spp_from_taxon

boolean vector, default to FALSE. If TRUE, will get all species names from taxon names given in input. Must have same length as input. If input is a newick string , with some clades it will be converted to phylo object phy, and the order of get_spp_from_taxon will match phy$tip.label.

verbose

Boolean. If TRUE, it gives printed updates to the user.

Value

A phylogeny with branch lengths proportional to relative substitution rate.


phylotastic/datelife documentation built on Jan. 22, 2019, 12:29 a.m.