get_all_calibrations: Get all calibrations from chronograms in a database...

Description Usage Arguments Value

View source: R/all_calibrations.R

Description

Get all calibrations from chronograms in a database (specified in cache).

Usage

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get_all_calibrations(input = c("Rhea americana", "Pterocnemia pennata",
  "Struthio camelus"), partial = TRUE, use_tnrs = FALSE,
  approximate_match = TRUE, update_cache = FALSE,
  cache = get("opentree_chronograms"), verbose = FALSE)

Arguments

input

vector of names, a newick string, or a phylo object

partial

Boolean; default TRUE: use source trees even if they only match some of the desired taxa

use_tnrs

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

approximate_match

Boolean; default TRUE: use a slower TNRS to correct mispellings, increasing the chance of matches (including false matches)

update_cache

default to FALSE

cache

The cached set of chronograms and other info from data(opentree_chronograms)

verbose

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

Value

A data_frame of calibrations


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