use_all_calibrations: Use all calibrations from chronograms in a database to date a...

Description Usage Arguments Details Value

View source: R/all_calibrations.R

Description

Use all calibrations from chronograms in a database to date a tree.

Usage

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use_all_calibrations(phy = make_bold_otol_tree(c("Rhea americana",
  "Struthio camelus", "Gallus gallus"), chronogram = FALSE, verbose =
  FALSE), partial = TRUE, use_tnrs = FALSE, approximate_match = TRUE,
  update_cache = FALSE, cache = get("opentree_chronograms"),
  expand = 0.1, giveup = 100, verbose = FALSE)

Arguments

phy

A phylo object

partial

If TRUE, use source trees even if they only match some of the desired taxa

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)

update_cache

default to FALSE

cache

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

expand

How much to expand by each step to get consistent calibrations

giveup

How many expansions to try before giving up

verbose

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

Details

This will try to use the calibrations as fixed ages. If that fails (often due to conflict between calibrations), it will expand the range of the minage and maxage and try again. And repeat. expand sets the expansion value: should be between 0 and 1

Value

list with chronogram, original calibrations, and expanded calibrations


phylotastic/datelife documentation built on Jan. 14, 2019, 9:56 p.m.