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Date a given tree topology using a combined set of given calibrations

Source: R/calibrations_use.R
use_calibrations.Rd

use_calibrations combines all given calibrations and uses them as constraints to perform a dating analysis on a given tree topology, using BLADJ if it has no branch lengths, or PATHd8 if the given tree topology has initial branch lengths.

Usage

use_calibrations(
  phy = NULL,
  calibrations = NULL,
  dating_method = "bladj",
  type = "median",
  ...
)

Arguments

phy

A phylo object to use as tree topology.

calibrations

A calibrations object, an output of get_all_calibrations().

dating_method

Tree dating algorithm to use. Options are "bladj" or "pathd8" (Webb et al., 2008, doi:10.1093/bioinformatics/btn358 ; Britton et al., 2007, doi:10.1080/10635150701613783 ).

type

The type of age to use as calibration. Options are "median", "mean", "min", or "max".

...

Arguments passed on to use_calibrations_pathd8

expand

How much to expand by each step to get consistent calibrations. Should be between 0 and 1.

giveup

How many expansions to try before giving up

Value

A phylo object with branch lengths proportional to time.

Details

If phy has no branch lengths, dating_method is ignores, and the function applies secondary calibrations to date the tree with the BLADJ algorithm. See make_bladj_tree() and use_calibrations_bladj(). If phy has branch lengths, the function can use the PATHd8 algorithm. See use_calibrations_pathd8().

More

The output object stores the used calibrations and dating_method as attributes(output)$datelife_calibrations and attributes(output)$dating_method.