use_calibrations: Date a given tree topology using a combined set of given...

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

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

Description

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, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bioinformatics/btn358")}; Britton et al., 2007, \Sexpr[results=rd]{tools:::Rd_expr_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

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().

Value

A phylo object with branch lengths proportional to time.

More

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

phylotastic/datelife documentation built on June 9, 2024, 6:50 p.m.