use_calibrations_each: Date a given tree topology by using a given list of...

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

Date a given tree topology by using a given list of calibrations independently, to generate multiple hypothesis of time of divergence

Description

use_calibrations_each wraps use_calibrations to take each set of given calibrations and use it independently as constraints for BLADJ or PATHd8 to date a given tree topology.

Usage

use_calibrations_each(phy = NULL, calibrations = NULL, ...)

Arguments

phy	A phylo object to use as tree topology.
calibrations	A calibrations object, an output of get_all_calibrations().
...	Arguments passed on to use_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".

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 multiPhylo object of trees 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.

datelife documentation built on July 10, 2023, 2:02 a.m.