datelife_use_datelifequery: Generate one or multiple chronograms for a set of taxon names...

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

Generate one or multiple chronograms for a set of taxon names given as a datelifeQuery object.

Description

datelife_use gets secondary calibrations available for any pair of given taxon names, mined from the opentree_chronograms object, congruifies them, and uses them to date a given tree topology with the algorithm defined in dating_method. If no tree topology is provided, it will attempt to get one for the given taxon names from Open Tree of Life synthetic tree, using make_bold_otol_tree().

Usage

datelife_use_datelifequery(
  datelife_query = NULL,
  dating_method = "bladj",
  each = FALSE
)

Arguments

datelife_query	A datelifeQuery object, usually an output of make_datelife_query().
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")}).
each	Boolean, default to FALSE: all calibrations are returned in the same data.frame. If TRUE, calibrations from each chronogram are returned in separate data frames.

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 or multiPhylo 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 Jan. 17, 2024, 11:10 p.m.