datelife (version 0.6.8)

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

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(input = NULL, each = FALSE, dating_method = "bladj", ...)

Value

A phylo or multiPhylo object with branch lengths proportional to time.

Arguments

input

One of the following:

A character vector

With taxon names as a single comma separated starting or concatenated with c().

A phylogenetic tree with taxon names as tip labels

As a phylo or multiPhylo object, OR as a newick character string.

A datelifeQuery object

An output from make_datelife_query().

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.

dating_method

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

...

Arguments passed on to make_datelife_query

use_tnrs

Whether to use Open Tree of Life's Taxonomic Name Resolution Service (TNRS) to process input taxon names. Default to TRUE, it corrects misspellings and taxonomic name variations with tnrs_match(), a wrapper of rotl::tnrs_match_names().

get_spp_from_taxon

Whether to search ages for all species belonging to a given taxon or not. Default to FALSE. If TRUE, it must have same length as input. If input is a newick string with some clades it will be converted to a phylo object, and the order of get_spp_from_taxon will match phy$tip.label.

reference_taxonomy

A character vector specifying the reference taxonomy to use for TNRS. Options are "ott", "ncbi", "gbif" or "irmng". The function defaults to "ott".

More

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

Details

If input is a vector of taxon names, the function will attempt to reconstruct a BOLD tree with make_bold_otol_tree() to get a tree with branch lengths. If it fails, it will get an Open Tree of Life synthetic tree topology. The function then calls use_calibrations().