get_datelife_result: Get a patristic matrix of time of lineage divergence data for...
In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

get_datelife_result

R Documentation

Get a patristic matrix of time of lineage divergence data for a given set of taxon names

Description

get_datelife_result takes as input a vector of taxon names, a newick string, a phylo object, or adatelifeQuery object. It searches the chronogram database specified in cache for chronograms matching two or more given taxon names. For each matching chronogram, it extracts time of lineage divergence data and stores it as a patristic matrix. It then lists all resulting patristic matrices. Each list element is named with the study citation of the source chronogram.

Usage

get_datelife_result(
  input = NULL,
  partial = TRUE,
  cache = "opentree_chronograms",
  update_opentree_chronograms = FALSE,
  ...
)

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()`.
`partial`	Whether to return or exclude partially matching source chronograms, i.e, those that match some and not all of taxa given in `datelife_query`. Options are `TRUE` or `FALSE`. Defaults to `TRUE`: return all matching source chronograms.
`cache`	A character vector of length one, with the name of the data object to cache. Default to `"opentree_chronograms"`, a data object storing Open Tree of Life's database chronograms and other associated information.
`update_opentree_chronograms`	Whether to update the chronogram database or not. Defaults to `FALSE`.
`...`	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".