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Get a list of patristic matrices from a given datelifeQuery object

Source: R/datelife_result.R
get_datelife_result_datelifequery.Rd

Get a list of patristic matrices from a given datelifeQuery object

Usage

get_datelife_result_datelifequery(
  datelife_query = NULL,
  partial = TRUE,
  cache = "opentree_chronograms",
  update_opentree_chronograms = FALSE,
  ...
)

Arguments

datelife_query

A datelifeQuery object, usually an output of 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

input

Taxon names as one of the following:

A character vector of taxon names

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.

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".

Value

A datelifeResult object -- a named list of patristic matrices.

Details

If there is just one taxon name in input$cleaned_names, the function will run make_datelife_query() setting get_spp_from_taxon = TRUE. The datelifeQuery used as input can be accessed with attributes(datelifeResult)$query.