R: Get a list of patristic matrices from a given 'datelifeQuery'...

get_datelife_result_datelifequery {datelife}

R Documentation

Get a list of patristic matrices from a given `datelifeQuery` object

Description

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".

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.

Value

A datelifeResult object – a named list of patristic matrices.