make_datelife_query: Cleans taxon names from input character vector, phylo object...

Description Usage Arguments Value

View source: R/datelife.R

Description

Cleans taxon names from input character vector, phylo object or newick character string. Process the two latter with input_process first.

Usage

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make_datelife_query(input = c("Rhea americana", "Pterocnemia pennata",
  "Struthio camelus"), use_tnrs = FALSE, approximate_match = TRUE,
  get_spp_from_taxon = FALSE, verbose = FALSE, ...)

Arguments

input

Target taxa names as a character vector, a newick character string, or a phylo object.

use_tnrs

If TRUE, use OpenTree's services to resolve names. This can dramatically improve the chance of matches, but also take much longer.

approximate_match

If TRUE, use a slower TNRS to correct mispellings, increasing the chance of matches (including false matches).

get_spp_from_taxon

boolean vector, default to FALSE. If TRUE, will get all species names from taxon names given in input. Must have same length as input. If input is a newick string , with some clades it will be converted to phylo object phy, and the order of get_spp_from_taxon will match phy$tip.label.

verbose

Boolean. If TRUE, it gives printed updates to the user.

...

Arguments passed on to rphylotastic::taxon_get_species

filters

A character vector of strings to exclude.

Value

A list with the phy (or NA, if no tree) and cleaned vector of taxa


phylotastic/datelife documentation built on Jan. 14, 2019, 9:56 p.m.