set_taxonomicCoverage: set_taxonomicCoverage

In EML: Read and Write Ecological Metadata Language Files

set_taxonomicCoverage

Description

set_taxonomicCoverage

Usage

set_taxonomicCoverage(sci_names, expand = FALSE, db = "itis")

Arguments

sci_names	string (space separated) or list or data frame of scientific names for species covered.
expand	Set to TRUE to use '[taxadb]' to expand sci_names into full taxonomic classifications
db	The taxonomic database to query (when expand is set to TRUE). See ‘[taxadb::filter_name]' for valid options. Defaults to ’itis'.

Details

Turn a data.frame or a list of scientific names into a taxonomicCoverage block sci_names can be a space-separated character string or a data frame with column names as rank name or a list of user-defined taxonomicClassification

Value

a taxonomicCoverage object for EML

Note

If "sci_names" is a data frame, column names of the data frame are rank names. For user-defined "sci_names", users must make sure that the order of rank names they specify is from high to low. Ex. "Kingdom","Phylum","Class","Order","Family","Genus","Species","Common" EML permits any rank names provided they go in descending order.

Examples

taxon_coverage <- set_taxonomicCoverage("Macrocystis pyrifera")

sci_names <- data.frame(
  Kingdom = "Plantae",
  Phylum = "Phaeophyta",
  Class = "Phaeophyceae",
  Order = "Laminariales",
  Family = "Lessoniaceae",
  Genus = "Macrocystis",
  specificEpithet = "pyrifera"
)
taxon_coverage <- set_taxonomicCoverage(sci_names)

 # Examples that may take > 5s

## use a list of lists for multiple species
sci_names <- list(list(
  Kingdom = "Plantae",
  Phylum = "Phaeophyta",
  Class = "Phaeophyceae",
  Order = "Laminariales",
  Family = "Lessoniaceae",
  Genus = "Macrocystis",
  specificEpithet = "pyrifera"
))
set_taxonomicCoverage(sci_names)

EML documentation built on April 29, 2022, 1:06 a.m.