set_taxonomicCoverage

0th

Percentile

set_taxonomicCoverage

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.

Aliases
  • set_taxonomicCoverage
Examples
# NOT RUN {
sci_names <- data.frame(
  Kingdom = "Plantae",
  Phylum = "Phaeophyta",
  Class = "Phaeophyceae",
  Order = "Laminariales",
  Family = "Lessoniaceae",
  Genus = "Macrocystis",
  Species = "pyrifera"
)
taxon_coverage <- set_taxonomicCoverage(sci_names)

# }
# NOT RUN {
 # Examples that may take > 5s

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

# }
Documentation reproduced from package EML, version 2.0.4, License: MIT + file LICENSE

Community examples

Looks like there are no examples yet.