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'.

Value

a taxonomicCoverage object for EML

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

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)
#> $taxonomicClassification
#> $taxonomicClassification[[1]]
#> $taxonomicClassification[[1]]$taxonRankName
#> [1] "Kingdom"
#> 
#> $taxonomicClassification[[1]]$taxonRankValue
#> [1] "Plantae"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonRankName
#> [1] "Phylum"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonRankValue
#> [1] "Phaeophyta"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonRankName
#> [1] "Class"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonRankValue
#> [1] "Phaeophyceae"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonRankName
#> [1] "Order"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonRankValue
#> [1] "Laminariales"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonRankName
#> [1] "Family"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonRankValue
#> [1] "Lessoniaceae"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonRankName
#> [1] "Genus"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonRankValue
#> [1] "Macrocystis"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonRankName
#> [1] "specificEpithet"
#> 
#> $taxonomicClassification[[1]]$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonomicClassification$taxonRankValue
#> [1] "pyrifera"
#> 
#> 
#> 
#> 
#> 
#> 
#> 
#> 
#>