Study Taxon List

Takes input phylogenies or vectors of taxon names, checks against taxonomic database, returns vector of cleaned taxonomic names (using gnr_resolve) for use in spocc queries, as well as warnings if there are invalid names.

Usage

studyTaxonList(x = NULL, datasources = "GBIF Backbone Taxonomy")

Arguments

x

A phylogeny of class 'phylo' or a vector of class 'character' containing the names of taxa of interest

datasources

A vector of taxonomic data sources implemented in gnr_resolve. You can see the list using taxize::gnr_datasources().

Value

An object of class occCiteData containing the type of inquiry the user has made –a phylogeny or a vector of names– and a data frame containing input taxa names, the closest match according to gnr_resolve, and a list of taxonomic data sources that contain the matching name.

Examples

## Inputting a vector of taxon names
studyTaxonList(
  x = c(
    "Buteo buteo",
    "Buteo buteo hartedi",
    "Buteo japonicus"
  ),
  datasources = c("National Center for Biotechnology Information")
)
#> An object of class "occCiteData"
#> Slot "userQueryType":
#> [1] "User-supplied list of taxa."
#> 
#> Slot "userSpecTaxonomy":
#> [1] "National Center for Biotechnology Information"
#> 
#> Slot "cleanedTaxonomy":
#>            Input Name           Best Match
#> 1         Buteo buteo          Buteo buteo
#> 2 Buteo buteo hartedi Buteo buteo harterti
#> 3     Buteo japonicus      Buteo japonicus
#>                  Taxonomic Databases w/ Matches
#> 1 National Center for Biotechnology Information
#> 2 National Center for Biotechnology Information
#> 3 National Center for Biotechnology Information
#> 
#> Slot "occSources":
#> logical(0)
#> 
#> Slot "occCiteSearchDate":
#> character(0)
#> 
#> Slot "occResults":
#> list()
#> 

# \donttest{
## Inputting a phylogeny
phylogeny <- ape::read.nexus(
  system.file("extdata/Fish_12Tax_time_calibrated.tre",
    package = "occCite"
  )
)
phylogeny <- ape::extract.clade(phylogeny, 18)
studyTaxonList(
  x = phylogeny,
  datasources = c("GBIF Backbone Taxonomy")
)
#> An object of class "occCiteData"
#> Slot "userQueryType":
#> [1] "User-supplied phylogeny."
#> 
#> Slot "userSpecTaxonomy":
#> [1] "GBIF Backbone Taxonomy"
#> 
#> Slot "cleanedTaxonomy":
#>                   Input Name                                    Best Match
#> 1           Istiompax_indica               Istiompax indica (Cuvier, 1832)
#> 2             Kajikia_albida                   Kajikia albida (Poey, 1860)
#> 3              Kajikia_audax                Kajikia audax (Philippi, 1887)
#> 4 Tetrapturus_angustirostris       Tetrapturus angustirostris Tanaka, 1915
#> 5         Tetrapturus_belone           Tetrapturus belone Rafinesque, 1810
#> 6        Tetrapturus_georgii                Tetrapturus georgii Lowe, 1841
#> 7      Tetrapturus_pfluegeri Tetrapturus pfluegeri Robins & de Sylva, 1963
#>   Taxonomic Databases w/ Matches
#> 1         GBIF Backbone Taxonomy
#> 2         GBIF Backbone Taxonomy
#> 3         GBIF Backbone Taxonomy
#> 4         GBIF Backbone Taxonomy
#> 5         GBIF Backbone Taxonomy
#> 6         GBIF Backbone Taxonomy
#> 7         GBIF Backbone Taxonomy
#> 
#> Slot "occSources":
#> logical(0)
#> 
#> Slot "occCiteSearchDate":
#> character(0)
#> 
#> Slot "occResults":
#> list()
#> 
# }