Study Taxon List

Takes input phylogenies or vectors of taxon names, checks against taxonomic database, returns vector of cleaned taxonomic names (using taxize::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 taxize::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 taxize::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")
)
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> 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 Taxonomic Databases w/ Matches
#> 1         Buteo buteo         Buteo buteo                 Not rectified.
#> 2 Buteo buteo hartedi Buteo buteo hartedi                 Not rectified.
#> 3     Buteo japonicus     Buteo japonicus                 Not rectified.
#> 
#> 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")
)
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> handled warning: Package taxize unavailable. Skipping taxonomic rectification.
#> 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
#> 2             Kajikia_albida             Kajikia_albida
#> 3              Kajikia_audax              Kajikia_audax
#> 4 Tetrapturus_angustirostris Tetrapturus_angustirostris
#> 5         Tetrapturus_belone         Tetrapturus_belone
#> 6        Tetrapturus_georgii        Tetrapturus_georgii
#> 7      Tetrapturus_pfluegeri      Tetrapturus_pfluegeri
#>   Taxonomic Databases w/ Matches
#> 1                 Not rectified.
#> 2                 Not rectified.
#> 3                 Not rectified.
#> 4                 Not rectified.
#> 5                 Not rectified.
#> 6                 Not rectified.
#> 7                 Not rectified.
#> 
#> Slot "occSources":
#> logical(0)
#> 
#> Slot "occCiteSearchDate":
#> character(0)
#> 
#> Slot "occResults":
#> list()
#> 
# }