Used to store the names of taxon databases defined in db_ref. Primarily
used in other classes like taxon_id to define databases for each item.
Usage
taxon_db(db = character(), .names = NULL, ...)See also
Other classes:
[.taxa_classification(),
classification(),
taxon(),
taxon_authority(),
taxon_id(),
taxon_rank()
Examples
# Making new objects
x <- taxon_db(c('ncbi', 'ncbi', 'itis'))
x
#> <taxon_db[3]>
#> [1] ncbi ncbi itis
# Manipulating objects
as.character(x)
#> [1] "ncbi" "ncbi" "itis"
x[2:3]
#> <taxon_db[2]>
#> [1] ncbi itis
x[2:3] <- 'nbn'
names(x) <- c('a', 'b', 'c')
x['b']
#> <taxon_db[1]>
#> b
#> nbn
x['b'] <- 'nbn'
x[x == 'itis'] <- 'gbif'
# Using as columns in tables
tibble::tibble(x = x, y = 1:3)
#> # A tibble: 3 × 2
#> x y
#> <tax_db> <int>
#> 1 ncbi 1
#> 2 nbn 2
#> 3 nbn 3
data.frame(x = x, y = 1:3)
#> x y
#> 1 ncbi 1
#> 2 nbn 2
#> 3 nbn 3
# Converting to tables
tibble::as_tibble(x)
#> # A tibble: 3 × 1
#> tax_db
#> <chr>
#> 1 ncbi
#> 2 nbn
#> 3 nbn
as_data_frame(x)
#> tax_db
#> 1 ncbi
#> 2 nbn
#> 3 nbn
# Trying to use an invalid database generates an error
# x <- taxon_db(c('ncbi', 'ncbi', 'my_custom_db'))
# x[x == 'itis'] <- 'my_custom_db'
# Listing known databases and their properties
db_ref$get()
#> <taxon_db_def[8]>
#> _____________________ ncbi ______________________
#> url: http://www.ncbi.nlm.nih.gov/taxonomy
#> desc: NCBI Taxonomy Database
#> id_regex: [0-9]+
#> rank_levels:
#>
#> _____________________________ gbif _____________________________
#> url: http://www.gbif.org/developer/species
#> desc: GBIF Taxonomic Backbone
#> id_regex: [0-9]+
#> rank_levels: kingdom < phylum < order < family < genus < species
#>
#> _________________________________ bold _________________________________
#> url: http://www.boldsystems.org
#> desc: Barcode of Life
#> id_regex: [0-9]+
#> rank_levels: phylum < class < order < family < subfamily < genus < spec…
#>
#> ___________________ col ___________________
#> url: http://www.catalogueoflife.org
#> desc: Catalogue of Life
#> id_regex: [a-z0-9]{32}
#> rank_levels:
#>
#> ______________ eol ______________
#> url: http://eol.org
#> desc: Encyclopedia of Life
#> id_regex: [0-9]+
#> rank_levels:
#>
#> ____________________ nbn ____________________
#> url: https://nbn.org.uk
#> desc: UK National Biodiversity Network
#> id_regex: [A-Z]{5}[0-9]{10}
#> rank_levels:
#>
#> ________________ tps ________________
#> url: http://www.tropicos.org/
#> desc: Tropicos
#> id_regex: [0-9]+
#> rank_levels:
#>
#> _______________________ itis _______________________
#> url: http://www.itis.gov
#> desc: Integrated Taxonomic Information System
#> id_regex: [0-9]+
#> rank_levels:
# Adding and using a new database
db_ref$set(name = 'my_custom_db', desc = 'I just made this up')
db_ref$get()
#> <taxon_db_def[9]>
#> _____________________ ncbi ______________________
#> url: http://www.ncbi.nlm.nih.gov/taxonomy
#> desc: NCBI Taxonomy Database
#> id_regex: [0-9]+
#> rank_levels:
#>
#> _____________________________ gbif _____________________________
#> url: http://www.gbif.org/developer/species
#> desc: GBIF Taxonomic Backbone
#> id_regex: [0-9]+
#> rank_levels: kingdom < phylum < order < family < genus < species
#>
#> _________________________________ bold _________________________________
#> url: http://www.boldsystems.org
#> desc: Barcode of Life
#> id_regex: [0-9]+
#> rank_levels: phylum < class < order < family < subfamily < genus < spec…
#>
#> ___________________ col ___________________
#> url: http://www.catalogueoflife.org
#> desc: Catalogue of Life
#> id_regex: [a-z0-9]{32}
#> rank_levels:
#>
#> ______________ eol ______________
#> url: http://eol.org
#> desc: Encyclopedia of Life
#> id_regex: [0-9]+
#> rank_levels:
#>
#> ____________________ nbn ____________________
#> url: https://nbn.org.uk
#> desc: UK National Biodiversity Network
#> id_regex: [A-Z]{5}[0-9]{10}
#> rank_levels:
#>
#> ________________ tps ________________
#> url: http://www.tropicos.org/
#> desc: Tropicos
#> id_regex: [0-9]+
#> rank_levels:
#>
#> _______________________ itis _______________________
#> url: http://www.itis.gov
#> desc: Integrated Taxonomic Information System
#> id_regex: [0-9]+
#> rank_levels:
#>
#> _________ my_custom_db _________
#> url: NA
#> desc: I just made this up
#> id_regex: NA
#> rank_levels:
x <- taxon_db(c('ncbi', 'ncbi', 'my_custom_db'))