Used to store the ID corresponding to taxa, either arbitrary or from a
particular taxonomy database. This is typically used to store taxon IDs in
taxon objects.
Usage
taxon_id(id = character(), db = "", .names = NULL)Arguments
- id
Zero or more taxonomic ids. Inputs will be transformed to a character vector if possible.
- db
The name(s) of the database(s) associated with the IDs. If not
NA(the default), the input must consist of names of databases in db_ref$get().- .names
The names that will be applied to the vector.
See also
Other classes:
[.taxa_classification(),
classification(),
taxon(),
taxon_authority(),
taxon_db(),
taxon_rank()
Examples
# Making new objects
x <- taxon_id(c('A', 'B', 'C'))
x <- taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi')
x <- taxon_id(c('9606', '1386', '4890', '4345'),
db = c('ncbi', 'ncbi', 'itis', 'itis'))
names(x) <- c('a', 'b', 'c', 'd')
# Manipulating objects
as.character(x)
#> a b c d
#> "9606" "1386" "4890" "4345"
x[2:3]
#> <taxon_id[2]>
#> b c
#> 1386 (ncbi) 4890 (itis)
x[2:3] <- 'ABC'
x[c('a', 'c')] <- '123'
x[['b']] <- taxon_id('123423', db = 'ncbi')
tax_db(x)
#> <taxon_db[4]>
#> a b c d
#> ncbi itis
tax_db(x) <- 'nbn'
c(x, x)
#> <taxon_id[8]>
#> a b c d a b
#> 123 (nbn) 123423 (nbn) 123 (nbn) 4345 (nbn) 123 (nbn) 123423 (nbn)
#> c d
#> 123 (nbn) 4345 (nbn)
# Using as columns in tables
tibble::tibble(x = x, y = 1:4)
#> # A tibble: 4 × 2
#> x y
#> <tax_id> <int>
#> 1 123 (nbn) 1
#> 2 123423 (nbn) 2
#> 3 123 (nbn) 3
#> 4 4345 (nbn) 4
data.frame(x = x, y = 1:4)
#> x y
#> 1 123 (nbn) 1
#> 2 123423 (nbn) 2
#> 3 123 (nbn) 3
#> 4 4345 (nbn) 4
# Convert to tables
tibble::as_tibble(x)
#> # A tibble: 4 × 2
#> tax_id tax_db
#> <chr> <chr>
#> 1 123 nbn
#> 2 123423 nbn
#> 3 123 nbn
#> 4 4345 nbn
as_data_frame(x)
#> tax_id tax_db
#> 1 123 nbn
#> 2 123423 nbn
#> 3 123 nbn
#> 4 4345 nbn
# Trying to use an invalid ID with a specified database causes an error
#taxon_id('NOLETTERS', db = 'ncbi')