taxon_id: Taxon ID class

In ropenscilabs/taxa: Classes for Storing and Manipulating Taxonomic Data

Taxon ID class

Description

\Sexpr[results=rd, stage=render]{taxa:::lifecycle("maturing")}

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.

Value

An S3 object of class taxa_taxon_id

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)
x[2:3]
x[2:3] <- 'ABC'
x[c('a', 'c')] <- '123'
x[['b']] <- taxon_id('123423', db = 'ncbi')
tax_db(x)
tax_db(x) <- 'nbn'
c(x, x)

# Using as columns in tables
tibble::tibble(x = x, y = 1:4)
data.frame(x = x, y = 1:4)

# Convert to tables
tibble::as_tibble(x)
as_data_frame(x)

# Trying to use an invalid ID with a specified database causes an error
#taxon_id('NOLETTERS', db = 'ncbi')

ropenscilabs/taxa documentation built on Feb. 23, 2024, 6:31 p.m.