tax_id: Set and get taxon IDs

In taxa: Classes for Storing and Manipulating Taxonomic Data

Set and get taxon IDs

Description

Set and get the taxon IDs in objects that have them, such as taxon objects.

Usage

## S3 method for class 'taxa_classification'
tax_id(x)

## S3 replacement method for class 'taxa_classification'
tax_id(x) <- value

tax_id(x)

tax_id(x) <- value

## S3 method for class 'taxa_taxon'
tax_id(x)

## S3 replacement method for class 'taxa_taxon'
tax_id(x) <- value

## S3 method for class 'taxa_taxonomy'
tax_id(x)

## S3 replacement method for class 'taxa_taxonomy'
tax_id(x) <- value

Arguments

x	An object with taxon IDs.
value	The taxon IDs to set. Inputs will be coerced into a taxon_id vector.

Examples

x <- taxon(name = c('Homo sapiens', 'Bacillus', 'Ascomycota', 'Ericaceae'),
           rank = c('species', 'genus', 'phylum', 'family'),
           id = taxon_id(c('9606', '1386', '4890', '4345'), db = 'ncbi'),
           auth = c('Linnaeus, 1758', 'Cohn 1872', NA, 'Juss., 1789'))

tax_id(x)
tax_id(x) <- paste0('00', tax_id(x))
tax_id(x)[1] <- '00000'

taxa documentation built on April 12, 2022, 9:06 a.m.