Skip to contents

Set and get taxon IDs

Source: R/classification.R, R/getter_setter_s3_generics.R, R/taxon.R, and 1 more
tax_id.Rd

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

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

# S3 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)
#> <taxon_id[4]>
#> [1] 9606 (ncbi) 1386 (ncbi) 4890 (ncbi) 4345 (ncbi)
tax_id(x) <- paste0('00', tax_id(x))
tax_id(x)[1] <- '00000'