taxon | R Documentation |
Used to store information about taxa, such as names, ranks, and IDs.
taxon(name = character(0), rank = NA, id = NA, auth = NA, .names = NA, ...)
name |
The names of taxa. Inputs with be coerced into a character vector if anything else is given. |
rank |
The ranks of taxa. Inputs with be coerced into a taxon_rank vector if anything else is given. |
id |
The ids of taxa. These should be unique identifier and are usually associated with a database. Inputs with be coerced into a taxon_id vector if anything else is given. |
auth |
The authority of the taxon. Inputs with be coerced into a taxon_authority vector if anything else is given. |
.names |
The names of the vector. |
... |
Additional arguments. |
An S3
object of class taxa_taxon
Other classes:
[.taxa_classification()
,
classification()
,
taxon_authority()
,
taxon_db()
,
taxon_id()
,
taxon_rank()
# Create taxon name vector x <- taxon(c('A', 'B', 'C')) 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')) names(x) <- c('a', 'b', 'c', 'd') # Get parts of the taxon name vector tax_name(x) tax_rank(x) tax_id(x) tax_db(x) tax_auth(x) tax_author(x) tax_date(x) tax_cite(x) # Set parts of the taxon name vector tax_name(x) <- tolower(tax_name(x)) tax_rank(x)[1] <- NA tax_name(x)['b'] <- 'Billy' tax_id(x) <- '9999' tax_db(x) <- 'itis' tax_auth(x) <- NA tax_author(x)[2:3] <- c('Joe', 'Billy') tax_date(x) <- c('1999', '2013', '1796', '1899') tax_cite(x)[1] <- 'Linnaeus, C. (1771). Mantissa plantarum altera generum.' # Manipulate taxon name vectors x[1:3] x[tax_rank(x) > 'family'] x['b'] <- NA x[c('c', 'd')] <- 'unknown' is.na(x) # Use as columns in tables tibble::tibble(x = x, y = 1:4) data.frame(x = x, y = 1:4) # Converting to tables tibble::as_tibble(x) as_data_frame(x)
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