<a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle"> <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
Usage
tax_iucn_code_pq(
physeq = NULL,
taxnames = NULL,
taxonomic_rank = "currentCanonicalSimple",
add_to_phyloseq = NULL,
col_prefix = NULL,
discard_genus_alone = identical(taxonomic_rank, "currentCanonicalSimple"),
discard_NA = TRUE
)Arguments
- physeq
(optional) A phyloseq object. Either `physeq` or `taxnames` must be provided, but not both.
- taxnames
(optional) A character vector of taxonomic names.
- taxonomic_rank
(Character, default "currentCanonicalSimple") The column(s) present in the @tax_table slot of the phyloseq object. Can be a vector of two columns (e.g. c("Genus", "Species")).
- add_to_phyloseq
(logical, default TRUE when physeq is provided, FALSE when taxnames is provided) If TRUE, add a new column (iucn_code) in the tax_table of the phyloseq object. Automatically set to TRUE when a phyloseq object is provided and FALSE when taxnames is provided. Cannot be TRUE if `taxnames` is provided.
- col_prefix
A character string to be added as a prefix to the new columns names added to the tax_table slot of the phyloseq object (default: NULL).
- discard_genus_alone
(logical, default `TRUE` when `taxonomic_rank == "currentCanonicalSimple"`). Passed to [taxonomic_rank_to_taxnames()].
- discard_NA
(logical, default `TRUE`). Passed to [taxonomic_rank_to_taxnames()].
Value
Either a tibble (if add_to_phyloseq = FALSE) or a new phyloseq object, if add_to_phyloseq = TRUE, with 1 new column (iucn_code) in the tax_table.
Examples
if (FALSE) { # \dontrun{
data_fungi_mini_cleanNames <-
gna_verifier_pq(data_fungi_mini) |>
tax_iucn_code_pq()
table(data_fungi_mini_cleanNames@tax_table[, "iucn_code"])
# Using taxnames vector (returns a tibble)
tax_iucn_code_pq(taxnames = c("Amanita muscaria", "Boletus edulis"))
} # }