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Add sensible taxon name to taxon table

Source: R/adders_taxa.R
add_taxon_name.Rd

add_taxon_name() creates sensible taxa names by -under default conditions- combining the genus name with a number. The number is only added if there is more than one taxon of that genus. The number indicates the rank of abundance, with 1 indicating the taxon with the highest mean relative abundance within the genus. If genus classification is not available the next most detailed taxonomic rank which is available is used. The sensible taxon name is added to the taxon table under the column name taxon_name.

Usage

add_taxon_name(ta, method = "mean_rel_abundance", include_species = FALSE)

Arguments

ta

A tidytacos object.

method

The method by which to arrange the taxon names. Currently only mean_rel_abundance.

include_species

Whether to include the species name or not.

Value

A tidytacos object.

See also

Other taxa-modifiers: add_mean_rel_abundance(), add_prevalence(), add_taxon_name_color()

Examples

urt_g <- urt %>% add_taxon_name()
# add the species name if present (which is often uncertain in amplicon data)
urt_s <- urt %>% add_taxon_name(include_species = TRUE)