listTaxa: Lists all unique taxonomic names in a Taxonomy at a given...

In reptalex/phylofactor: phylofactor

Lists all unique taxonomic names in a Taxonomy at a given level

Description

Lists all unique taxonomic names in a Taxonomy at a given level

Usage

listTaxa(s, minimum.level = 1, common.name = F, uniques = F)

Arguments

s	Character vector of taxonomic names. First row is species IDs, second row is their taxonomy. This function assumes greengenes-compatible taxonomic strings
minimum.level	Integer. Minimum number of taxonomic levels to include counting from highest to lowest.
common.name	logical whether or not to return the common name in the list of taxa
uniques	logical whether or not to trim taxonomic names to only unique entries

Value

list of taxonomic strings for all taxa up to speficied level.

Examples

data(FTmicrobiome)
sapply(FTmicrobiome$taxonomy[,2],as.character) %>%
   listTaxa(minimum.level=2,uniques=TRUE)

reptalex/phylofactor documentation built on Feb. 28, 2024, 3:19 p.m.