Agglomerate and merge a phyloseq object

Agglomerates by rank_names() and then merges them into a phyloseq object.

add_ranks(ps = ps, ranks = c(rank_names(ps)),
  replace_ASV_names = TRUE, verbose = TRUE)

Arguments

ps	A `phyloseq` object that contains a `tax_table`.
ranks	A vector of taxonomic rank names found in `rank_names`. Defaults to all available ranks (`Phylum` through `Genus`).
replace_ASV_names	Logical. If TRUE, ASVs will be named with a unique and the lowest taxonomic rank available.
verbose	Logical. If FALSE, messages will be supressed.

This function returns the input phyloseq object with additional taxa that are the agglomerated taxa at the taxonomic levels provided.

ps <- add_ranks(ps, ranks = c("Genus", "Family"))
#> Error in add_ranks(ps, ranks = c("Genus", "Family")): object 'ps' not found