Function reference • yatah

Filter taxonomy

is_lineage(): Test if a string is a lineage

is_clade(): Test if a lineage belongs to a clade

is_rank() is_at_least_rank(): Test if a lineage goes down to a specified rank

Extract clades and ranks

get_all_clades(): Extract all clades present in the lineages

get_clade(): Extract the clade of a desired rank in a lineage

get_last_clade(): Extract the last clade of a lineage

get_last_rank(): Extract the last rank of a lineage

Trim lineages

trim_rank(): Trim lineages until a specified rank

trim_void(): Trim void ranks in lineages

trim_common(): Trim lineages until the shallowest common rank.

Convert into other formats

taxtable(): Taxonomic table

taxtree(): Taxonomic tree

Dataset

all_ranks: Ranks handled by yatah

abundances: Abundance table for 199 samples.