get_ott_taxonomy

get_ott_taxonomy

get_ott_taxonomy(dir = NULL, quiet = FALSE, filter_unplaced = TRUE)

Arguments

dir

a directory containing the open tree of life taxonomy files obtained from the download_ott_taxonomy function

quiet

Whether progress should be printed to console

filter_unplaced

Whether to filter 'bad' entries. These include incertae_sedis major_rank_conflict unplaced environmental inconsistent extinct hidden hybrid not_otu viral barren See: https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/taxon-flags.md for more info