get_ntaxa: Count number of unique taxa

In ropensci/phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Count number of unique taxa

Description

Count the number of unique taxa represented by cluster(s) or sequences in phylota table Use rnk to specify a taxonomic level to count. If NULL counts will be made to the lowest level reported on NCBI.

Usage

get_ntaxa(phylota, cid = NULL, sid = NULL, rnk = NULL, keep_higher = FALSE)

Arguments

phylota	Phylota object
cid	Cluster ID(s)
sid	Sequence ID(s)
rnk	Taxonomic rank
keep_higher	Keep higher taxonomic ranks?

Value

vector

See Also

Other tools-public: calc_mad(), calc_wrdfrq(), drop_by_rank(), drop_clstrs(), drop_sqs(), get_clstr_slot(), get_nsqs(), get_sq_slot(), get_stage_times(), get_tx_slot(), get_txids(), is_txid_in_clstr(), is_txid_in_sq(), list_clstrrec_slots(), list_ncbi_ranks(), list_seqrec_slots(), list_taxrec_slots(), plot_phylota_pa(), plot_phylota_treemap(), read_phylota(), write_sqs()

Examples

data('bromeliads')
# how many species are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'species'))
# how many genera are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'genus'))
# how many families are there?
(get_ntaxa(phylota = bromeliads, cid = '0', rnk = 'family'))
# use list_ncbi_ranks() to see available rank names
(list_ncbi_ranks())

ropensci/phylotaR documentation built on July 9, 2023, 3:17 p.m.