get_summary_df: Generate a summary dataframe from the result of run_TS

In fcampelo/TaxonSampling: Hierarchical Taxonomic Sampling for Maximized Diversity at All Levels

Description

Returns a summary data frame containing relevant counts for each taxID associated with the sequences passed to [get_counts()] (parameters 'ids_df' or 'ids_file') in the pre-processing stage before the call to [run_TS()].

Usage

get_summary_df(taxlist)

Arguments

taxlist

list object of class _taxonsampling_, returned by [run_TS()]

Value

Data frame containing fields '$taxID', '$level' (taxonomic level), '$name' (scientific name), 'species_count' (total number of species or leaf nodes under that taxonomy ID), '$sample_count' (number of sampled species or leaf nodes under that taxonomy ID) and '$seq_count' (number of available sequences under that taxonomy ID, passed in the call to [get_counts()]).

fcampelo/TaxonSampling documentation built on Jan. 29, 2022, 7:11 a.m.