get_species_counts: Return the count of known species in each taxon

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

Description

This function processes a list of NCBI Taxon IDs and known number of species and determines the count of species under each taxon

Usage

get_species_counts(taxlist, spp_df = NULL, spp_file = NULL, verbose = TRUE)

Arguments

taxlist	a list object of class _taxonsampling_, containing (at least) a field '$countIDs', a numeric vector with the counts of the number of taxonomy IDs belonging to each taxon (calculated as part of [get_taxonomy_counts()]).
spp_df	two-column data frame with the input taxon IDs in the first column, and the corresponding number of known species in the second column. Ignored if 'ids_file' is not 'NULL'.
spp_file	path to a tab-separated file containng two two columns, with the input taxon IDs in the first column, and the corresponding number of known species in the second column.
verbose	logical: regulates function echoing to console.

Value

Input object 'taxlist' updated to contain the additional fields:

• 'spp_df': two-column data frame with the input taxon IDs in the first column, and the corresponding number of known species in the second column. Filtered to have only the IDs present in '$countIDs'.

• '$countSpp', a numeric vector with the counts of (known) species for each taxon from 'taxlist$countIDs'.

franciscolobo/TaxonSampling documentation built on Dec. 31, 2021, 12:04 a.m.