Description Usage Arguments Value
View source: R/get_taxID_spp_counts.R
Extract the species count for each taxonomy ID in the _nodes_ structure of the NCBI taxonomy.
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taxonomy_path |
path to folder containing the NCBI taxonomy files (i.e., the extracted contents of _taxdump.zip_, which can be downloaded from <ftp://ftp.ncbi.nih.gov/pub/taxonomy/> or retrieved using [retrieve_NCBI_taxonomy()]). Ignored if 'nodes' is not 'NULL'. |
nodes |
data.frame containing the pre-processed information about the NCBI taxonomy structure. This can be generated, e.g., by using [CHNOSZ::getnodes()]. |
out_file |
path to file for saving the output (saved as a tsv file). Ignored if 'NULL'. |
start_from_species |
logical. If 'TRUE' the counting starts at the 'species' level - i.e., taxon IDs below species (e.g., 'subspecies') receive a count of zero and are not included in the other counts. If 'FALSE', counting starts at the terminal nodes of the taxonomy, regardless of taxonomic level). |
what |
what to calculate? Accepts '"spp_counts"' for returning the count of species / leaf nodes per taxon ID, or '"ancestry"' for returning the ancestry list. |
verbose |
logical: regulates function echoing to console. |
either a data frame with species counts per taxon ID or a list with the ancestry of each taxonomic ID.
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