taxonbridge (version 1.0.5)

load_taxonomies: Load and merge GBIF and NCBI taxonomic data

Description

Load and merge GBIF and NCBI taxonomic data

Usage

load_taxonomies(GBIF_path, NCBI_path)

Arguments

GBIF_path

Path to the GBIF backbone taxonomy (compressed or uncompressed).

NCBI_path

Path to the NCBI taxonomy (compressed or uncompressed).

Value

A tibble containing merged GBIF and NCBI taxonomic data.

Details

This method parses and merges a GBIF Taxon.tsv file (see download_gbif()) and a Taxonkit (https://bioinf.shenwei.me/taxonkit/download/) output file obtained by running: taxonkit list --ids 1 | taxonkit lineage --show-lineage-taxids --show-lineage-ranks --show-rank --show-name > All.lineages.tsv on NCBI data dump files (see download_ncbi()).

Examples

# NOT RUN {
load_taxonomies("path/to/GBIF/Taxon.tsv","path/to/NCBI-Taxonkit/All.lineages.tsv")
# }
# NOT RUN {
load_taxonomies(download_gbif(), download_ncbi(taxonkitpath = "/path/to/taxonkit"))
# }