Create Custom Taxonomies Based on the NCBI Taxonomy and GBIF Backbone Taxonomy

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Documentation for package ‘taxonbridge’ version 1.2.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotate	Annotate a custom taxonomy
dedupe	Remove duplicate scientific names in a taxonomy
download_gbif	Download the GBIF backbone taxonomy
download_ncbi	Download the NCBI taxonomy
fuzzy_search	Match misspelled or partial scientific names
get_inconsistencies	Detect candidate inconsistencies and ambiguity between NCBI and GBIF data
get_lineages	Get entries that have lineage information for both the GBIF and NCBI data
get_status	Filter a custom taxonomy by GBIF taxonomic status/synonym
get_taxa	A helper function to filter on GBIF and NCBI taxa names
get_validity	Validate entries of a merged taxonomy
load_population	Load previously merged GBIF and NCBI taxonomies
load_sample	Load an example of previously merged GBIF and NCBI taxonomies
load_taxonomies	Load and merge GBIF and NCBI taxonomic data
plot_mdb	Generic for plot_mdb methods
prepare_comparable_rank_dist	Get comparable NCBI and GBIF taxonomic ranks
prepare_rank_dist	Get all NCBI and GBIF taxonomic ranks
term_conversion	Convert GBIF terms to NCBI terms