reformat_hierarchy: Reformat hierarchy

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

Reformat hierarchy

Description

Reformat hierarchy

Usage

reformat_hierarchy(
  x,
  db = NULL,
  quiet = FALSE,
  ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species"),
  multithread = FALSE
)

Arguments

x	A DNAbin with names formatted Accession|taxid;taxonomy
db	A database file generated by get_ncbi_taxonomy or get_ott_lineage. Required if get_lineage is TRUE
quiet	Whether progress should be printed to console
ranks	The taxonomic ranks to return in the output names
multithread	Whether multithreading should be used, if TRUE the number of cores will be automatically detected (Maximum available cores - 1), or provide a numeric vector to manually set the number of cores to use. Default is FALSE (single thread) This argument may alternatively be a 'cluster' object, in which case it is the user's responsibility to close the socket connection at the conclusion of the operation, for example by running parallel::stopCluster(cores).

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.