Reformat hierarchy

Reformat hierarchy

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).