Get taxa at specific scientific ranks

Get taxa at specific scientific ranks

Usage

taxa_at(
  x,
  rank,
  db = "ncbi",
  missing = "lower",
  verbose = TRUE,
  warn = TRUE,
  ...
)

Arguments

x

(character) Vector of taxon keys (ids) for the given database. required

rank

(character) A target rank for which to fetch data. required

db

(character) The database to search, one of ncbi, itis, gbif, col, or wfo

missing

(character) if no data found at the given rank and input key, should we get the next closest lower than that given in rank, or higher. one of lower (default), higher.

verbose

(logical) Print verbose messages

warn

(logical) If TRUE, raise a warning if any taxon IDs can not be found

...

Additional arguments passed to database specific classification functions

Value

list of data.frame's for each input taxon key, where each data.frame has fields: name, rank, id. When no results found, an empty data.frame

Examples

if (FALSE) { # \dontrun{
taxa_at(186803, rank = "order", db = "ncbi", missing = "lower")
taxa_at(c(186803, 541000, 216572, 186804, 31979,  186806),
 rank = "family", missing = "lower")
taxa_at(c(154395, 154357, 23041, 154396), rank = "family", db="itis")
taxa_at(c('wfo-4000032377', 'wfo-0000541830'), rank = "family", db = "wfo")
taxa_at("wfo-7000000057", rank = "order", db = "wfo")
taxa_at(2877951, rank = "phylum", db = "gbif")
taxa_at(c(2877951, 5386), rank = "family", db = "gbif")
taxa_at(c("C66T4", "C7ZVH", "TP"), rank = "family", db = "col")
} # }