This function is different from downstream() in that it only
collects immediate taxonomic children, while downstream()
collects taxonomic names down to a specified taxonomic rank, e.g.,
getting all species in a family.
children(...)
# S3 method for default
children(sci_id, db = NULL, rows = NA, x = NULL, ...)
# S3 method for tsn
children(sci_id, db = NULL, ...)
# S3 method for wormsid
children(sci_id, db = NULL, ...)
# S3 method for ids
children(sci_id, db = NULL, ...)
# S3 method for uid
children(sci_id, db = NULL, ...)
# S3 method for boldid
children(sci_id, db = NULL, ...)Further args passed on to ritis::hierarchy_down(),
ncbi_children(), worrms::wm_children(), bold_children()
See those functions for what parameters can be passed on.
Vector of taxa names (character) or IDs (character or numeric) to query.
character; database to query. One or more of itis,
ncbi, worms, or bold. Note that each taxonomic data
source has their own identifiers, so that if you provide the wrong
db value for the identifier you could get a result, but it will
likely be wrong (not what you were expecting). If using ncbi, we recommend
getting an API key; see taxize-authentication
(numeric) Any number from 1 to infinity. If the default NA, all rows are considered. Note that this parameter is ignored if you pass in a taxonomic id of any of the acceptable classes: tsn. NCBI has a method for this function but rows doesn't work.
Deprecated, see sci_id
A named list of data.frames with the children names of every supplied taxa. You get an NA if there was no match in the database.
note that with db = "ncbi", we set ambiguous = TRUE; that is, children
taxa with words like "unclassified", "unknown", "uncultured", "sp." are
NOT removed
BEWARE: db="bold" scrapes the BOLD website, so may be unstable. That is,
one day it may work, and the next it may fail. Open an issue if you
encounter an error: https://github.com/ropensci/taxize/issues
if (FALSE) {
# Plug in taxonomic IDs
children(161994, db = "itis")
children(8028, db = "ncbi")
## works with numeric if as character as well
children(161994, db = "itis")
children(88899, db = "bold")
children(as.boldid(88899))
# Plug in taxon names
children("Salmo", db = 'itis')
children("Salmo", db = 'ncbi')
children("Salmo", db = 'worms')
children("Salmo", db = 'bold')
# Plug in IDs
(id <- get_wormsid("Gadus"))
children(id)
# Many taxa
sp <- c("Tragia", "Schistocarpha", "Encalypta")
children(sp, db = 'itis')
# Two data sources
(ids <- get_ids("Apis", db = c('ncbi','itis')))
children(ids)
## same result
children(get_ids("Apis", db = c('ncbi','itis')))
# Use the rows parameter
children("Poa", db = 'itis')
children("Poa", db = 'itis', rows=1)
# use curl options
res <- children("Poa", db = 'itis', rows=1, verbose = TRUE)
}