classification: Retrieve the taxonomic hierarchy for a given taxon ID.

Description

Retrieve the taxonomic hierarchy for a given taxon ID.

Usage

classification(...)
## S3 method for class 'default':
classification(x, db = NULL, callopts = list(),
  return_id = TRUE, rows = NA, ...)
## S3 method for class 'tsn':
classification(id, callopts = list(), return_id = TRUE, ...)
## S3 method for class 'uid':
classification(id, callopts = list(), return_id = TRUE, ...)
## S3 method for class 'eolid':
classification(id, key = NULL, callopts = list(),
  return_id = TRUE, ...)
## S3 method for class 'colid':
classification(id, start = NULL, checklist = NULL,
  callopts = list(), return_id = TRUE, ...)
## S3 method for class 'tpsid':
classification(id, key = NULL, callopts = list(),
  return_id = TRUE, ...)
## S3 method for class 'gbifid':
classification(id, callopts = list(), return_id = TRUE,
  ...)
## S3 method for class 'nbnid':
classification(id, callopts = list(), return_id = TRUE, ...)
## S3 method for class 'ids':
classification(id, ...)
cbind.classification(x)
rbind.classification(x)
cbind.classification_ids(...)
rbind.classification_ids(...)

Arguments

...

Other arguments passed to get_tsn, get_uid, get_eolid,

Vector of taxa names (character) or IDs (character or numeric) to query.

character; database to query. either ncbi, itis, eol, col, tropicos, gbif, or nbn. Note that each taxonomic data source has their own identifiers, so that if you pr

callopts

Curl options passed on to GET

return_id

(logical) If TRUE (default), return the taxon id as well as the name and rank of taxa in the lineage returned.

rows

(numeric) Any number from 1 to inifity. If the default NA, all rows are considered. Note that this parameter is ignored if you pass in a taxonomic id instead of a name of class character.

character; identifiers, returned by get_tsn, get_uid, get_eolid,

key

Your API key; loads from .Rprofile.

start

The first record to return. If omitted, the results are returned from the first record (start=0). This is useful if the total number of results is larger than the maximum number of results returned by a single Web service query (currently the maximum numb

checklist

character; The year of the checklist to query, if you want a specific year's checklist instead of the lastest as default (numeric).

Value

A named list of data.frames with the taxonomic classification of every supplied taxa.

Details

If IDs are supplied directly (not from the get_* functions) you must specify the type of ID. There is a timeout of 1/3 seconds between querries to NCBI.

BEWARE: Right now, NBN doesn't return the queried taxon in the classification. But you can attach it yourself quite easily of course. This behavior is different from the other data sources.

Examples

Run this code

# Plug in taxon IDs
classification(9606, db = 'ncbi')
classification(c(9606, 55062), db = 'ncbi')
classification(129313, db = 'itis')
classification(57361017, db = 'eol')
classification(c(2704179, 2441176), db = 'gbif')
classification(25509881, db = 'tropicos')
classification("NBNSYS0000004786", db = 'nbn')
## works the same if IDs are in class character
classification(c("2704179", "2441176"), db = 'gbif')

# Plug in taxon names
## in this case, we use get_*() fxns internally to first get taxon IDs
classification(c("Chironomus riparius", "aaa vva"), db = 'ncbi')
classification(c("Chironomus riparius", "aaa vva"), db = 'ncbi', verbose=FALSE)
classification(c("Chironomus riparius", "aaa vva"), db = 'itis')
classification(c("Chironomus riparius", "aaa vva"), db = 'itis', verbose=FALSE)
classification(c("Chironomus riparius", "aaa vva"), db = 'eol')
classification(c("Chironomus riparius", "aaa vva"), db = 'col')
classification("Alopias vulpinus", db = 'nbn')
classification(c("Chironomus riparius", "aaa vva"), db = 'col', verbose=FALSE)
classification(c("Chironomus riparius", "asdfasdfsfdfsd"), db = 'gbif')
classification("Poa annua", db = 'tropicos')

# Use methods for get_uid, get_tsn, get_eolid, get_colid, get_tpsid
classification(get_uid(c("Chironomus riparius", "Puma concolor")))

classification(get_uid(c("Chironomus riparius", "aaa vva")))
classification(get_tsn(c("Chironomus riparius", "aaa vva")))
classification(get_tsn(c("Chironomus riparius", "aaa vva"), verbose = FALSE))
classification(get_eolid(c("Chironomus riparius", "aaa vva")))
classification(get_colid(c("Chironomus riparius", "aaa vva")))
classification(get_tpsid(c("Poa annua", "aaa vva")))
classification(get_gbifid(c("Poa annua", "Bison bison")))

# Pass many ids from class "ids"
(out <- get_ids(names="Puma concolor", db = c('ncbi','gbif')))
(cl <- classification(out))

# Bind width-wise from class classification_ids
cbind(cl)

# Bind length-wise
rbind(cl)

# Many names to get_ids
(out <- get_ids(names=c("Puma concolor","Accipiter striatus"), db = c('ncbi','itis','col')))
(cl <- classification(out))
rbind(cl)
## cbind with so many names results in some messy data
cbind(cl)
## so you can turn off return_id
cbind( classification(out, return_id=FALSE) )

# rbind and cbind on class classification (from a call to get_colid, get_tsn, etc.
# - other than get_ids)
(cl_col <- classification(get_colid(c("Puma concolor","Accipiter striatus"))))
rbind(cl_col)
cbind(cl_col)

(cl_uid <- classification(get_uid(c("Puma concolor","Accipiter striatus")), return_id=FALSE))
rbind(cl_uid)
cbind(cl_uid)
## cbind works a bit odd when there are lots of ranks without names
(cl_uid <- classification(get_uid(c("Puma concolor","Accipiter striatus")), return_id=TRUE))
cbind(cl_uid)

(cl_tsn <- classification(get_tsn(c("Puma concolor","Accipiter striatus"))))
rbind(cl_tsn)
cbind(cl_tsn)

(tsns <- get_tsn(c("Puma concolor","Accipiter striatus")))
(cl_tsns <- classification(tsns))
cbind(cl_tsns)

# NBN data
(res <- classification(c("Alopias vulpinus","Pinus sylvestris"), db = 'nbn'))
rbind(res)
cbind(res)

# Return taxonomic IDs
## the return_id parameter is logical, and you can turn it on or off. It's TRUE by default
classification(c("Alopias vulpinus","Pinus sylvestris"), db = 'ncbi', return_id = TRUE)
classification(c("Alopias vulpinus","Pinus sylvestris"), db = 'ncbi', return_id = FALSE)

# Use rows parameter to select certain
classification('Poa annua', db = 'tropicos')
classification('Poa annua', db = 'tropicos', rows=1:4)
classification('Poa annua', db = 'tropicos', rows=1)
classification('Poa annua', db = 'tropicos', rows=6)

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