taxize (version 0.2.2)

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

Arguments

x

character; taxons to query.

db

character; database to query. either ncbi, itis, eol, col, tropicos, gbif.

id

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

...

Other arguments passed to get_tsn, get_uid, get_eolid,

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 maxi

checklist

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

key

Your API key; loads from .Rprofile.

callopts

Further args passed on to httr::GET.

Value

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

See Also

get_tsn, get_uid, get_eolid, get_colid, get_tpsid, get_gbifid

Examples

# Plug in taxon names directly
classification(c("Chironomus riparius", "aaa vva"), db = 'ncbi')
classification(c("Chironomus riparius", "aaa vva"), db = 'itis')
classification(c("Chironomus riparius", "aaa vva"), db = 'eol')
classification(c("Chironomus riparius", "aaa vva"), db = 'col')
classification(c("Chironomus riparius", "asdfasdfsfdfsd"), db = 'gbif')
classification(c("Poa annua", "aaa vva"), 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_eolid(c("Chironomus riparius", "aaa vva")))
classification(get_colid(c("Chironomus riparius", "aaa vva")))
classification(get_tpsid(c("Poa annua", "aaa vva")))

# 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(cl)

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

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