Retrieve the taxonomic hierarchy for a given taxon ID.
Retrieve the taxonomic hierarchy for a given taxon ID.
classification(...) ## Default S3 method: classification( sci_id, db = NULL, callopts = list(), return_id = TRUE, rows = NA, x = NULL, ... ) ## S3 method for class 'tsn' classification(id, return_id = TRUE, ...) ## S3 method for class 'uid' classification( id, callopts = list(), return_id = TRUE, batch_size = 50, max_tries = 3, ... ) ## S3 method for class 'eolid' classification(id, callopts = list(), return_id = TRUE, ...) ## S3 method for class 'tpsid' classification(id, 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 'tolid' classification(id, callopts = list(), return_id = TRUE, ...) ## S3 method for class 'wormsid' classification(id, callopts = list(), return_id = TRUE, ...) ## S3 method for class 'natservid' classification(id, callopts = list(), return_id = TRUE, ...) ## S3 method for class 'boldid' classification(id, callopts = list(), return_id = TRUE, ...) ## S3 method for class 'wiki' classification(id, callopts = list(), return_id = TRUE, ...) ## S3 method for class 'pow' classification(id, callopts = list(), return_id = TRUE, ...) ## S3 method for class 'ids' classification(id, ...) ## S3 method for class 'classification' cbind(...) ## S3 method for class 'classification' rbind(...) ## S3 method for class 'classification_ids' cbind(...) ## S3 method for class 'classification_ids' rbind(...)
... |
For |
sci_id |
Vector of taxa names (character) or IDs (character or numeric)
to query. For |
db |
character; database to query. either |
callopts |
Curl options passed on to crul::verb-GET |
return_id |
(logical) If |
rows |
(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 instead of a name of class character. |
x |
Deprecated, see |
id |
character; identifiers, returned by |
batch_size |
(numeric) For NCBI queries, specify the number of IDs to lookup for each query. |
max_tries |
(numeric) For NCBI queries, the number of times a particular query will be attempted, assuming the first does not work. |
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
queries 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.
A named list of data.frames with the taxonomic classification of every supplied taxa.
It may happen sometimes that you get more results back from your query than will show in the data.frame on screen. Our advice is to refine your query in those cases. On a data source basis we can attempt to help make it easier to refine queries, whether it be with the data provider (unlikely to happen), or in the code in this package (more likely) - let us know if you run into too many results problem and we'll see what we can do.
EOL does not have very good failure behavior. For example, if you submit an ID that does not exist they'll return a 500 HTTP error, which is not an appropriate error; it's probably that that ID does not exist in their database, but we can't know for sure. Isn't that fun?
In case you run into NCBI errors due to your rate limit being exceeded, see
taxize_options(), where you can set ncbi_sleep.
We hard code http_version = 2L to use HTTP/1.1 in HTTP requests to
the Entrez API. See curl::curl_symbols('CURL_HTTP_VERSION')
## Not run:
# Plug in taxon IDs
classification(9606, db = 'ncbi')
classification(c(9606, 55062), db = 'ncbi')
classification(129313, db = 'itis')
classification(6985636, db = 'eol')
classification(126436, db = 'worms')
classification('Helianthus annuus', db = 'pow')
classification('Helianthus', db = 'pow')
classification('Asteraceae', db = 'pow')
classification("134717", db = 'natserv')
classification(c(2704179, 6162875, 8286319, 2441175, 731), db = 'gbif')
classification(25509881, db = 'tropicos')
classification("NBNSYS0000004786", db = 'nbn')
classification(as.nbnid("NBNSYS0000004786"), db = 'nbn')
classification(3930798, db = 'tol')
## works the same if IDs are in class character
classification(c("2704179", "2441176"), db = 'gbif')
classification("Agapostemon", db = "bold")
# wikispecies
classification("Malus domestica", db = "wiki")
classification("Pinus contorta", db = "wiki")
classification("Pinus contorta", db = "wiki", wiki_site = "commons")
classification("Pinus contorta", db = "wiki", wiki_site = "pedia")
classification("Pinus contorta", db = "wiki", wiki_site = "pedia",
wiki = "fr")
classification(get_wiki("Malus domestica", "commons"))
classification(get_wiki("Malus domestica", "species"))
classification(c("Pinus contorta", "Malus domestica"), db = "wiki")
# Plug in taxon names
## in this case, we use get_*() fxns internally to first get taxon IDs
classification("Oncorhynchus mykiss", db = "eol")
classification(c("Chironomus riparius", "aaa vva"), db = 'ncbi')
classification(c("Chironomus riparius", "aaa vva"), db = 'ncbi',
messages=FALSE)
classification(c("Chironomus riparius", "aaa vva"), db = 'itis')
classification(c("Chironomus riparius", "aaa vva"), db = 'itis',
messages=FALSE)
classification(c("Chironomus riparius", "aaa vva"), db = 'eol')
classification("Alopias vulpinus", db = 'nbn')
classification('Gadus morhua', db = 'worms')
classification('Aquila chrysaetos', db = 'natserv')
classification('Gadus morhua', db = 'natserv')
classification('Pomatomus saltatrix', db = 'natserv')
classification('Aquila chrysaetos', db = 'natserv')
classification(c("Chironomus riparius", "asdfasdfsfdfsd"), db = 'gbif')
classification("Chironomus", db = 'tol')
classification("Poa annua", db = 'tropicos')
# Use methods for get_uid, get_tsn, get_eolid, 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"),
messages = FALSE))
classification(get_eolid(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("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(c("Puma concolor","Accipiter striatus"),
db = c('ncbi','itis')))
(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) )
(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)
# Queries of many IDs are processed in batches for NCBI
ids <- c("13083", "2650392", "1547764", "230054", "353934", "656984",
"271789", "126272", "184644", "73213", "662816", "1161803", "1239353",
"59420", "665675", "866969", "1091219", "1431218", "1471898",
"864321", "251768", "2486276", "2068772", "1825808", "2006532",
"128287", "1195738", "1084683", "1886461", "508296", "377247",
"1489665", "329325", "219243", "1176946", "339893", "197933",
"174510", "1704048", "212897", "154842", "1239280", "260135",
"405735", "1566412", "2083462", "651348", "983204", "165380",
"2338856", "2068760", "167262", "34229", "1213340", "478939",
"1933585", "49951", "1277794", "1671089", "1502538", "362355",
"746473", "242879", "158219", "313664", "2093188", "1541232",
"584742", "1331091", "147639", "284492", "75642", "1412882",
"391782", "1406855", "434506", "2053357", "217315", "1444328",
"329249", "2294004", "84942", "324458", "538247", "69452", "49170",
"1993845", "261646", "127633", "228146", "1420004", "1629772",
"577055", "697062", "231660", "648380", "554953", "746496", "2602969")
result <- classification(ids, db = 'ncbi')
## End(Not run)
## Not run:
# Fails without db param set
# classification(315576)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.