Title: | Taxonomic Information from Around the Web |
---|---|
Description: | Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. |
Authors: | Scott Chamberlain [aut] , Eduard Szoecs [aut], Zachary Foster [aut, cre], Zebulun Arendsee [aut], Carl Boettiger [ctb], Karthik Ram [ctb], Ignasi Bartomeus [ctb], John Baumgartner [ctb], James O'Donnell [ctb], Jari Oksanen [ctb], Bastian Greshake Tzovaras [ctb], Philippe Marchand [ctb], Vinh Tran [ctb], Maëlle Salmon [ctb], Gaopeng Li [ctb], Matthias Grenié [ctb], rOpenSci [fnd] (https://ropensci.org/) |
Maintainer: | Zachary Foster <[email protected]> |
License: | MIT + file LICENSE |
Version: | 0.9.102 |
Built: | 2024-09-12 20:02:03 UTC |
Source: | https://github.com/ropensci/taxize |
This package interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.
Allows users to search over many websites for species names (scientific and common) and download up- and downstream taxonomic hierarchical information - and many other things.
The functions in the package that hit a specific API have a prefix and suffix
separated by an underscore. They follow the format of service_whatitdoes
.
For example, gnr_resolve
uses the Global Names Resolver API to resolve
species names.
General functions in the package that don't hit a specific API don't have
two words separated by an underscore, e.g., classification
You need API keys for some data sources. See taxize-authentication for more information.
API | prefix | SOAP? |
Encyclopedia of Life (EOL) | eol | FALSE |
Integrated Taxonomic Information Service (ITIS) | itis | FALSE |
Global Names Resolver (from EOL/GBIF) | gnr | FALSE |
Global Names Index (from EOL/GBIF) | gni | FALSE |
IUCN Red List | iucn | FALSE |
Tropicos (from Missouri Botanical Garden) | tp | FALSE |
Theplantlist.org | tpl | FALSE |
National Center for Biotechnology Information | ncbi | FALSE |
CANADENSYS Vascan name search API | vascan | FALSE |
International Plant Names Index (IPNI) | ipni | FALSE |
World Register of Marine Species (WoRMS) | worms | TRUE |
Barcode of Life Data Systems (BOLD) | bold | FALSE |
Pan-European Species directories Infrastructure (PESI) | pesi | TRUE |
Mycobank | myco | TRUE |
National Biodiversity Network (UK) | nbn | FALSE |
Index Fungorum | fg | FALSE |
EU BON | eubon | FALSE |
Index of Names (ION) | ion | FALSE |
Open Tree of Life (TOL) | tol | FALSE |
World Register of Marine Species (WoRMS) | worms | FALSE |
NatureServe | natserv | FALSE |
If the source above has a TRUE
in the SOAP?
column, it is not available
in this package. They are available from a different package called taxizesoap.
See the GitHub repo for how to install https://github.com/ropensci/taxizesoap
COL introduced rate limiting recently in 2019 - which has made the API essentially unusable - CoL+ is coming soon and we'll incorporate it here when it's stable. See https://github.com/ropensci/colpluz for the R implementation for CoL+
Scott Chamberlain
Eduard Szoecs [email protected]
Zachary Foster [email protected]
Carl Boettiger [email protected]
Karthik Ram [email protected]
Ignasi Bartomeus [email protected]
John Baumgartner [email protected]
James O'Donnell [email protected]
Useful links:
Report bugs at https://github.com/ropensci/taxize/issues
Generic names and their replacements from the Angiosperm Phylogeny Group III system of flowering plant classification.
apgOrders(...) apgFamilies(...)
apgOrders(...) apgFamilies(...)
... |
Curl args passed on to crul::verb-GET |
http://www.mobot.org/MOBOT/research/APweb/
## Not run: head(apgOrders()) head(apgFamilies()) ## End(Not run)
## Not run: head(apgOrders()) head(apgFamilies()) ## End(Not run)
Family names and their replacements from the Angiosperm Phylogeny Website system of flowering plant classification.
A data frame with 1705 rows and 6 variables:
family
: family name
synonym
: if accepted=FALSE
, this is the accepted name;
if accepted=TRUE
, this is NA
, and the name in family
is accepted
order
: order name for the family
accepted
: logical, if name in family
column is accepted or not
original
: original data record from APG website, mapping
name in family
column to a new name, if there is one
accepted_name
: accepted name. accepted names, combining those that
are accepted from family
column, with the new name from synonym
if applicable
This dataset is from Version 14, incorporated on 2020-06-03,
generated using apgFamilies()
(update script in inst/ignore/apg_script.R)
http://www.mobot.org/MOBOT/research/APweb/
Lookup in the APGIII taxonomy and replace family names
apg_lookup(taxa, rank = "family")
apg_lookup(taxa, rank = "family")
taxa |
(character) Taxonomic name to lookup a synonym for in APGIII taxonomy. |
rank |
(character) Taxonomic rank to lookup a synonym for. One of family or order. |
Internally in this function, we use the datasets apg_families
and apg_orders - see their descriptions for the data in them.
The functions apgOrders()
apgFamilies()
are for scraping
current content from the http://www.mobot.org/MOBOT/research/APweb/
website
The datasets used in this function are from the most recent version of APGIII, Version 14 (http://www.mobot.org/MOBOT/research/APweb/)
A APGIII family or order name, the original name if the name is the same as APG has, or NA if no match found
# New name found apg_lookup(taxa = "Hyacinthaceae", rank = "family") # Name is the same apg_lookup(taxa = "Poaceae", rank = "family") apg_lookup(taxa = "Asteraceae", rank = "family") # Name not found apg_lookup(taxa = "Foobar", rank = "family") # New name found apg_lookup(taxa = "Acerales", rank = "order") # Name is the same apg_lookup(taxa = "Acorales", rank = "order") # Name not found apg_lookup(taxa = "Foobar", rank = "order")
# New name found apg_lookup(taxa = "Hyacinthaceae", rank = "family") # Name is the same apg_lookup(taxa = "Poaceae", rank = "family") apg_lookup(taxa = "Asteraceae", rank = "family") # Name not found apg_lookup(taxa = "Foobar", rank = "family") # New name found apg_lookup(taxa = "Acerales", rank = "order") # Name is the same apg_lookup(taxa = "Acorales", rank = "order") # Name not found apg_lookup(taxa = "Foobar", rank = "order")
Order names and their replacements from the Angiosperm Phylogeny Website system of flowering plant classification.
A data frame with 576 rows and 5 variables:
order
: order name
synonym
: if accepted=FALSE
, this is the accepted name;
if accepted=TRUE
, this is NA
, and the name in order
is accepted
accepted
: logical, if name in order
column is accepted or not
original
: original data record from APG website, mapping
name in order
column to a new name, if there is one
accepted_name
: accepted name. accepted names, combining those that
are accepted from order
column, with the new name from synonym
if applicable
This dataset is from Version 14, incorporated on 2020-06-03,
generated using apgOrders()
(update script in inst/ignore/apg_script.R)
http://www.mobot.org/MOBOT/research/APweb/
Retrieve all taxa names downstream in hierarchy for BOLD
bold_downstream(id, downto, intermediate = FALSE, ...)
bold_downstream(id, downto, intermediate = FALSE, ...)
id |
(integer) One or more BOLD taxonomic identifiers |
downto |
(character) The taxonomic level you want to go down to.
See examples below. The taxonomic level IS case sensitive, and you do have
to spell it correctly. See |
intermediate |
(logical) If |
... |
crul options passed on to crul::verb-GET |
BEWARE: This function 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
data.frame of taxonomic information downstream to family from e.g.,
Order, Class, etc., or if intermediated=TRUE
, list of length two,
with target taxon rank names, and intermediate names.
## Not run: ## the genus Gadus bold_downstream(id = 3451, downto="species") bold_downstream(id = 443, downto="genus") bold_downstream(id = 443, downto="genus", intermediate=TRUE) ## End(Not run)
## Not run: ## the genus Gadus bold_downstream(id = 3451, downto="species") bold_downstream(id = 443, downto="genus") bold_downstream(id = 443, downto="genus", intermediate=TRUE) ## End(Not run)
Search Barcode of Life for taxonomic IDs
bold_search( sci = NULL, id = NULL, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, response = FALSE, name = NULL, ... )
bold_search( sci = NULL, id = NULL, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, response = FALSE, name = NULL, ... )
sci |
(character) One or more scientific names. |
id |
(integer) One or more BOLD taxonomic identifiers. |
fuzzy |
(logical) Whether to use fuzzy search or not (default: |
dataTypes |
(character) Specifies the datatypes that will be returned.
See Details for options. This variable is ignored if |
includeTree |
(logical) If TRUE (default: FALSE), returns a list containing
information for parent taxa as well as the specified taxon. Only used if |
response |
(logical) Note that response is the object that returns from the curl call, useful for debugging, and getting detailed info on the API call. |
name |
Deprecated, see |
... |
named curl options passed on to crul::verb-GET |
You must provide one of sci
or id
to this function. The other
parameters are optional. Note that when passing in sci
, fuzzy
can be used
as well, while if id
is passed, then fuzzy
is ignored, and dataTypes
includeTree
can be used.
Options for dataTypes
parameter:
all returns all data
basic returns basic taxon information
images returns specimen image. Includes copyright information, image URL, image metadata.
stats Returns specimen and sequence statistics. Includes public species count, public BIN count, public marker counts, public record count, specimen count, sequenced specimen count, barcode specimen count, species count, barcode species count.
geo Returns collection site information. Includes country, collection site map.
sequencinglabs Returns sequencing labs. Includes lab name, record count.
depository Returns specimen depositories. Includes depository name, record count.
thirdparty Returns information from third parties. Includes wikipedia summary, wikipedia URL, GBIF map.
A list of data.frame's.
http://www.boldsystems.org/index.php/resources/api
## Not run: # A basic example bold_search(sci="Apis") bold_search(sci="Agapostemon") bold_search(sci="Poa") # Fuzzy search head(bold_search(sci="Po", fuzzy=TRUE)) head(bold_search(sci="Aga", fuzzy=TRUE)) # Many names bold_search(sci=c("Apis","Puma concolor")) nms <- names_list('species') bold_search(sci=nms) # Searching by ID - dataTypes can be used, and includeTree can be used bold_search(id=88899) bold_search(id=88899, dataTypes="stats") bold_search(id=88899, dataTypes="geo") bold_search(id=88899, dataTypes="basic") bold_search(id=88899, includeTree=TRUE) ## End(Not run)
## Not run: # A basic example bold_search(sci="Apis") bold_search(sci="Agapostemon") bold_search(sci="Poa") # Fuzzy search head(bold_search(sci="Po", fuzzy=TRUE)) head(bold_search(sci="Aga", fuzzy=TRUE)) # Many names bold_search(sci=c("Apis","Puma concolor")) nms <- names_list('species') bold_search(sci=nms) # Searching by ID - dataTypes can be used, and includeTree can be used bold_search(id=88899) bold_search(id=88899, dataTypes="stats") bold_search(id=88899, dataTypes="geo") bold_search(id=88899, dataTypes="basic") bold_search(id=88899, includeTree=TRUE) ## End(Not run)
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(...) ## Default S3 method: children(sci_id, db = NULL, rows = NA, x = NULL, ...) ## S3 method for class 'tsn' children(sci_id, db = NULL, ...) ## S3 method for class 'wormsid' children(sci_id, db = NULL, ...) ## S3 method for class 'ids' children(sci_id, db = NULL, ...) ## S3 method for class 'uid' children(sci_id, db = NULL, ...) ## S3 method for class 'boldid' children(sci_id, db = NULL, ...)
children(...) ## Default S3 method: children(sci_id, db = NULL, rows = NA, x = NULL, ...) ## S3 method for class 'tsn' children(sci_id, db = NULL, ...) ## S3 method for class 'wormsid' children(sci_id, db = NULL, ...) ## S3 method for class 'ids' children(sci_id, db = NULL, ...) ## S3 method for class 'uid' children(sci_id, db = NULL, ...) ## S3 method for class 'boldid' children(sci_id, db = NULL, ...)
... |
Further args passed on to |
sci_id |
Vector of taxa names (character) or IDs (character or numeric) to query. |
db |
character; database to query. One or more of |
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 of any of the acceptable classes: tsn. NCBI has a method for this function but rows doesn't work. |
x |
Deprecated, see |
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
## Not run: # 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) ## End(Not run)
## Not run: # 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) ## End(Not run)
This function converts a list of hierarchies for individual species into a single species by taxonomic level matrix, then calculates a distance matrix based on taxonomy alone, and outputs either a phylo or dist object. See details for more information.
class2tree(input, varstep = TRUE, check = TRUE, remove_shared = FALSE, ...) ## S3 method for class 'classtree' plot(x, ...) ## S3 method for class 'classtree' print(x, ...)
class2tree(input, varstep = TRUE, check = TRUE, remove_shared = FALSE, ...) ## S3 method for class 'classtree' plot(x, ...) ## S3 method for class 'classtree' print(x, ...)
input |
List of classification data.frame's from the function
|
varstep |
Vary step lengths between successive levels relative to proportional loss of the number of distinct classes. |
check |
If TRUE, remove all redundant levels which are different for all rows or constant for all rows and regard each row as a different basal taxon (species). If FALSE all levels are retained and basal taxa (species) also must be coded as variables (columns). You will get a warning if species are not coded, but you can ignore this if that was your intention. |
remove_shared |
If |
... |
Further arguments passed on to hclust. |
x |
Input object to print or plot - output from class2tree function. |
See vegan::taxa2dist()
. Thanks to Jari Oksanen for
making the taxa2dist function and pointing it out, and Clarke & Warwick
(1998, 2001), which taxa2dist was based on.
The taxonomy tree created is not only based on the clustering of the
taxonomy ranks (e.g. strain, species, genus, ...), but it also utilizes the
actual taxon clades (e.g. mammals, plants or reptiles, etc.). The process of
this function is as following: First, all possible taxonomy ranks and their
corresponding IDs for each given taxon will be collected from the input.
Then, the rank vectors of all taxa will be aligned, so that they together
will become a matrix where columns are ordered taxonomy ranks of all taxa and
rows are the rank vectors of those taxa. After that, the rank matrix will be
converted into taxonomy ID matrix, any missing rank will have a pseudo
ID from the previous rank. Finally, this taxonomy ID matrix will be used to
cluster taxa that have similar taxonomy hierarchy together.
An object of class "classtree" with slots:
phylo - The resulting object, a phylo object
classification - The classification data.frame, with taxa as rows, and different classification levels as columns
distmat - Distance matrix
names - The names of the tips of the phylogeny
Note that when you execute the resulting object, you only get the phylo object. You can get to the other 3 slots by calling them directly, like output$names, etc.
## Not run: spnames <- c('Quercus robur', 'Iris oratoria', 'Arachis paraguariensis', 'Helianthus annuus','Madia elegans','Lupinus albicaulis', 'Pinus lambertiana') out <- classification(spnames, db='itis') tr <- class2tree(out) plot(tr) spnames <- c('Klattia flava', 'Trollius sibiricus', 'Arachis paraguariensis', 'Tanacetum boreale', 'Gentiana yakushimensis','Sesamum schinzianum', 'Pilea verrucosa','Tibouchina striphnocalyx','Lycium dasystemum', 'Berkheya echinacea','Androcymbium villosum', 'Helianthus annuus','Madia elegans','Lupinus albicaulis', 'Pinus lambertiana') out <- classification(spnames, db='ncbi') tr <- class2tree(out) plot(tr) ## End(Not run)
## Not run: spnames <- c('Quercus robur', 'Iris oratoria', 'Arachis paraguariensis', 'Helianthus annuus','Madia elegans','Lupinus albicaulis', 'Pinus lambertiana') out <- classification(spnames, db='itis') tr <- class2tree(out) plot(tr) spnames <- c('Klattia flava', 'Trollius sibiricus', 'Arachis paraguariensis', 'Tanacetum boreale', 'Gentiana yakushimensis','Sesamum schinzianum', 'Pilea verrucosa','Tibouchina striphnocalyx','Lycium dasystemum', 'Berkheya echinacea','Androcymbium villosum', 'Helianthus annuus','Madia elegans','Lupinus albicaulis', 'Pinus lambertiana') out <- classification(spnames, db='ncbi') tr <- class2tree(out) plot(tr) ## End(Not run)
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(...)
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')
get_tsn()
, get_uid()
, get_eolid()
,
get_tpsid()
, get_gbifid()
, get_wormsid()
, get_natservid()
,
get_boldid()
, get_wiki()
, get_pow()
## 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)
## 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)
Get scientific names from common names.
comm2sci(...) ## Default S3 method: comm2sci( com, db = "ncbi", itisby = "search", simplify = TRUE, commnames = NULL, ... ) ## S3 method for class 'tsn' comm2sci(id, db = "ncbi", itisby = "search", simplify = TRUE, ...) ## S3 method for class 'uid' comm2sci(id, db = "ncbi", itisby = "search", simplify = TRUE, ...)
comm2sci(...) ## Default S3 method: comm2sci( com, db = "ncbi", itisby = "search", simplify = TRUE, commnames = NULL, ... ) ## S3 method for class 'tsn' comm2sci(id, db = "ncbi", itisby = "search", simplify = TRUE, ...) ## S3 method for class 'uid' comm2sci(id, db = "ncbi", itisby = "search", simplify = TRUE, ...)
... |
Further arguments passed on to internal methods. |
com |
One or more common names or partial names. |
db |
Data source, one of "ncbi" (default), "itis", "tropicos", "eol", or "worms". If using ncbi, we recommend getting an API key; see taxize-authentication |
itisby |
Search for common names across entire names (search, default), at beginning of names (begin), or at end of names (end). |
simplify |
(logical) If |
commnames |
Deprecated, see |
id |
For data sources ITIS and NCBI you can pass in common names
directly, and use get_uid()
or get_tsn()
to get ids first, then pass in
to this fxn.
For the other data sources, you can only pass in common names directly.
If simplify=TRUE
, a list of scientific names, with list
labeled by your input names. If simplify=FALSE
, a data.frame with
columns that vary by data source. character(0)
on no match
See taxize-authentication for help on authentication
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')
In case you run into errors due to your rate limit being exceeded, see
taxize_options()
, where you can set ncbi_sleep
.
Scott Chamberlain
## Not run: comm2sci(com='american black bear') comm2sci(com='american black bear', simplify = FALSE) comm2sci(com='black bear', db='itis') comm2sci(com='american black bear', db='itis') comm2sci(com='annual blue grass', db='tropicos') comm2sci(com=c('annual blue grass','tree of heaven'), db='tropicos') comm2sci('blue whale', db = "worms") comm2sci(c('blue whale', 'dwarf surfclam'), db = "worms") # ncbi: pass in uid's from get_uid() directly x <- get_uid("western capercaillie", modifier = "Common Name") comm2sci(x) # itis: pass in tsn's from get_tsn() directly x <- get_tsn(c("Louisiana black bear", "american crow"), searchtype = "common") comm2sci(x) ## End(Not run)
## Not run: comm2sci(com='american black bear') comm2sci(com='american black bear', simplify = FALSE) comm2sci(com='black bear', db='itis') comm2sci(com='american black bear', db='itis') comm2sci(com='annual blue grass', db='tropicos') comm2sci(com=c('annual blue grass','tree of heaven'), db='tropicos') comm2sci('blue whale', db = "worms") comm2sci(c('blue whale', 'dwarf surfclam'), db = "worms") # ncbi: pass in uid's from get_uid() directly x <- get_uid("western capercaillie", modifier = "Common Name") comm2sci(x) # itis: pass in tsn's from get_tsn() directly x <- get_tsn(c("Louisiana black bear", "american crow"), searchtype = "common") comm2sci(x) ## End(Not run)
This function uses a while loop to continually collect children taxa down
to the taxonomic rank that you specify in the downto
parameter. You
can get data from ITIS (itis), GBIF (gbif), NCBI (ncbi), WORMS (worms),
or BOLD (bold). There is no method exposed by these four
services for getting taxa at a specific taxonomic rank, so we do it
ourselves here.
downstream(...) ## Default S3 method: downstream( sci_id, db = NULL, downto = NULL, intermediate = FALSE, rows = NA, x = NULL, ... ) ## S3 method for class 'tsn' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...) ## S3 method for class 'gbifid' downstream( sci_id, db = NULL, downto = NULL, intermediate = FALSE, limit = 100, start = NULL, ... ) ## S3 method for class 'uid' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...) ## S3 method for class 'wormsid' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...) ## S3 method for class 'boldid' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...) ## S3 method for class 'ids' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...)
downstream(...) ## Default S3 method: downstream( sci_id, db = NULL, downto = NULL, intermediate = FALSE, rows = NA, x = NULL, ... ) ## S3 method for class 'tsn' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...) ## S3 method for class 'gbifid' downstream( sci_id, db = NULL, downto = NULL, intermediate = FALSE, limit = 100, start = NULL, ... ) ## S3 method for class 'uid' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...) ## S3 method for class 'wormsid' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...) ## S3 method for class 'boldid' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...) ## S3 method for class 'ids' downstream(sci_id, db = NULL, downto = NULL, intermediate = FALSE, ...)
... |
Further args passed on to |
sci_id |
Vector of taxa names (character) or IDs (character or numeric) to query. |
db |
character; database to query. One or more of |
downto |
What taxonomic rank to go down to. One of: 'superkingdom', 'kingdom', 'subkingdom','infrakingdom','phylum','division','subphylum', 'subdivision','infradivision', 'superclass','class','subclass','infraclass', 'superorder','order','suborder','infraorder','superfamily','family', 'subfamily','tribe','subtribe','genus','subgenus','section','subsection', 'species group','species','subspecies','variety','form','subvariety','race', 'stirp', 'morph','aberration','subform', 'unspecified', 'no rank' |
intermediate |
(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 of any of the acceptable classes: tsn. |
x |
Deprecated, see |
limit |
Number of records to return. Applies to gbif only.
default: 100. max: 1000. use in combination with the |
start |
Record number to start at. Applies to gbif only. default: 0.
use in combination with the |
A named list of data.frames with the downstream names of every supplied taxa. You get an NA if there was no match in the database.
See taxize-authentication for help on authentication
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
## Not run: # Plug in taxon IDs downstream(125732, db = 'worms', downto = 'species') downstream(3451, db = 'bold', downto = 'species') if (interactive()) { # Plug in taxon names downstream("Apis", db = 'ncbi', downto = 'species') downstream("Apis", db = 'itis', downto = 'species') downstream("Apis", db = 'bold', downto = 'species') downstream("Gadus", db = 'worms', downto = 'species') downstream(c("Apis","Epeoloides"), db = 'itis', downto = 'species') downstream("Ursus", db = 'gbif', downto = 'species') downstream(get_gbifid("Ursus"), db = 'gbif', downto = 'species') # Many taxa sp <- names_list("genus", 3) downstream(sp, db = 'itis', downto = 'species') downstream(sp, db = 'gbif', downto = 'species') # Both data sources ids <- get_ids("Apis", db = c('gbif','itis')) downstream(ids, downto = 'species') ## same result downstream(get_ids("Apis", db = c('gbif','itis')), downto = 'species') # Collect intermediate names ## itis downstream('Bangiophyceae', db="itis", downto="genus") downstream('Bangiophyceae', db="itis", downto="genus", intermediate=TRUE) downstream(get_tsn('Bangiophyceae'), downto="genus") downstream(get_tsn('Bangiophyceae'), downto="genus", intermediate=TRUE) # Use the rows parameter ## note how in the second function call you don't get the prompt downstream("Poa", db = 'gbif', downto="species") downstream("Poa", db = 'gbif', downto="species", rows=1) # use curl options res <- downstream("Apis", db = 'gbif', downto = 'species', verbose = TRUE) # Pagination # GBIF limits queries to a maximum of 1000 records per request, so if # there's more than 1000, use the start parameter # Piper, taxonKey = 3075433 z1 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000) z2 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000, start=1000) z3 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000, start=2000) z4 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000, start=3000) NROW(rbind(z1[[1]], z2[[1]], z3[[1]], z4[[1]])) } ## End(Not run)
## Not run: # Plug in taxon IDs downstream(125732, db = 'worms', downto = 'species') downstream(3451, db = 'bold', downto = 'species') if (interactive()) { # Plug in taxon names downstream("Apis", db = 'ncbi', downto = 'species') downstream("Apis", db = 'itis', downto = 'species') downstream("Apis", db = 'bold', downto = 'species') downstream("Gadus", db = 'worms', downto = 'species') downstream(c("Apis","Epeoloides"), db = 'itis', downto = 'species') downstream("Ursus", db = 'gbif', downto = 'species') downstream(get_gbifid("Ursus"), db = 'gbif', downto = 'species') # Many taxa sp <- names_list("genus", 3) downstream(sp, db = 'itis', downto = 'species') downstream(sp, db = 'gbif', downto = 'species') # Both data sources ids <- get_ids("Apis", db = c('gbif','itis')) downstream(ids, downto = 'species') ## same result downstream(get_ids("Apis", db = c('gbif','itis')), downto = 'species') # Collect intermediate names ## itis downstream('Bangiophyceae', db="itis", downto="genus") downstream('Bangiophyceae', db="itis", downto="genus", intermediate=TRUE) downstream(get_tsn('Bangiophyceae'), downto="genus") downstream(get_tsn('Bangiophyceae'), downto="genus", intermediate=TRUE) # Use the rows parameter ## note how in the second function call you don't get the prompt downstream("Poa", db = 'gbif', downto="species") downstream("Poa", db = 'gbif', downto="species", rows=1) # use curl options res <- downstream("Apis", db = 'gbif', downto = 'species', verbose = TRUE) # Pagination # GBIF limits queries to a maximum of 1000 records per request, so if # there's more than 1000, use the start parameter # Piper, taxonKey = 3075433 z1 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000) z2 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000, start=1000) z3 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000, start=2000) z4 <- downstream(3075433, db = 'gbif', downto = "species", limit=1000, start=3000) NROW(rbind(z1[[1]], z2[[1]], z3[[1]], z4[[1]])) } ## End(Not run)
Given the identifier for a data object, return all metadata about the object
eol_dataobjects(id, taxonomy = TRUE, language = NULL, ...)
eol_dataobjects(id, taxonomy = TRUE, language = NULL, ...)
id |
(character) The EOL data object identifier |
taxonomy |
(logical) Whether to return any taxonomy details from
different taxon hierarchy providers, in an array named |
language |
(character) provides the results in the specified language. one of ms, de, en, es, fr, gl, it, nl, nb, oc, pt-BR, sv, tl, mk, sr, uk, ar, zh-Hans, zh-Hant, ko |
... |
Curl options passed on to crul::HttpClient |
It's possible to return JSON or XML with the EOL API. However, this function only returns JSON for now.
A list, optionally with a data.frame if taxonomy=TRUE
## Not run: eol_dataobjects(id = 7561533) # curl options eol_dataobjects(id = 7561533, verbose = TRUE) ## End(Not run)
## Not run: eol_dataobjects(id = 7561533) # curl options eol_dataobjects(id = 7561533, verbose = TRUE) ## End(Not run)
Search for pages in EOL database using a taxonconceptID.
eol_pages( taxonconceptID, images_per_page = NULL, images_page = NULL, videos_per_page = NULL, videos_page = NULL, sounds_per_page = NULL, sounds_page = NULL, maps_per_page = NULL, maps_page = NULL, texts_per_page = NULL, texts_page = NULL, subjects = "overview", licenses = "all", details = FALSE, common_names = FALSE, synonyms = FALSE, references = FALSE, taxonomy = TRUE, vetted = 0, cache_ttl = NULL, ... )
eol_pages( taxonconceptID, images_per_page = NULL, images_page = NULL, videos_per_page = NULL, videos_page = NULL, sounds_per_page = NULL, sounds_page = NULL, maps_per_page = NULL, maps_page = NULL, texts_per_page = NULL, texts_page = NULL, subjects = "overview", licenses = "all", details = FALSE, common_names = FALSE, synonyms = FALSE, references = FALSE, taxonomy = TRUE, vetted = 0, cache_ttl = NULL, ... )
taxonconceptID |
(numeric) a taxonconceptID, which is also the page number |
images_per_page |
(integer) number of returned image objects (0-75) |
images_page |
(integer) images page |
videos_per_page |
(integer) number of returned video objects (0-75) |
videos_page |
(integer) videos page |
sounds_per_page |
(integer) number of returned sound objects (0-75) |
sounds_page |
(integer) sounds page |
maps_per_page |
(integer) number of returned map objects (0-75) |
maps_page |
(integer) maps page |
texts_per_page |
(integer) number of returned text objects (0-75) |
texts_page |
(integer) texts page |
subjects |
'overview' (default) to return the overview text (if exists), a pipe | delimited list of subject names from the list of EOL accepted subjects (e.g. TaxonBiology, FossilHistory), or 'all' to get text in any subject. Always returns an overview text as a first result (if one exists in the given context). |
licenses |
A pipe | delimited list of licenses or 'all' (default) to get objects under any license. Licenses abbreviated cc- are all Creative Commons licenses. Visit their site for more information on the various licenses they offer. |
details |
Include all metadata for data objects. (Default: |
common_names |
Return all common names for the page's taxon
(Default: |
synonyms |
Return all synonyms for the page's taxon
(Default: |
references |
Return all references for the page's taxon
(Default: |
taxonomy |
(logical) Whether to return any taxonomy details from
different taxon hierarchy providers, in an array named |
vetted |
If 'vetted' is given a value of '1', then only trusted
content will be returned. If 'vetted' is '2', then only trusted and
unreviewed content will be returned (untrusted content will not be returned).
The default is to return all content. (Default: |
cache_ttl |
The number of seconds you wish to have the response cached. |
... |
Curl options passed on to crul::HttpClient |
It's possible to return JSON or XML with the EOL API. However, this function only returns JSON for now.
JSON list object, or data.frame.
## Not run: (pageid <- eol_search('Pomatomus')$pageid[1]) x <- eol_pages(taxonconceptID = pageid) x x$scinames z <- eol_pages(taxonconceptID = pageid, synonyms = TRUE) z$synonyms z <- eol_pages(taxonconceptID = pageid, common_names = TRUE) z$vernacular ## End(Not run)
## Not run: (pageid <- eol_search('Pomatomus')$pageid[1]) x <- eol_pages(taxonconceptID = pageid) x x$scinames z <- eol_pages(taxonconceptID = pageid, synonyms = TRUE) z$synonyms z <- eol_pages(taxonconceptID = pageid, common_names = TRUE) z$vernacular ## End(Not run)
Search for terms in EOL database.
eol_search( sci, page = 1, exact = NULL, filter_tid = NULL, filter_heid = NULL, filter_by_string = NULL, cache_ttl = NULL, terms = NULL, ... )
eol_search( sci, page = 1, exact = NULL, filter_tid = NULL, filter_heid = NULL, filter_by_string = NULL, cache_ttl = NULL, terms = NULL, ... )
sci |
(character) scientific name |
page |
A maximum of 30 results are returned per page. This parameter allows you to fetch more pages of results if there are more than 30 matches (Default 1) |
exact |
Will find taxon pages if the preferred name or any synonym or common name exactly matches the search term. |
filter_tid |
Given an EOL page ID, search results will be limited to members of that taxonomic group |
filter_heid |
Given a Hierarchy Entry ID, search results will be limited to members of that taxonomic group |
filter_by_string |
Given a search term, an exact search will be made and that matching page will be used as the taxonomic group against which to filter search results |
cache_ttl |
The number of seconds you wish to have the response cached. |
terms |
Deprecated, see |
... |
Curl options passed on to crul::HttpClient |
It's possible to return JSON or XML with the EOL API. However, this function only returns JSON for now.
A data frame with four columns:
pageid: pageid, this is the same as the eolid you can get from
get_eolid()
name: taxonomic name, may or may not contain the taxonomic authority
link: URL for the taxon in question
content: a string of semi-colon separated names. it's not clear to us what these represent exactly, but figured why not give it to users in case some may find it useful
## Not run: eol_search(sci='Homo') eol_search(sci='Salix', verbose = TRUE) eol_search(sci='Ursus americanus') eol_search('Pinus contorta') ## End(Not run)
## Not run: eol_search(sci='Homo') eol_search(sci='Salix', verbose = TRUE) eol_search(sci='Ursus americanus') eol_search('Pinus contorta') ## End(Not run)
EUBON capabilities
eubon_capabilities(...)
eubon_capabilities(...)
... |
Curl options passed on to crul::verb-GET |
https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html
Other eubon-methods:
eubon_children()
,
eubon_hierarchy()
,
eubon_search()
## Not run: eubon_capabilities() ## End(Not run)
## Not run: eubon_capabilities() ## End(Not run)
EUBON children
eubon_children(id, providers = NULL, timeout = 0, ...)
eubon_children(id, providers = NULL, timeout = 0, ...)
id |
(character) identifier for the taxon. (LSID, DOI, URI, or any other identifier used by the checklist provider) |
providers |
(character) A list of provider id strings concatenated by comma characters. The default : "pesi,bgbm-cdm-server[col] will be used if this parameter is not set. A list of all available provider ids can be obtained from the '/capabilities' service end point. Providers can be nested, that is a parent provider can have sub providers. If the id of the parent provider is supplied all subproviders will be queried. The query can also be restricted to one or more subproviders by using the following syntax: parent-id[sub-id-1,sub-id2,...] |
timeout |
(numeric) The maximum of milliseconds to wait for responses from any of the providers. If the timeout is exceeded the service will just return the responses that have been received so far. The default timeout is 0 ms (wait for ever) |
... |
Curl options passed on to crul::verb-GET |
a data.frame or an empty list if no results found
There is no pagination in this method, so you may or may not be getting all the results for a search. Sorry, out of our control
https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html
Other eubon-methods:
eubon_capabilities()
,
eubon_hierarchy()
,
eubon_search()
## Not run: x <- eubon_children(id = "urn:lsid:marinespecies.org:taxname:126141", providers = 'worms') head(x) ## End(Not run)
## Not run: x <- eubon_children(id = "urn:lsid:marinespecies.org:taxname:126141", providers = 'worms') head(x) ## End(Not run)
EUBON hierarchy
eubon_hierarchy(id, providers = "pesi", timeout = 0, ...)
eubon_hierarchy(id, providers = "pesi", timeout = 0, ...)
id |
(character) identifier for the taxon. (LSID, DOI, URI, or any other identifier used by the checklist provider) |
providers |
(character) A list of provider id strings concatenated by comma characters. The default : "pesi,bgbm-cdm-server[col]" will be used if this parameter is not set. A list of all available provider ids can be obtained from the '/capabilities' service end point. Providers can be nested, that is a parent provider can have sub providers. If the id of the parent provider is supplied all subproviders will be queried. The query can also be restricted to one or more subproviders by using the following syntax: parent-id[sub-id-1,sub-id2,...] |
timeout |
(numeric) The maximum of milliseconds to wait for responses from any of the providers. If the timeout is exceeded the service will just return the responses that have been received so far. The default timeout is 0 ms (wait for ever) |
... |
Curl options passed on to crul::verb-GET |
There is no pagination in this method, so you may or may not be getting all the results for a search. Sorry, out of our control
https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html
Other eubon-methods:
eubon_capabilities()
,
eubon_children()
,
eubon_search()
## Not run: eubon_hierarchy(id = "urn:lsid:marinespecies.org:taxname:126141", 'worms') eubon_hierarchy(id = "urn:lsid:marinespecies.org:taxname:274350", 'worms') ## End(Not run)
## Not run: eubon_hierarchy(id = "urn:lsid:marinespecies.org:taxname:126141", 'worms') eubon_hierarchy(id = "urn:lsid:marinespecies.org:taxname:274350", 'worms') ## End(Not run)
EUBON taxonomy search
eubon_search( query, providers = "pesi", searchMode = "scientificNameExact", addSynonymy = FALSE, addParentTaxon = FALSE, timeout = 0, dedup = NULL, limit = 20, page = 1, ... )
eubon_search( query, providers = "pesi", searchMode = "scientificNameExact", addSynonymy = FALSE, addParentTaxon = FALSE, timeout = 0, dedup = NULL, limit = 20, page = 1, ... )
query |
(character) The scientific name to search for. For example: "Bellis perennis", "Prionus" or "Bolinus brandaris". This is an exact search so wildcard characters are not supported |
providers |
(character) A list of provider id strings concatenated by comma characters. The default : "pesi,bgbm-cdm-server[col]" will be used if this parameter is not set. A list of all available provider ids can be obtained from the '/capabilities' service end point. Providers can be nested, that is a parent provider can have sub providers. If the id of the parent provider is supplied all subproviders will be queried. The query can also be restricted to one or more subproviders by using the following syntax: parent-id[sub-id-1,sub-id2,...] |
searchMode |
(character) Specifies the searchMode. Possible search
modes are: |
addSynonymy |
(logical) Indicates whether the synonymy of the accepted
taxon should be included into the response. Turning this option on may
cause an increased response time. Default: |
addParentTaxon |
(logical) Indicates whether the the parent taxon of
the accepted taxon should be included into the response. Turning this option
on may cause a slightly increased response time. Default: |
timeout |
(numeric) The maximum of milliseconds to wait for responses from any of the providers. If the timeout is exceeded the service will just return the responses that have been received so far. The default timeout is 0 ms (wait for ever) |
dedup |
(character) Allows to deduplicate the results by making use of a deduplication strategy. The deduplication is done by comparing specific properties of the taxon:
|
limit |
(numeric/integer) number of records to retrieve. default: 20.
This only affects the search mode |
page |
(numeric/integer) page to retrieve. default: 1. This only
affects the search mode |
... |
Curl options passed on to crul::verb-GET |
https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html
Other eubon-methods:
eubon_capabilities()
,
eubon_children()
,
eubon_hierarchy()
## Not run: eubon_search("Prionus") eubon_search("Salmo", "pesi") eubon_search("Salmo", c("pesi", "worms")) eubon_search("Salmo", "worms", "scientificNameLike") eubon_search("Salmo", "worms", "scientificNameLike", limit = 3) eubon_search("Salmo", "worms", "scientificNameLike", limit = 20, page = 2) eubon_search("Salmo", "worms", addSynonymy = TRUE) eubon_search("Salmo", "worms", addParentTaxon = TRUE) ## End(Not run)
## Not run: eubon_search("Prionus") eubon_search("Salmo", "pesi") eubon_search("Salmo", c("pesi", "worms")) eubon_search("Salmo", "worms", "scientificNameLike") eubon_search("Salmo", "worms", "scientificNameLike", limit = 3) eubon_search("Salmo", "worms", "scientificNameLike", limit = 20, page = 2) eubon_search("Salmo", "worms", addSynonymy = TRUE) eubon_search("Salmo", "worms", addParentTaxon = TRUE) ## End(Not run)
Search for taxonomic names in Index Fungorum
fg_name_search(q, anywhere = TRUE, limit = 10, ...) fg_author_search(q, anywhere = TRUE, limit = 10, ...) fg_epithet_search(q, anywhere = TRUE, limit = 10, ...) fg_name_by_key(key, ...) fg_name_full_by_lsid(lsid, ...) fg_all_updated_names(date, ...) fg_deprecated_names(date, ...)
fg_name_search(q, anywhere = TRUE, limit = 10, ...) fg_author_search(q, anywhere = TRUE, limit = 10, ...) fg_epithet_search(q, anywhere = TRUE, limit = 10, ...) fg_name_by_key(key, ...) fg_name_full_by_lsid(lsid, ...) fg_all_updated_names(date, ...) fg_deprecated_names(date, ...)
q |
(character) Query term |
anywhere |
(logical) Default: |
limit |
(integer) Number of results to return. max limit value appears to be 6000, not positive about that though |
... |
Curl options passed on to crul::verb-GET |
key |
(character) A IndexFungorum taxon key |
lsid |
(character) an LSID, e.,g. "urn:lsid:indexfungorum.org:names:81085" |
date |
(character) Date, of the form YYYMMDD |
A data.frame
, or NULL
if no results
http://www.indexfungorum.org/, API docs: http://www.indexfungorum.org/ixfwebservice/fungus.asmx
## Not run: # NameSearch fg_name_search(q = "Gymnopus", limit = 2, verbose = TRUE) fg_name_search(q = "Gymnopus") # EpithetSearch fg_epithet_search(q = "phalloides") # NameByKey fg_name_by_key(17703) # NameFullByKey fg_name_full_by_lsid("urn:lsid:indexfungorum.org:names:81085") # AllUpdatedNames fg_all_updated_names(date = gsub("-", "", Sys.Date() - 2)) # DeprecatedNames fg_deprecated_names(date=20151001) # AuthorSearch fg_author_search(q = "Fayod", limit = 2) ## End(Not run)
## Not run: # NameSearch fg_name_search(q = "Gymnopus", limit = 2, verbose = TRUE) fg_name_search(q = "Gymnopus") # EpithetSearch fg_epithet_search(q = "phalloides") # NameByKey fg_name_by_key(17703) # NameFullByKey fg_name_full_by_lsid("urn:lsid:indexfungorum.org:names:81085") # AllUpdatedNames fg_all_updated_names(date = gsub("-", "", Sys.Date() - 2)) # DeprecatedNames fg_deprecated_names(date=20151001) # AuthorSearch fg_author_search(q = "Fayod", limit = 2) ## End(Not run)
Retrieve all taxonomic names downstream in hierarchy for GBIF
gbif_downstream( id, downto, intermediate = FALSE, limit = 100, start = NULL, key = NULL, ... )
gbif_downstream( id, downto, intermediate = FALSE, limit = 100, start = NULL, key = NULL, ... )
id |
A taxonomic serial number. |
downto |
The taxonomic level you want to go down to. See examples below.
The taxonomic level IS case sensitive, and you do have to spell it
correctly. See |
intermediate |
(logical) If TRUE, return a list of length two with target taxon rank names, with additional list of data.frame's of intermediate taxonomic groups. Default: FALSE |
limit |
Number of records to return. default: 100. max: 1000. use in
combination with the |
start |
Record number to start at. default: 0. use in combination
with the |
key |
Deprecated, see |
... |
Further args passed on to |
Sometimes records don't have a canonicalName
entry which is
what we look for. In that case we grab the scientificName
entry.
You can see the type of name colleceted in the column name_type
data.frame of taxonomic information downstream to family from e.g.,
Order, Class, etc., or if intermediated=TRUE
, list of length two,
with target taxon rank names, and intermediate names.
Scott Chamberlain
## Not run: ## the plant class Bangiophyceae gbif_downstream(id = 198, downto="genus") gbif_downstream(id = 198, downto="genus", intermediate=TRUE) # families downstream from the family Strepsiptera (twisted wing parasites) gbif_downstream(id = 1227, "family") ## here, intermediate leads to the same result as the target gbif_downstream(id = 1227, "family", intermediate=TRUE) if (interactive()) { # Lepidoptera gbif_downstream(id = 797, "family") # get species downstream from the genus Ursus gbif_downstream(id = 2433406, "species") # get tribes down from the family Apidae gbif_downstream(id = 7799978, downto="species") gbif_downstream(id = 7799978, downto="species", intermediate=TRUE) # names that don't have canonicalname entries for some results # Myosotis: key 2925668 key <- 2925668 res <- gbif_downstream(key, downto = "species") res2 <- downstream(key, db = "gbif", downto = "species") # Pagination # GBIF limits queries to a maximum of 1000 records per request, so if # there's more than 1000, use the start parameter # Piper, taxonKey = 3075433 x1 <- gbif_downstream(id = 3075433, downto = "species", limit=1000) x2 <- gbif_downstream(id = 3075433, downto = "species", limit=1000, start=1000) x3 <- gbif_downstream(id = 3075433, downto = "species", limit=1000, start=2000) x4 <- gbif_downstream(id = 3075433, downto = "species", limit=1000, start=3000) rbind(x1, x2, x3, x4) } ## End(Not run)
## Not run: ## the plant class Bangiophyceae gbif_downstream(id = 198, downto="genus") gbif_downstream(id = 198, downto="genus", intermediate=TRUE) # families downstream from the family Strepsiptera (twisted wing parasites) gbif_downstream(id = 1227, "family") ## here, intermediate leads to the same result as the target gbif_downstream(id = 1227, "family", intermediate=TRUE) if (interactive()) { # Lepidoptera gbif_downstream(id = 797, "family") # get species downstream from the genus Ursus gbif_downstream(id = 2433406, "species") # get tribes down from the family Apidae gbif_downstream(id = 7799978, downto="species") gbif_downstream(id = 7799978, downto="species", intermediate=TRUE) # names that don't have canonicalname entries for some results # Myosotis: key 2925668 key <- 2925668 res <- gbif_downstream(key, downto = "species") res2 <- downstream(key, db = "gbif", downto = "species") # Pagination # GBIF limits queries to a maximum of 1000 records per request, so if # there's more than 1000, use the start parameter # Piper, taxonKey = 3075433 x1 <- gbif_downstream(id = 3075433, downto = "species", limit=1000) x2 <- gbif_downstream(id = 3075433, downto = "species", limit=1000, start=1000) x3 <- gbif_downstream(id = 3075433, downto = "species", limit=1000, start=2000) x4 <- gbif_downstream(id = 3075433, downto = "species", limit=1000, start=3000) rbind(x1, x2, x3, x4) } ## End(Not run)
This is a taxize version of the same function in the rgbif
package so as to not have to
import rgbif and thus require GDAL binary installation.
gbif_name_usage( key = NULL, name = NULL, data = "all", language = NULL, datasetKey = NULL, uuid = NULL, sourceId = NULL, rank = NULL, shortname = NULL, start = NULL, limit = 20, ... )
gbif_name_usage( key = NULL, name = NULL, data = "all", language = NULL, datasetKey = NULL, uuid = NULL, sourceId = NULL, rank = NULL, shortname = NULL, start = NULL, limit = 20, ... )
key |
(numeric) A GBIF key for a taxon |
name |
(character) Filters by a case insensitive, canonical namestring, e.g. 'Puma concolor' |
data |
(character) Specify an option to select what data is returned. See Description below. |
language |
(character) Language, default is english |
datasetKey |
(character) Filters by the dataset's key (a uuid) |
uuid |
(character) A uuid for a dataset. Should give exact same results as datasetKey. |
sourceId |
(numeric) Filters by the source identifier. Not used right now. |
rank |
(character) Taxonomic rank. Filters by taxonomic rank as one of: CLASS, CULTIVAR, CULTIVAR_GROUP, DOMAIN, FAMILY, FORM, GENUS, INFORMAL, INFRAGENERIC_NAME, INFRAORDER, INFRASPECIFIC_NAME, INFRASUBSPECIFIC_NAME, KINGDOM, ORDER, PHYLUM, SECTION, SERIES, SPECIES, STRAIN, SUBCLASS, SUBFAMILY, SUBFORM, SUBGENUS, SUBKINGDOM, SUBORDER, SUBPHYLUM, SUBSECTION, SUBSERIES, SUBSPECIES, SUBTRIBE, SUBVARIETY, SUPERCLASS, SUPERFAMILY, SUPERORDER, SUPERPHYLUM, SUPRAGENERIC_NAME, TRIBE, UNRANKED, VARIETY |
shortname |
(character) A short name..need more info on this? |
start |
Record number to start at |
limit |
Number of records to return |
... |
Curl options passed on to crul::HttpClient |
A list of length two. The first element is metadata. The second is either a data.frame (verbose=FALSE, default) or a list (verbose=TRUE)
https://www.gbif.org/developer/summary
Parse taxon names using the GBIF name parser.
gbif_parse(scientificname, ...)
gbif_parse(scientificname, ...)
scientificname |
(character) scientific names |
... |
Further args passed on to crul::verb-POST |
A data.frame
containing fields extracted from parsed
taxon names. Fields returned are the union of fields extracted from
all species names in scientificname
.
John Baumgartner [email protected]
https://www.gbif.org/tools/name-parser/about
## Not run: gbif_parse(scientificname='x Agropogon littoralis') gbif_parse(c('Arrhenatherum elatius var. elatius', 'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale', 'Vanessa atalanta (Linnaeus, 1758)')) ## End(Not run)
## Not run: gbif_parse(scientificname='x Agropogon littoralis') gbif_parse(c('Arrhenatherum elatius var. elatius', 'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale', 'Vanessa atalanta (Linnaeus, 1758)')) ## End(Not run)
Get NCBI taxonomy UID from GenBankID
genbank2uid(id, batch_size = 100, key = NULL, ...)
genbank2uid(id, batch_size = 100, key = NULL, ...)
id |
A GenBank accession alphanumeric string, or a gi numeric string. |
batch_size |
The number of queries to submit at a time. |
key |
(character) NCBI Entrez API key. optional. See Details. |
... |
Curl args passed on to crul::HttpClient |
See https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html for help on why there are two identifiers, and the difference between them.
one or more NCBI taxonomic IDs
See taxize-authentication for help on authentication. We recommend getting an API key.
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')
In case you run into errors due to your rate limit being exceeded, see
taxize_options()
, where you can set ncbi_sleep
.
## Not run: # with accession numbers genbank2uid(id = 'AJ748748') genbank2uid(id = 'Y13155') genbank2uid(id = 'X78312') genbank2uid(id = 'KM495596') # with gi numbers genbank2uid(id = 62689767) genbank2uid(id = 22775511) genbank2uid(id = 156446673) # pass in many accession or gi numbers genbank2uid(c(62689767,156446673)) genbank2uid(c('X78312','KM495596')) genbank2uid(list('X78312',156446673)) # curl options res <- genbank2uid(id = 156446673, verbose = TRUE) ## End(Not run)
## Not run: # with accession numbers genbank2uid(id = 'AJ748748') genbank2uid(id = 'Y13155') genbank2uid(id = 'X78312') genbank2uid(id = 'KM495596') # with gi numbers genbank2uid(id = 62689767) genbank2uid(id = 22775511) genbank2uid(id = 156446673) # pass in many accession or gi numbers genbank2uid(c(62689767,156446673)) genbank2uid(c('X78312','KM495596')) genbank2uid(list('X78312',156446673)) # curl options res <- genbank2uid(id = 156446673, verbose = TRUE) ## End(Not run)
Get the BOLD (Barcode of Life) code for a search term.
get_boldid( sci, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, ask = TRUE, messages = TRUE, rows = NA, rank = NULL, division = NULL, parent = NULL, searchterm = NULL, ... ) as.boldid(x, check = TRUE) ## S3 method for class 'boldid' as.boldid(x, check = TRUE) ## S3 method for class 'character' as.boldid(x, check = TRUE) ## S3 method for class 'list' as.boldid(x, check = TRUE) ## S3 method for class 'numeric' as.boldid(x, check = TRUE) ## S3 method for class 'data.frame' as.boldid(x, check = TRUE) ## S3 method for class 'boldid' as.data.frame(x, ...) get_boldid_( sci, messages = TRUE, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, rows = NA, searchterm = NULL, ... )
get_boldid( sci, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, ask = TRUE, messages = TRUE, rows = NA, rank = NULL, division = NULL, parent = NULL, searchterm = NULL, ... ) as.boldid(x, check = TRUE) ## S3 method for class 'boldid' as.boldid(x, check = TRUE) ## S3 method for class 'character' as.boldid(x, check = TRUE) ## S3 method for class 'list' as.boldid(x, check = TRUE) ## S3 method for class 'numeric' as.boldid(x, check = TRUE) ## S3 method for class 'data.frame' as.boldid(x, check = TRUE) ## S3 method for class 'boldid' as.data.frame(x, ...) get_boldid_( sci, messages = TRUE, fuzzy = FALSE, dataTypes = "basic", includeTree = FALSE, rows = NA, searchterm = NULL, ... )
sci |
character; A vector of scientific names. Or,
a |
fuzzy |
(logical) Whether to use fuzzy search or not (default: FALSE). |
dataTypes |
(character) Specifies the datatypes that will be returned.
See |
includeTree |
(logical) If TRUE (default: FALSE), returns a list containing information for parent taxa as well as the specified taxon. |
ask |
logical; should get_tsn be run in interactive mode? If TRUE and more than one TSN is found for teh species, the user is asked for input. If FALSE NA is returned for multiple matches. |
messages |
logical; should progress be printed? |
rows |
numeric; Any number from 1 to infinity. If the default NA, all rows are
considered. Note that this function still only gives back a boldid class object with one
to many identifiers. See |
rank |
(character) A taxonomic rank name. See rank_ref for possible
options. Though note that some data sources use atypical ranks, so inspect the
data itself for options. Optional. See |
division |
(character) A division (aka phylum) name. Optional. See |
parent |
(character) A parent name (i.e., the parent of the target search
taxon). Optional. See |
searchterm |
Deprecated, see |
... |
Curl options passed on to |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only used in
|
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
The parameters division
, parent
, and rank
are not used in the search to
the data provider, but are used in filtering the data down to a subset that
is closer to the target you want. For all these parameters, you can use
regex strings since we use grep()
internally to match. Filtering narrows
down to the set that matches your query, and removes the rest.
Other taxonomic-ids:
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: get_boldid(sci = "Agapostemon") get_boldid(sci = "Chironomus riparius") get_boldid(c("Chironomus riparius","Quercus douglasii")) splist <- names_list('species') get_boldid(splist, messages=FALSE) # Fuzzy searching get_boldid(sci="Osmi", fuzzy=TRUE) # Get back a subset get_boldid(sci="Osmi", fuzzy=TRUE, rows = 1) get_boldid(sci="Osmi", fuzzy=TRUE, rows = 1:10) get_boldid(sci=c("Osmi","Aga"), fuzzy=TRUE, rows = 1) get_boldid(sci=c("Osmi","Aga"), fuzzy=TRUE, rows = 1:3) # found get_boldid('Epicordulia princeps') get_boldid('Arigomphus furcifer') # When not found get_boldid("howdy") get_boldid(c("Chironomus riparius", "howdy")) get_boldid("Cordulegaster erronea") get_boldid("Nasiaeshna pentacantha") # Narrow down results to a division or rank, or both ## Satyrium example ### Results w/o narrowing get_boldid("Satyrium") ### w/ phylum get_boldid("Satyrium", division = "Plantae") get_boldid("Satyrium", division = "Animalia") ## Rank example get_boldid("Osmia", fuzzy = TRUE) get_boldid("Osmia", fuzzy = TRUE, rank = "genus") # Fuzzy filter on any filtering fields ## uses grep on the inside get_boldid("Satyrium", division = "anim") get_boldid("Aga", fuzzy = TRUE, parent = "*idae") # Convert a boldid without class information to a boldid class as.boldid(get_boldid("Agapostemon")) # already a boldid, returns the same as.boldid(get_boldid(c("Agapostemon","Quercus douglasii"))) # same as.boldid(1973) # numeric as.boldid(c(1973,101009,98597)) # numeric vector, length > 1 as.boldid("1973") # character as.boldid(c("1973","101009","98597")) # character vector, length > 1 as.boldid(list("1973","101009","98597")) # list, either numeric or character ## dont check, much faster as.boldid("1973", check=FALSE) as.boldid(1973, check=FALSE) as.boldid(c("1973","101009","98597"), check=FALSE) as.boldid(list("1973","101009","98597"), check=FALSE) (out <- as.boldid(c(1973,101009,98597))) data.frame(out) as.boldid( data.frame(out) ) # Get all data back get_boldid_("Osmia", fuzzy=TRUE, rows=1:5) get_boldid_("Osmia", fuzzy=TRUE, rows=1) get_boldid_(c("Osmi","Aga"), fuzzy=TRUE, rows = 1:3) ## End(Not run)
## Not run: get_boldid(sci = "Agapostemon") get_boldid(sci = "Chironomus riparius") get_boldid(c("Chironomus riparius","Quercus douglasii")) splist <- names_list('species') get_boldid(splist, messages=FALSE) # Fuzzy searching get_boldid(sci="Osmi", fuzzy=TRUE) # Get back a subset get_boldid(sci="Osmi", fuzzy=TRUE, rows = 1) get_boldid(sci="Osmi", fuzzy=TRUE, rows = 1:10) get_boldid(sci=c("Osmi","Aga"), fuzzy=TRUE, rows = 1) get_boldid(sci=c("Osmi","Aga"), fuzzy=TRUE, rows = 1:3) # found get_boldid('Epicordulia princeps') get_boldid('Arigomphus furcifer') # When not found get_boldid("howdy") get_boldid(c("Chironomus riparius", "howdy")) get_boldid("Cordulegaster erronea") get_boldid("Nasiaeshna pentacantha") # Narrow down results to a division or rank, or both ## Satyrium example ### Results w/o narrowing get_boldid("Satyrium") ### w/ phylum get_boldid("Satyrium", division = "Plantae") get_boldid("Satyrium", division = "Animalia") ## Rank example get_boldid("Osmia", fuzzy = TRUE) get_boldid("Osmia", fuzzy = TRUE, rank = "genus") # Fuzzy filter on any filtering fields ## uses grep on the inside get_boldid("Satyrium", division = "anim") get_boldid("Aga", fuzzy = TRUE, parent = "*idae") # Convert a boldid without class information to a boldid class as.boldid(get_boldid("Agapostemon")) # already a boldid, returns the same as.boldid(get_boldid(c("Agapostemon","Quercus douglasii"))) # same as.boldid(1973) # numeric as.boldid(c(1973,101009,98597)) # numeric vector, length > 1 as.boldid("1973") # character as.boldid(c("1973","101009","98597")) # character vector, length > 1 as.boldid(list("1973","101009","98597")) # list, either numeric or character ## dont check, much faster as.boldid("1973", check=FALSE) as.boldid(1973, check=FALSE) as.boldid(c("1973","101009","98597"), check=FALSE) as.boldid(list("1973","101009","98597"), check=FALSE) (out <- as.boldid(c(1973,101009,98597))) data.frame(out) as.boldid( data.frame(out) ) # Get all data back get_boldid_("Osmia", fuzzy=TRUE, rows=1:5) get_boldid_("Osmia", fuzzy=TRUE, rows=1) get_boldid_(c("Osmi","Aga"), fuzzy=TRUE, rows = 1:3) ## End(Not run)
Note that EOL doesn't expose an API endpoint for directly querying for EOL
taxon ID's, so we first use the function eol_search()
to find pages that deal with the species of interest, then use
eol_pages()
to find the actual taxon IDs.
get_eolid( sci_com, ask = TRUE, messages = TRUE, rows = NA, rank = NULL, data_source = NULL, sciname = NULL, ... ) as.eolid(x, check = TRUE) ## S3 method for class 'eolid' as.eolid(x, check = TRUE) ## S3 method for class 'character' as.eolid(x, check = TRUE) ## S3 method for class 'list' as.eolid(x, check = TRUE) ## S3 method for class 'numeric' as.eolid(x, check = TRUE) ## S3 method for class 'data.frame' as.eolid(x, check = TRUE) ## S3 method for class 'eolid' as.data.frame(x, ...) get_eolid_(sci_com, messages = TRUE, rows = NA, sciname = NULL, ...)
get_eolid( sci_com, ask = TRUE, messages = TRUE, rows = NA, rank = NULL, data_source = NULL, sciname = NULL, ... ) as.eolid(x, check = TRUE) ## S3 method for class 'eolid' as.eolid(x, check = TRUE) ## S3 method for class 'character' as.eolid(x, check = TRUE) ## S3 method for class 'list' as.eolid(x, check = TRUE) ## S3 method for class 'numeric' as.eolid(x, check = TRUE) ## S3 method for class 'data.frame' as.eolid(x, check = TRUE) ## S3 method for class 'eolid' as.data.frame(x, ...) get_eolid_(sci_com, messages = TRUE, rows = NA, sciname = NULL, ...)
sci_com |
character; one or more scientific or common names. Or,
a |
ask |
logical; should get_eolid be run in interactive mode? If TRUE and more than one ID is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches. |
messages |
logical; If |
rows |
numeric; Any number from 1 to infinity. If the default NA, all
rows are considered. Note that this function still only gives back a eolid
class object with one to many identifiers. See
|
rank |
(character) A taxonomic rank name. See rank_ref
for possible options. Though note that some data sources use atypical ranks,
so inspect the data itself for options. Optional. See |
data_source |
(character) A data source inside of EOL. These are
longish names like e.g., "Barcode of Life Data Systems" or
"USDA PLANTS images". Optional. See |
sciname |
Deprecated, see |
... |
Further args passed on to |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only
used in |
EOL is a bit odd in that they have page IDs for each taxon, but
then within that, they have taxon ids for various taxa within that page
(e.g., GBIF and NCBI each have a taxon they refer to within the
page [i.e., taxon]). And we need the taxon ids from a particular data
provider (e.g, NCBI) to do other things, like get a higher classification
tree. However, humans want the page id, not the taxon id. So, the
id returned from this function is the taxon id, not the page id. You can
get the page id for a taxon by using eol_search()
and
'eol_pages()
, and the URI returned in the attributes for a
taxon will lead you to the taxon page, and the ID in the URL is the
page id.
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
The parameters rank
and data_source
are not used in the
search to the data provider, but are used in filtering the data down to a
subset that is closer to the target you want. For all these parameters,
you can use regex strings since we use grep()
internally to
match. Filtering narrows down to the set that matches your query, and
removes the rest.
Scott Chamberlain
Other taxonomic-ids:
get_boldid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: get_eolid(sci_com='Pinus contorta') get_eolid(sci_com='Puma concolor') get_eolid(c("Puma concolor", "Pinus contorta")) # specify rows to limit choices available get_eolid('Poa annua') get_eolid('Poa annua', rows=1) get_eolid('Poa annua', rows=2) get_eolid('Poa annua', rows=1:2) # When not found get_eolid(sci_com="uaudnadndj") get_eolid(c("Chironomus riparius", "uaudnadndj")) # filter results to a rank or data source, or both get_eolid("Satyrium") get_eolid("Satyrium", rank = "genus") get_eolid("Satyrium", data_source = "INAT") get_eolid("Satyrium", rank = "genus", data_source = "North Pacific Species List") # Convert a eolid without class information to a eolid class # already a eolid, returns the same as.eolid(get_eolid("Chironomus riparius")) # same as.eolid(get_eolid(c("Chironomus riparius","Pinus contorta"))) # numeric as.eolid(10247706) # numeric vector, length > 1 as.eolid(c(6985636,12188704,10247706)) # character as.eolid("6985636") # character vector, length > 1 as.eolid(c("6985636","12188704","10247706")) # list, either numeric or character as.eolid(list("6985636","12188704","10247706")) ## dont check, much faster as.eolid("6985636", check=FALSE) as.eolid(6985636, check=FALSE) as.eolid(c("6985636","12188704","10247706"), check=FALSE) as.eolid(list("6985636","12188704","10247706"), check=FALSE) (out <- as.eolid(c(6985636,12188704,10247706))) data.frame(out) as.eolid( data.frame(out) ) # Get all data back get_eolid_("Poa annua") get_eolid_("Poa annua", rows=2) get_eolid_("Poa annua", rows=1:2) get_eolid_(c("asdfadfasd", "Pinus contorta")) ## End(Not run)
## Not run: get_eolid(sci_com='Pinus contorta') get_eolid(sci_com='Puma concolor') get_eolid(c("Puma concolor", "Pinus contorta")) # specify rows to limit choices available get_eolid('Poa annua') get_eolid('Poa annua', rows=1) get_eolid('Poa annua', rows=2) get_eolid('Poa annua', rows=1:2) # When not found get_eolid(sci_com="uaudnadndj") get_eolid(c("Chironomus riparius", "uaudnadndj")) # filter results to a rank or data source, or both get_eolid("Satyrium") get_eolid("Satyrium", rank = "genus") get_eolid("Satyrium", data_source = "INAT") get_eolid("Satyrium", rank = "genus", data_source = "North Pacific Species List") # Convert a eolid without class information to a eolid class # already a eolid, returns the same as.eolid(get_eolid("Chironomus riparius")) # same as.eolid(get_eolid(c("Chironomus riparius","Pinus contorta"))) # numeric as.eolid(10247706) # numeric vector, length > 1 as.eolid(c(6985636,12188704,10247706)) # character as.eolid("6985636") # character vector, length > 1 as.eolid(c("6985636","12188704","10247706")) # list, either numeric or character as.eolid(list("6985636","12188704","10247706")) ## dont check, much faster as.eolid("6985636", check=FALSE) as.eolid(6985636, check=FALSE) as.eolid(c("6985636","12188704","10247706"), check=FALSE) as.eolid(list("6985636","12188704","10247706"), check=FALSE) (out <- as.eolid(c(6985636,12188704,10247706))) data.frame(out) as.eolid( data.frame(out) ) # Get all data back get_eolid_("Poa annua") get_eolid_("Poa annua", rows=2) get_eolid_("Poa annua", rows=1:2) get_eolid_(c("asdfadfasd", "Pinus contorta")) ## End(Not run)
Get the GBIF backbone taxon ID from taxonomic names.
get_gbifid( sci, ask = TRUE, messages = TRUE, rows = NA, phylum = NULL, class = NULL, order = NULL, family = NULL, rank = NULL, method = "backbone", sciname = NULL, ... ) as.gbifid(x, check = FALSE) ## S3 method for class 'gbifid' as.gbifid(x, check = FALSE) ## S3 method for class 'character' as.gbifid(x, check = TRUE) ## S3 method for class 'list' as.gbifid(x, check = TRUE) ## S3 method for class 'numeric' as.gbifid(x, check = TRUE) ## S3 method for class 'data.frame' as.gbifid(x, check = TRUE) ## S3 method for class 'gbifid' as.data.frame(x, ...) get_gbifid_( sci, messages = TRUE, rows = NA, method = "backbone", sciname = NULL )
get_gbifid( sci, ask = TRUE, messages = TRUE, rows = NA, phylum = NULL, class = NULL, order = NULL, family = NULL, rank = NULL, method = "backbone", sciname = NULL, ... ) as.gbifid(x, check = FALSE) ## S3 method for class 'gbifid' as.gbifid(x, check = FALSE) ## S3 method for class 'character' as.gbifid(x, check = TRUE) ## S3 method for class 'list' as.gbifid(x, check = TRUE) ## S3 method for class 'numeric' as.gbifid(x, check = TRUE) ## S3 method for class 'data.frame' as.gbifid(x, check = TRUE) ## S3 method for class 'gbifid' as.data.frame(x, ...) get_gbifid_( sci, messages = TRUE, rows = NA, method = "backbone", sciname = NULL )
sci |
(character) one or more scientific names. Or, a |
ask |
logical; should get_gbifid be run in interactive mode? If TRUE and more than one ID is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches. |
messages |
logical; If TRUE the actual taxon queried is printed on the console. |
rows |
numeric; Any number from 1 to infinity. If the default NA, all rows are considered.
Note that this function still only gives back a gbifid class object with one to many identifiers.
See |
phylum |
(character) A phylum (aka division) name. Optional. See |
class |
(character) A class name. Optional. See |
order |
(character) An order name. Optional. See |
family |
(character) A family name. Optional. See |
rank |
(character) A taxonomic rank name. See rank_ref for possible
options. Though note that some data sources use atypical ranks, so inspect the
data itself for options. Optional. See |
method |
(character) one of "backbone" or "lookup". See Details. |
sciname |
Deprecated, see |
... |
Ignored |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only used in
|
Internally in this function we use a function to search GBIF's taxonomy, and if we find an exact match we return the ID for that match. If there isn't an exact match we return the options to you to pick from.
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
"backbone" uses the /species/match
GBIF API route, matching against their
backbone taxonomy. We turn on fuzzy matching by default, as the search without
fuzzy against backbone is quite narrow. "lookup" uses the /species/search
GBIF API route, doing a full text search of name usages covering scientific
and vernacular named, species descriptions, distributions and the entire
classification.
The parameters phylum
, class
, order
, family
, and rank
are not used
in the search to the data provider, but are used in filtering the data down
to a subset that is closer to the target you want. For all these parameters,
you can use regex strings since we use grep()
internally to match.
Filtering narrows down to the set that matches your query, and removes the rest.
Scott Chamberlain,
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: get_gbifid(sci='Poa annua') get_gbifid(sci='Pinus contorta') get_gbifid(sci='Puma concolor') #lots of queries spp <- names_list("species", 10) res <- get_gbifid(spp) res xx <- taxon_last() xx # multiple names get_gbifid(c("Poa annua", "Pinus contorta")) # specify rows to limit choices available get_gbifid(sci='Pinus') get_gbifid(sci='Pinus', rows=10) get_gbifid(sci='Pinus', rows=1:3) # When not found, NA given get_gbifid(sci="uaudnadndj") get_gbifid(c("Chironomus riparius", "uaudnadndj")) # Narrow down results to a division or rank, or both ## Satyrium example ### Results w/o narrowing get_gbifid("Satyrium") ### w/ phylum get_gbifid("Satyrium", phylum = "Tracheophyta") get_gbifid("Satyrium", phylum = "Arthropoda") ### w/ phylum & rank get_gbifid("Satyrium", phylum = "Arthropoda", rank = "genus") ## Rank example get_gbifid("Poa", method = "lookup") get_gbifid("Poa", method = "lookup", rank = "genus") get_gbifid("Poa", method = "lookup", family = "Thripidae") # Fuzzy filter on any filtering fields ## uses grep on the inside get_gbifid("Satyrium", phylum = "arthropoda") get_gbifid("A*", method = "lookup", order = "*tera") get_gbifid("A*", method = "lookup", order = "*ales") # Convert a uid without class information to a uid class as.gbifid(get_gbifid("Poa annua")) # already a uid, returns the same as.gbifid(get_gbifid(c("Poa annua","Puma concolor"))) # same as.gbifid(2704179) # numeric as.gbifid(c(2704179,2435099,3171445)) # numeric vector, length > 1 as.gbifid("2704179") # character as.gbifid(c("2704179","2435099","3171445")) # character vector, length > 1 as.gbifid(list("2704179","2435099","3171445")) # list, either numeric or character ## dont check, much faster as.gbifid("2704179", check=FALSE) as.gbifid(2704179, check=FALSE) as.gbifid(2704179, check=FALSE) as.gbifid(c("2704179","2435099","3171445"), check=FALSE) as.gbifid(list("2704179","2435099","3171445"), check=FALSE) (out <- as.gbifid(c(2704179,2435099,3171445))) data.frame(out) as.uid( data.frame(out) ) # Get all data back get_gbifid_("Puma concolor") get_gbifid_(c("Pinus", "uaudnadndj")) get_gbifid_(c("Pinus", "Puma"), rows=5) get_gbifid_(c("Pinus", "Puma"), rows=1:5) # use curl options invisible(get_gbifid("Quercus douglasii", verbose = TRUE)) ## End(Not run)
## Not run: get_gbifid(sci='Poa annua') get_gbifid(sci='Pinus contorta') get_gbifid(sci='Puma concolor') #lots of queries spp <- names_list("species", 10) res <- get_gbifid(spp) res xx <- taxon_last() xx # multiple names get_gbifid(c("Poa annua", "Pinus contorta")) # specify rows to limit choices available get_gbifid(sci='Pinus') get_gbifid(sci='Pinus', rows=10) get_gbifid(sci='Pinus', rows=1:3) # When not found, NA given get_gbifid(sci="uaudnadndj") get_gbifid(c("Chironomus riparius", "uaudnadndj")) # Narrow down results to a division or rank, or both ## Satyrium example ### Results w/o narrowing get_gbifid("Satyrium") ### w/ phylum get_gbifid("Satyrium", phylum = "Tracheophyta") get_gbifid("Satyrium", phylum = "Arthropoda") ### w/ phylum & rank get_gbifid("Satyrium", phylum = "Arthropoda", rank = "genus") ## Rank example get_gbifid("Poa", method = "lookup") get_gbifid("Poa", method = "lookup", rank = "genus") get_gbifid("Poa", method = "lookup", family = "Thripidae") # Fuzzy filter on any filtering fields ## uses grep on the inside get_gbifid("Satyrium", phylum = "arthropoda") get_gbifid("A*", method = "lookup", order = "*tera") get_gbifid("A*", method = "lookup", order = "*ales") # Convert a uid without class information to a uid class as.gbifid(get_gbifid("Poa annua")) # already a uid, returns the same as.gbifid(get_gbifid(c("Poa annua","Puma concolor"))) # same as.gbifid(2704179) # numeric as.gbifid(c(2704179,2435099,3171445)) # numeric vector, length > 1 as.gbifid("2704179") # character as.gbifid(c("2704179","2435099","3171445")) # character vector, length > 1 as.gbifid(list("2704179","2435099","3171445")) # list, either numeric or character ## dont check, much faster as.gbifid("2704179", check=FALSE) as.gbifid(2704179, check=FALSE) as.gbifid(2704179, check=FALSE) as.gbifid(c("2704179","2435099","3171445"), check=FALSE) as.gbifid(list("2704179","2435099","3171445"), check=FALSE) (out <- as.gbifid(c(2704179,2435099,3171445))) data.frame(out) as.uid( data.frame(out) ) # Get all data back get_gbifid_("Puma concolor") get_gbifid_(c("Pinus", "uaudnadndj")) get_gbifid_(c("Pinus", "Puma"), rows=5) get_gbifid_(c("Pinus", "Puma"), rows=1:5) # use curl options invisible(get_gbifid("Quercus douglasii", verbose = TRUE)) ## End(Not run)
get_*()
functionsIncluding outputs from get_*()
functions, as well as their
attributes, and all exception behaviors.
This document applies to the following functions:
Each output from get_*()
functions have the following attributes:
match (character) - the reason for NA, either 'not found', 'found' or
if ask = FALSE
then 'NA due to ask=FALSE')
multiple_matches (logical) - Whether multiple matches were returned by
the data source.
This can be TRUE
, even if you get 1 name back because we try to pattern
match the name to see if there's any direct matches. So sometimes this
attribute is TRUE
, as well as pattern_match
, which then returns 1
resulting name without user prompt.
pattern_match (logical) - Whether a pattern match was made.
If TRUE
thenmultiple_matches
must be TRUE
, and we found a perfect match
to your name, ignoring case. If FALSE
, there wasn't a direct match, and
likely you need to pick from many choices or further parameters can be used
to limit results
uri (character) - The URI where more information can be read on the taxon
includes the taxonomic identifier in the URL somewhere. This may be missing
if the value returned is NA
The following are the various ways in which get_*()
functions behave:
success - the value returned is a character string or numeric
no matches found - you'll get an NA, refine your search or possible the taxon searched for does not exist in the database you're using
more than on match and ask = FALSE
- if there's more than one matching
result, and you have set ask = FALSE
, then we can't determine the single
match to return, so we give back NA
. However, in this case we do set the
match
attribute to say NA due to ask=FALSE & > 1 result
so it's very
clear what happened - and you can even programatically check this as well
NA due to some other reason - some get_*()
functions have additional
parameters for filtering taxa. It's possible that even though there's
results (that is, found
will say TRUE
), you can get back an NA. This is
most likely if the parameter filters taxa after they are returned from the
data provider and the value passed to the parameter leads to no matches.
This is a convenience function to get identifiers across all data sources.
You can use other get_*
functions to get identifiers from specific
sources if you like.
get_ids( sci_com, db = c("itis", "ncbi", "eol", "tropicos", "gbif", "nbn", "pow"), suppress = FALSE, names = NULL, ... ) get_ids_( sci_com, db = get_ids_dbs, rows = NA, suppress = FALSE, names = NULL, ... )
get_ids( sci_com, db = c("itis", "ncbi", "eol", "tropicos", "gbif", "nbn", "pow"), suppress = FALSE, names = NULL, ... ) get_ids_( sci_com, db = get_ids_dbs, rows = NA, suppress = FALSE, names = NULL, ... )
sci_com |
(character) Taxonomic name to query. |
db |
(character) database to query. One or more of |
suppress |
(logical) suppress cli separators with the database
name being queried. default: |
names |
Deprecated, see |
... |
Other arguments passed to |
rows |
(numeric) Any number from 1 to infinity. If the default NA, all
rows are returned. When used in |
A vector of taxonomic identifiers, each retaining their respective S3 classes so that each element can be passed on to another function (see e.g.'s).
See taxize-authentication for help on authentication
There is a timeout of 1/3 seconds between queries to NCBI.
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: # Plug in taxon names directly # specify rows to limit choices available get_ids("Poa annua", db="eol", rows=1) get_ids("Poa annua", db="eol", rows=1:2) ## Or you can specify which source you want via the db parameter get_ids("Chironomus riparius", db = 'ncbi') get_ids("Salvelinus fontinalis", db = 'nbn') get_ids(c("Chironomus riparius", "Pinus contorta"), db = 'ncbi') get_ids("Pinus contorta", db = c('ncbi','eol','tropicos')) get_ids("ava avvva", db = c('ncbi','eol','tropicos')) # Pass on to other functions out <- get_ids("Pinus contorta", db = c('ncbi','eol','tropicos')) classification(out$ncbi) # Get all data back get_ids_(c("Chironomus riparius", "Pinus contorta"), db = 'nbn', rows=1:10) get_ids_(c("Chironomus riparius", "Pinus contorta"), db = c('nbn','gbif'), rows=1:10) # use curl options get_ids("Agapostemon", db = "ncbi", verbose = TRUE) ## End(Not run)
## Not run: # Plug in taxon names directly # specify rows to limit choices available get_ids("Poa annua", db="eol", rows=1) get_ids("Poa annua", db="eol", rows=1:2) ## Or you can specify which source you want via the db parameter get_ids("Chironomus riparius", db = 'ncbi') get_ids("Salvelinus fontinalis", db = 'nbn') get_ids(c("Chironomus riparius", "Pinus contorta"), db = 'ncbi') get_ids("Pinus contorta", db = c('ncbi','eol','tropicos')) get_ids("ava avvva", db = c('ncbi','eol','tropicos')) # Pass on to other functions out <- get_ids("Pinus contorta", db = c('ncbi','eol','tropicos')) classification(out$ncbi) # Get all data back get_ids_(c("Chironomus riparius", "Pinus contorta"), db = 'nbn', rows=1:10) get_ids_(c("Chironomus riparius", "Pinus contorta"), db = c('nbn','gbif'), rows=1:10) # use curl options get_ids("Agapostemon", db = "ncbi", verbose = TRUE) ## End(Not run)
Get a IUCN Redlist taxon
get_iucn(sci, messages = TRUE, key = NULL, x = NULL, ...) as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'iucn' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'character' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'list' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'numeric' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'data.frame' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'iucn' as.data.frame(x, ...)
get_iucn(sci, messages = TRUE, key = NULL, x = NULL, ...) as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'iucn' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'character' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'list' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'numeric' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'data.frame' as.iucn(x, check = TRUE, key = NULL) ## S3 method for class 'iucn' as.data.frame(x, ...)
sci |
(character) A vector of scientific names. Or, a
|
messages |
logical; should progress be printed? |
key |
(character) required. you IUCN Redlist API key. See rredlist::rredlist-package for help on authenticating with IUCN Redlist |
x |
For |
... |
Ignored |
check |
(logical) Check if ID matches any existing on the DB, only
used in |
There is no underscore method, because there's no real search for IUCN, that is, where you search for a string, and get back a bunch of results due to fuzzy matching. If that exists in the future we'll add an underscore method here.
IUCN ids only work with synonyms()
and sci2comm()
methods.
A vector of taxonomic identifiers as an S3 class.
Comes with the following attributes:
match (character) - the reason for NA, either 'not found',
'found' or if ask = FALSE
then 'NA due to ask=FALSE')
name (character) - the taxonomic name, which is needed in
synonyms()
and sci2comm()
methods since they
internally use rredlist functions which require the taxonomic name,
and not the taxonomic identifier
ri (character) - The URI where more information can be read on the taxon - includes the taxonomic identifier in the URL somewhere
multiple_matches and pattern_match do not apply here as in other get_*
methods since there is no IUCN Redlist search, so you either get a match or
you do not get a match.
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: get_iucn("Branta canadensis") get_iucn("Branta bernicla") get_iucn("Panthera uncia") # as coercion as.iucn(22732) as.iucn("22732") (res <- as.iucn(c(22679946, 22732, 22679935))) data.frame(res) as.iucn(data.frame(res)) ## End(Not run)
## Not run: get_iucn("Branta canadensis") get_iucn("Branta bernicla") get_iucn("Panthera uncia") # as coercion as.iucn(22732) as.iucn("22732") (res <- as.iucn(c(22679946, 22732, 22679935))) data.frame(res) as.iucn(data.frame(res)) ## End(Not run)
Get NatureServe taxonomic ID for a taxon name
get_natservid( sci_com, searchtype = "scientific", ask = TRUE, messages = TRUE, rows = NA, query = NULL, ... ) as.natservid(x, check = TRUE) ## S3 method for class 'natservid' as.natservid(x, check = TRUE) ## S3 method for class 'character' as.natservid(x, check = TRUE) ## S3 method for class 'list' as.natservid(x, check = TRUE) ## S3 method for class 'numeric' as.natservid(x, check = TRUE) ## S3 method for class 'data.frame' as.natservid(x, check = TRUE) ## S3 method for class 'natservid' as.data.frame(x, ...) get_natservid_( sci_com, searchtype = "scientific", messages = TRUE, rows = NA, query = NULL, ... )
get_natservid( sci_com, searchtype = "scientific", ask = TRUE, messages = TRUE, rows = NA, query = NULL, ... ) as.natservid(x, check = TRUE) ## S3 method for class 'natservid' as.natservid(x, check = TRUE) ## S3 method for class 'character' as.natservid(x, check = TRUE) ## S3 method for class 'list' as.natservid(x, check = TRUE) ## S3 method for class 'numeric' as.natservid(x, check = TRUE) ## S3 method for class 'data.frame' as.natservid(x, check = TRUE) ## S3 method for class 'natservid' as.data.frame(x, ...) get_natservid_( sci_com, searchtype = "scientific", messages = TRUE, rows = NA, query = NULL, ... )
sci_com |
character; A vector of common or scientific names. Or, a
|
searchtype |
character; One of 'scientific' (default) or 'common'. This doesn't affect the query to NatureServe - but rather affects what column of data is targeted in name filtering post data request. |
ask |
logical; should get_natservid be run in interactive mode?
If |
messages |
logical; should progress be printed? default: |
rows |
numeric; Any number from 1 to infinity. If the default NaN, all
rows are considered. Note that this function still only gives back a
natservid class object with one to many identifiers. See
|
query |
Deprecated, see |
... |
curl options passed on to crul::verb-POST |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only
used in |
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
Authentication no longer required
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: (x <- get_natservid("Helianthus annuus", verbose = TRUE)) attributes(x) attr(x, "match") attr(x, "multiple_matches") attr(x, "pattern_match") attr(x, "uri") get_natservid('Gadus morhua') get_natservid(c("Helianthus annuus", 'Gadus morhua')) # specify rows to limit choices available get_natservid('Ruby Quaker Moth', 'common') get_natservid('Ruby*', 'common') get_natservid('Ruby*', 'common', rows=1) get_natservid('Ruby*', 'common', rows=1:2) # When not found get_natservid("howdy") get_natservid(c('Gadus morhua', "howdy")) # Convert a natservid without class information to a natservid class # already a natservid, returns the same as.natservid(get_natservid('Pomatomus saltatrix')) # same as.natservid(get_natservid(c('Gadus morhua', 'Pomatomus saltatrix'))) # character as.natservid(101905) # character vector, length > 1 as.natservid(c(101905, 101998)) # list, either numeric or character as.natservid(list(101905, 101998)) ## dont check, much faster as.natservid(101905, check = FALSE) as.natservid(c(101905, 101998), check = FALSE) as.natservid(list(101905, 101998), check = FALSE) (out <- as.natservid(c(101905, 101998), check = FALSE)) data.frame(out) as.natservid( data.frame(out) ) # Get all data back get_natservid_("Helianthus") get_natservid_("Ruby*", searchtype = "common") get_natservid_("Ruby*", searchtype = "common", rows=1:3) ## End(Not run)
## Not run: (x <- get_natservid("Helianthus annuus", verbose = TRUE)) attributes(x) attr(x, "match") attr(x, "multiple_matches") attr(x, "pattern_match") attr(x, "uri") get_natservid('Gadus morhua') get_natservid(c("Helianthus annuus", 'Gadus morhua')) # specify rows to limit choices available get_natservid('Ruby Quaker Moth', 'common') get_natservid('Ruby*', 'common') get_natservid('Ruby*', 'common', rows=1) get_natservid('Ruby*', 'common', rows=1:2) # When not found get_natservid("howdy") get_natservid(c('Gadus morhua', "howdy")) # Convert a natservid without class information to a natservid class # already a natservid, returns the same as.natservid(get_natservid('Pomatomus saltatrix')) # same as.natservid(get_natservid(c('Gadus morhua', 'Pomatomus saltatrix'))) # character as.natservid(101905) # character vector, length > 1 as.natservid(c(101905, 101998)) # list, either numeric or character as.natservid(list(101905, 101998)) ## dont check, much faster as.natservid(101905, check = FALSE) as.natservid(c(101905, 101998), check = FALSE) as.natservid(list(101905, 101998), check = FALSE) (out <- as.natservid(c(101905, 101998), check = FALSE)) data.frame(out) as.natservid( data.frame(out) ) # Get all data back get_natservid_("Helianthus") get_natservid_("Ruby*", searchtype = "common") get_natservid_("Ruby*", searchtype = "common", rows=1:3) ## End(Not run)
Get the UK National Biodiversity Network ID from taxonomic names.
get_nbnid( sci_com, ask = TRUE, messages = TRUE, rec_only = FALSE, rank = NULL, rows = NA, name = NULL, ... ) as.nbnid(x, check = TRUE) ## S3 method for class 'nbnid' as.nbnid(x, check = TRUE) ## S3 method for class 'character' as.nbnid(x, check = TRUE) ## S3 method for class 'list' as.nbnid(x, check = TRUE) ## S3 method for class 'data.frame' as.nbnid(x, check = TRUE) ## S3 method for class 'nbnid' as.data.frame(x, ...) get_nbnid_( sci_com, messages = TRUE, rec_only = FALSE, rank = NULL, rows = NA, name = NULL, ... )
get_nbnid( sci_com, ask = TRUE, messages = TRUE, rec_only = FALSE, rank = NULL, rows = NA, name = NULL, ... ) as.nbnid(x, check = TRUE) ## S3 method for class 'nbnid' as.nbnid(x, check = TRUE) ## S3 method for class 'character' as.nbnid(x, check = TRUE) ## S3 method for class 'list' as.nbnid(x, check = TRUE) ## S3 method for class 'data.frame' as.nbnid(x, check = TRUE) ## S3 method for class 'nbnid' as.data.frame(x, ...) get_nbnid_( sci_com, messages = TRUE, rec_only = FALSE, rank = NULL, rows = NA, name = NULL, ... )
sci_com |
character; a vector of common or scientific names. Or, a
|
ask |
logical; should get_nbnid be run in interactive mode? If TRUE and more than one ID is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches. |
messages |
logical; If TRUE the actual taxon queried is printed on the console. |
rec_only |
(logical) If |
rank |
(character) If given, we attempt to limit the results to those taxa with the matching rank. |
rows |
numeric; Any number from 1 to infinity. If the default NA, all
rows are considered. Note that this function still only gives back a nbnid
class object with one to many identifiers. See
|
name |
Deprecated, see |
... |
Further args passed on to |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only
used in |
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
an object of class nbnid, a light wrapper around a character string that is the taxonomic ID - includes attributes with relavant metadata
Scott Chamberlain,
https://api.nbnatlas.org/
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
Other nbn:
nbn_classification()
,
nbn_search()
,
nbn_synonyms()
## Not run: get_nbnid(sci_com='Poa annua') get_nbnid(sci_com='Poa annua', rec_only=TRUE) get_nbnid(sci_com='Poa annua', rank='Species') get_nbnid(sci_com='Poa annua', rec_only=TRUE, rank='Species') get_nbnid(sci_com='Pinus contorta') # The NBN service handles common names too get_nbnid(sci_com='red-winged blackbird') # specify rows to limit choices available get_nbnid('Poa ann') get_nbnid('Poa ann', rows=1) get_nbnid('Poa ann', rows=25) get_nbnid('Poa ann', rows=1:2) # When not found get_nbnid(sci_com="uaudnadndj") get_nbnid(c("Zootoca vivipara", "uaudnadndj")) get_nbnid(c("Zootoca vivipara","Chironomus riparius", "uaudnadndj")) # Convert an nbnid without class information to a nbnid class as.nbnid(get_nbnid("Zootoca vivipara")) # already a nbnid, returns the same as.nbnid(get_nbnid(c("Zootoca vivipara","Pinus contorta"))) # same as.nbnid('NHMSYS0001706186') # character # character vector, length > 1 as.nbnid(c("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867")) # list as.nbnid(list("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867")) ## dont check, much faster as.nbnid('NHMSYS0001706186', check=FALSE) as.nbnid(list("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867"), check=FALSE) (out <- as.nbnid(c("NHMSYS0001706186","NHMSYS0000494848", "NBNSYS0000010867"))) data.frame(out) as.nbnid( data.frame(out) ) # Get all data back get_nbnid_("Zootoca vivipara") get_nbnid_("Poa annua", rows=2) get_nbnid_("Poa annua", rows=1:2) get_nbnid_(c("asdfadfasd","Pinus contorta"), rows=1:5) # use curl options invisible(get_nbnid("Quercus douglasii", verbose = TRUE)) ## End(Not run)
## Not run: get_nbnid(sci_com='Poa annua') get_nbnid(sci_com='Poa annua', rec_only=TRUE) get_nbnid(sci_com='Poa annua', rank='Species') get_nbnid(sci_com='Poa annua', rec_only=TRUE, rank='Species') get_nbnid(sci_com='Pinus contorta') # The NBN service handles common names too get_nbnid(sci_com='red-winged blackbird') # specify rows to limit choices available get_nbnid('Poa ann') get_nbnid('Poa ann', rows=1) get_nbnid('Poa ann', rows=25) get_nbnid('Poa ann', rows=1:2) # When not found get_nbnid(sci_com="uaudnadndj") get_nbnid(c("Zootoca vivipara", "uaudnadndj")) get_nbnid(c("Zootoca vivipara","Chironomus riparius", "uaudnadndj")) # Convert an nbnid without class information to a nbnid class as.nbnid(get_nbnid("Zootoca vivipara")) # already a nbnid, returns the same as.nbnid(get_nbnid(c("Zootoca vivipara","Pinus contorta"))) # same as.nbnid('NHMSYS0001706186') # character # character vector, length > 1 as.nbnid(c("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867")) # list as.nbnid(list("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867")) ## dont check, much faster as.nbnid('NHMSYS0001706186', check=FALSE) as.nbnid(list("NHMSYS0001706186","NHMSYS0000494848","NBNSYS0000010867"), check=FALSE) (out <- as.nbnid(c("NHMSYS0001706186","NHMSYS0000494848", "NBNSYS0000010867"))) data.frame(out) as.nbnid( data.frame(out) ) # Get all data back get_nbnid_("Zootoca vivipara") get_nbnid_("Poa annua", rows=2) get_nbnid_("Poa annua", rows=1:2) get_nbnid_(c("asdfadfasd","Pinus contorta"), rows=1:5) # use curl options invisible(get_nbnid("Quercus douglasii", verbose = TRUE)) ## End(Not run)
Get Kew's Plants of the World code for a taxon
get_pow( sci_com, accepted = FALSE, ask = TRUE, messages = TRUE, rows = NA, family_filter = NULL, rank_filter = NULL, x = NULL, ... ) as.pow(x, check = TRUE) ## S3 method for class 'pow' as.pow(x, check = TRUE) ## S3 method for class 'character' as.pow(x, check = TRUE) ## S3 method for class 'list' as.pow(x, check = TRUE) ## S3 method for class 'data.frame' as.pow(x, check = TRUE) ## S3 method for class 'pow' as.data.frame(x, ...) get_pow_(sci_com, messages = TRUE, rows = NA, x = NULL, ...)
get_pow( sci_com, accepted = FALSE, ask = TRUE, messages = TRUE, rows = NA, family_filter = NULL, rank_filter = NULL, x = NULL, ... ) as.pow(x, check = TRUE) ## S3 method for class 'pow' as.pow(x, check = TRUE) ## S3 method for class 'character' as.pow(x, check = TRUE) ## S3 method for class 'list' as.pow(x, check = TRUE) ## S3 method for class 'data.frame' as.pow(x, check = TRUE) ## S3 method for class 'pow' as.data.frame(x, ...) get_pow_(sci_com, messages = TRUE, rows = NA, x = NULL, ...)
sci_com |
character; A vector of common or scientific names. Or, a
|
accepted |
logical; If TRUE, removes names that are not accepted
valid names by ITIS. Set to |
ask |
logical; should |
messages |
logical; should progress be printed? |
rows |
numeric; Any number from 1 to infinity. If the default NA,
all rows are considered. Note that this function still only gives back
a pow class object with one to many identifiers. See
|
family_filter |
(character) A division (aka phylum) name to filter
data after retrieved from NCBI. Optional. See |
rank_filter |
(character) A taxonomic rank name to filter data after
retrieved from NCBI. See rank_ref for possible options.
Though note that some data sources use atypical ranks, so inspect the data
itself for options. Optional. See |
x |
For |
... |
Curl options passed on to crul::HttpClient |
check |
logical; Check if ID matches any existing on the DB, only
used in |
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
The parameters family_filter
anrank_filter
er are not
used in the search to the data provider, but are used in filtering the data down to a
subset that is closer to the target you want. For these two parameters,
you can use regex strings since we use grep()
internally to match.
Filtering narrows down to the set that matches your query, and removes the rest.
As of February 2019, KEW was limiting to 5 requests per second. Note that they may change that number in the future.
If you get errors that contain 429
you are hitting the rate limit, and you
can get around it by doing requests with Sys.sleep
in between requests.
Other pow:
pow_lookup()
,
pow_search()
,
pow_synonyms()
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: get_pow(sci_com="Helianthus") get_pow(c("Helianthus","Quercus douglasii")) # Get back a subset get_pow(sci_com="Helianthus", rows = 1) get_pow(sci_com="Helianthus", rows = 1:10) # When not found get_pow("howdy") get_pow(c("Helianthus annuus", "howdy")) # Narrow down results # to accepted names get_pow("Helianthus", accepted = TRUE) # to a kingom get_pow("Helianthus", rank_filter = "genus") # to accepted names and rank get_pow("Helianthus annuus", accepted = TRUE, rank_filter = "species") # to a family get_pow("flower", family_filter = "Acanthaceae") # Convert a pow without class information to a pow class z <- get_pow("Helianthus annuus", accepted = TRUE, rank_filter = "species") # already a pow, returns the same as.pow(z) as.pow("urn:lsid:ipni.org:names:119003-2") # character vector, length > 1 ids <- c("urn:lsid:ipni.org:names:119003-2","urn:lsid:ipni.org:names:328247-2") as.pow(ids) # list, with character strings as.pow(as.list(ids)) ## dont check, much faster as.pow("urn:lsid:ipni.org:names:119003-2", check=FALSE) as.pow(ids, check=FALSE) as.pow(as.list(ids), check=FALSE) (out <- as.pow(ids)) data.frame(out) as.pow( data.frame(out) ) # Get all data back get_pow_("Quercus", rows=1:5) get_pow_("Quercus", rows=1) get_pow_(c("Pinus", "Abies"), rows = 1:3) ## End(Not run)
## Not run: get_pow(sci_com="Helianthus") get_pow(c("Helianthus","Quercus douglasii")) # Get back a subset get_pow(sci_com="Helianthus", rows = 1) get_pow(sci_com="Helianthus", rows = 1:10) # When not found get_pow("howdy") get_pow(c("Helianthus annuus", "howdy")) # Narrow down results # to accepted names get_pow("Helianthus", accepted = TRUE) # to a kingom get_pow("Helianthus", rank_filter = "genus") # to accepted names and rank get_pow("Helianthus annuus", accepted = TRUE, rank_filter = "species") # to a family get_pow("flower", family_filter = "Acanthaceae") # Convert a pow without class information to a pow class z <- get_pow("Helianthus annuus", accepted = TRUE, rank_filter = "species") # already a pow, returns the same as.pow(z) as.pow("urn:lsid:ipni.org:names:119003-2") # character vector, length > 1 ids <- c("urn:lsid:ipni.org:names:119003-2","urn:lsid:ipni.org:names:328247-2") as.pow(ids) # list, with character strings as.pow(as.list(ids)) ## dont check, much faster as.pow("urn:lsid:ipni.org:names:119003-2", check=FALSE) as.pow(ids, check=FALSE) as.pow(as.list(ids), check=FALSE) (out <- as.pow(ids)) data.frame(out) as.pow( data.frame(out) ) # Get all data back get_pow_("Quercus", rows=1:5) get_pow_("Quercus", rows=1) get_pow_(c("Pinus", "Abies"), rows = 1:3) ## End(Not run)
Retrieve the Open Tree of Life Taxonomy (OTT) id of a taxon from OpenTreeOfLife
get_tolid(sci, ask = TRUE, messages = TRUE, rows = NA, sciname = NULL, ...) as.tolid(x, check = TRUE) ## S3 method for class 'tolid' as.tolid(x, check = TRUE) ## S3 method for class 'character' as.tolid(x, check = TRUE) ## S3 method for class 'list' as.tolid(x, check = TRUE) ## S3 method for class 'numeric' as.tolid(x, check = TRUE) ## S3 method for class 'data.frame' as.tolid(x, check = TRUE) ## S3 method for class 'tolid' as.data.frame(x, ...) get_tolid_(sci, messages = TRUE, rows = NA, sciname = NULL)
get_tolid(sci, ask = TRUE, messages = TRUE, rows = NA, sciname = NULL, ...) as.tolid(x, check = TRUE) ## S3 method for class 'tolid' as.tolid(x, check = TRUE) ## S3 method for class 'character' as.tolid(x, check = TRUE) ## S3 method for class 'list' as.tolid(x, check = TRUE) ## S3 method for class 'numeric' as.tolid(x, check = TRUE) ## S3 method for class 'data.frame' as.tolid(x, check = TRUE) ## S3 method for class 'tolid' as.data.frame(x, ...) get_tolid_(sci, messages = TRUE, rows = NA, sciname = NULL)
sci |
character; one or more scientific names. Or, a |
ask |
logical; should |
messages |
logical; should progress be printed? |
rows |
numeric; Any number from 1 to infinity. If the default NA, all
rows are considered. Note that this function still only gives back a tol
class object with one to many identifiers. See |
sciname |
Deprecated, see |
... |
Ignored |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only
used in |
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: get_tolid(sci = "Quercus douglasii") get_tolid(sci = "Chironomus riparius") get_tolid(c("Chironomus riparius","Quercus douglasii")) splist <- c("annona cherimola", 'annona muricata', "quercus robur", "shorea robusta", "pandanus patina", "oryza sativa", "durio zibethinus") get_tolid(splist, messages=FALSE) # specify rows to limit choices available get_tolid('Arni') get_tolid('Arni', rows=1) get_tolid('Arni', rows=1:2) # When not found get_tolid("howdy") get_tolid(c("Chironomus riparius", "howdy")) # Convert a tol without class information to a tol class as.tolid(get_tolid("Quercus douglasii")) # already a tol, returns the same as.tolid(get_tolid(c("Chironomus riparius","Pinus contorta"))) # same as.tolid(5907893) # numeric as.tolid(c(3930798,515712,872577)) # numeric vector, length > 1 as.tolid("3930798") # character as.tolid(c("3930798","515712","872577")) # character vector, length > 1 as.tolid(list("3930798","515712","872577")) # list, either numeric or character ## dont check, much faster as.tolid("3930798", check=FALSE) as.tolid(3930798, check=FALSE) as.tolid(c("3930798","515712","872577"), check=FALSE) as.tolid(list("3930798","515712","872577"), check=FALSE) (out <- as.tolid(c(3930798,515712,872577))) data.frame(out) as.tolid( data.frame(out) ) # Get all data back get_tolid_("Arni") get_tolid_("Arni", rows=1) get_tolid_("Arni", rows=1:2) get_tolid_(c("asdfadfasd","Pinus contorta")) ## End(Not run)
## Not run: get_tolid(sci = "Quercus douglasii") get_tolid(sci = "Chironomus riparius") get_tolid(c("Chironomus riparius","Quercus douglasii")) splist <- c("annona cherimola", 'annona muricata', "quercus robur", "shorea robusta", "pandanus patina", "oryza sativa", "durio zibethinus") get_tolid(splist, messages=FALSE) # specify rows to limit choices available get_tolid('Arni') get_tolid('Arni', rows=1) get_tolid('Arni', rows=1:2) # When not found get_tolid("howdy") get_tolid(c("Chironomus riparius", "howdy")) # Convert a tol without class information to a tol class as.tolid(get_tolid("Quercus douglasii")) # already a tol, returns the same as.tolid(get_tolid(c("Chironomus riparius","Pinus contorta"))) # same as.tolid(5907893) # numeric as.tolid(c(3930798,515712,872577)) # numeric vector, length > 1 as.tolid("3930798") # character as.tolid(c("3930798","515712","872577")) # character vector, length > 1 as.tolid(list("3930798","515712","872577")) # list, either numeric or character ## dont check, much faster as.tolid("3930798", check=FALSE) as.tolid(3930798, check=FALSE) as.tolid(c("3930798","515712","872577"), check=FALSE) as.tolid(list("3930798","515712","872577"), check=FALSE) (out <- as.tolid(c(3930798,515712,872577))) data.frame(out) as.tolid( data.frame(out) ) # Get all data back get_tolid_("Arni") get_tolid_("Arni", rows=1) get_tolid_("Arni", rows=1:2) get_tolid_(c("asdfadfasd","Pinus contorta")) ## End(Not run)
Get the NameID codes from Tropicos for taxonomic names.
get_tpsid( sci, ask = TRUE, messages = TRUE, key = NULL, rows = NA, family = NULL, rank = NULL, sciname = NULL, ... ) as.tpsid(x, check = TRUE) ## S3 method for class 'tpsid' as.tpsid(x, check = TRUE) ## S3 method for class 'character' as.tpsid(x, check = TRUE) ## S3 method for class 'list' as.tpsid(x, check = TRUE) ## S3 method for class 'numeric' as.tpsid(x, check = TRUE) ## S3 method for class 'data.frame' as.tpsid(x, check = TRUE) ## S3 method for class 'tpsid' as.data.frame(x, ...) get_tpsid_(sci, messages = TRUE, key = NULL, rows = NA, sciname = NULL, ...)
get_tpsid( sci, ask = TRUE, messages = TRUE, key = NULL, rows = NA, family = NULL, rank = NULL, sciname = NULL, ... ) as.tpsid(x, check = TRUE) ## S3 method for class 'tpsid' as.tpsid(x, check = TRUE) ## S3 method for class 'character' as.tpsid(x, check = TRUE) ## S3 method for class 'list' as.tpsid(x, check = TRUE) ## S3 method for class 'numeric' as.tpsid(x, check = TRUE) ## S3 method for class 'data.frame' as.tpsid(x, check = TRUE) ## S3 method for class 'tpsid' as.data.frame(x, ...) get_tpsid_(sci, messages = TRUE, key = NULL, rows = NA, sciname = NULL, ...)
sci |
(character) One or more scientific name's as a vector or list. Or,
a |
ask |
logical; should get_tpsid be run in interactive mode? If TRUE and more than one ID is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches. |
messages |
logical; If TRUE the actual taxon queried is printed on the console. |
key |
Your API key; see taxize-authentication |
rows |
numeric; Any number from 1 to infinity. If the default NA, all rows are considered.
Note that this function still only gives back a tpsid class object with one to many identifiers.
See |
family |
(character) A family name. Optional. See |
rank |
(character) A taxonomic rank name. See rank_ref for possible
options. Though note that some data sources use atypical ranks, so inspect the
data itself for options. Optional. See |
sciname |
Deprecated, see |
... |
Other arguments passed to |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only used in
|
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
The parameters family
anrank
nk are not used in the search to the data
provider, but are used in filtering the data down to a subset that is closer to the
target you want. For all these parameters,
you can use regex strings since we use grep()
internally to match.
Filtering narrows down to the set that matches your query, and removes the rest.
Scott Chamberlain,
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tsn()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: get_tpsid(sci='Poa annua') get_tpsid(sci='Pinus contorta') get_tpsid(c("Poa annua", "Pinus contorta")) # specify rows to limit choices available get_tpsid('Poa ann') get_tpsid('Poa ann', rows=1) get_tpsid('Poa ann', rows=25) get_tpsid('Poa ann', rows=1:2) # When not found, NA given (howdy is not a species name, and Chrinomus is a fly) get_tpsid("howdy") get_tpsid(c("Chironomus riparius", "howdy")) # Narrow down results to a division or rank, or both ## Satyrium example ### Results w/o narrowing get_tpsid("Satyrium") ### w/ rank get_tpsid("Satyrium", rank = "var.") get_tpsid("Satyrium", rank = "sp.") ## w/ family get_tpsid("Poa") get_tpsid("Poa", family = "Iridaceae") get_tpsid("Poa", family = "Orchidaceae") get_tpsid("Poa", family = "Orchidaceae", rank = "gen.") # Fuzzy filter on any filtering fields ## uses grep on the inside get_tpsid("Poa", family = "orchidaceae") get_tpsid("Aga", fuzzy = TRUE, parent = "*idae") # pass to classification function to get a taxonomic hierarchy classification(get_tpsid(sci='Poa annua')) # Convert a tpsid without class information to a tpsid class as.tpsid(get_tpsid("Pinus contorta")) # already a tpsid, returns the same as.tpsid(get_tpsid(c("Chironomus riparius","Pinus contorta"))) # same as.tpsid(24900183) # numeric as.tpsid(c(24900183,50150089,50079838)) # numeric vector, length > 1 as.tpsid("24900183") # character as.tpsid(c("24900183","50150089","50079838")) # character vector, length > 1 as.tpsid(list("24900183","50150089","50079838")) # list, either numeric or character ## dont check, much faster as.tpsid("24900183", check=FALSE) as.tpsid(24900183, check=FALSE) as.tpsid(c("24900183","50150089","50079838"), check=FALSE) as.tpsid(list("24900183","50150089","50079838"), check=FALSE) (out <- as.tpsid(c(24900183,50150089,50079838))) data.frame(out) as.tpsid( data.frame(out) ) # Get all data back get_tpsid_("Poa annua") get_tpsid_("Poa annua", rows=2) get_tpsid_("Poa annua", rows=1:2) get_tpsid_(c("asdfadfasd","Pinus contorta"), rows=1:5) # use curl options invisible(get_tpsid("Quercus douglasii", messages = TRUE)) ## End(Not run)
## Not run: get_tpsid(sci='Poa annua') get_tpsid(sci='Pinus contorta') get_tpsid(c("Poa annua", "Pinus contorta")) # specify rows to limit choices available get_tpsid('Poa ann') get_tpsid('Poa ann', rows=1) get_tpsid('Poa ann', rows=25) get_tpsid('Poa ann', rows=1:2) # When not found, NA given (howdy is not a species name, and Chrinomus is a fly) get_tpsid("howdy") get_tpsid(c("Chironomus riparius", "howdy")) # Narrow down results to a division or rank, or both ## Satyrium example ### Results w/o narrowing get_tpsid("Satyrium") ### w/ rank get_tpsid("Satyrium", rank = "var.") get_tpsid("Satyrium", rank = "sp.") ## w/ family get_tpsid("Poa") get_tpsid("Poa", family = "Iridaceae") get_tpsid("Poa", family = "Orchidaceae") get_tpsid("Poa", family = "Orchidaceae", rank = "gen.") # Fuzzy filter on any filtering fields ## uses grep on the inside get_tpsid("Poa", family = "orchidaceae") get_tpsid("Aga", fuzzy = TRUE, parent = "*idae") # pass to classification function to get a taxonomic hierarchy classification(get_tpsid(sci='Poa annua')) # Convert a tpsid without class information to a tpsid class as.tpsid(get_tpsid("Pinus contorta")) # already a tpsid, returns the same as.tpsid(get_tpsid(c("Chironomus riparius","Pinus contorta"))) # same as.tpsid(24900183) # numeric as.tpsid(c(24900183,50150089,50079838)) # numeric vector, length > 1 as.tpsid("24900183") # character as.tpsid(c("24900183","50150089","50079838")) # character vector, length > 1 as.tpsid(list("24900183","50150089","50079838")) # list, either numeric or character ## dont check, much faster as.tpsid("24900183", check=FALSE) as.tpsid(24900183, check=FALSE) as.tpsid(c("24900183","50150089","50079838"), check=FALSE) as.tpsid(list("24900183","50150089","50079838"), check=FALSE) (out <- as.tpsid(c(24900183,50150089,50079838))) data.frame(out) as.tpsid( data.frame(out) ) # Get all data back get_tpsid_("Poa annua") get_tpsid_("Poa annua", rows=2) get_tpsid_("Poa annua", rows=1:2) get_tpsid_(c("asdfadfasd","Pinus contorta"), rows=1:5) # use curl options invisible(get_tpsid("Quercus douglasii", messages = TRUE)) ## End(Not run)
Retrieve the taxonomic serial numbers (TSN) of a taxon from ITIS.
get_tsn( sci_com, searchtype = "scientific", accepted = FALSE, ask = TRUE, messages = TRUE, rows = NA, searchterm = NULL, ... ) as.tsn(x, check = TRUE) ## S3 method for class 'tsn' as.tsn(x, check = TRUE) ## S3 method for class 'character' as.tsn(x, check = TRUE) ## S3 method for class 'list' as.tsn(x, check = TRUE) ## S3 method for class 'numeric' as.tsn(x, check = TRUE) ## S3 method for class 'data.frame' as.tsn(x, check = TRUE) ## S3 method for class 'tsn' as.data.frame(x, ...) get_tsn_( sci_com, messages = TRUE, searchtype = "scientific", accepted = TRUE, rows = NA, searchterm = NULL, ... )
get_tsn( sci_com, searchtype = "scientific", accepted = FALSE, ask = TRUE, messages = TRUE, rows = NA, searchterm = NULL, ... ) as.tsn(x, check = TRUE) ## S3 method for class 'tsn' as.tsn(x, check = TRUE) ## S3 method for class 'character' as.tsn(x, check = TRUE) ## S3 method for class 'list' as.tsn(x, check = TRUE) ## S3 method for class 'numeric' as.tsn(x, check = TRUE) ## S3 method for class 'data.frame' as.tsn(x, check = TRUE) ## S3 method for class 'tsn' as.data.frame(x, ...) get_tsn_( sci_com, messages = TRUE, searchtype = "scientific", accepted = TRUE, rows = NA, searchterm = NULL, ... )
sci_com |
character; A vector of common or scientific names.
Or, a |
searchtype |
character; One of 'scientific' or 'common', or any unique abbreviation |
accepted |
logical; If TRUE, removes names that are not accepted valid
names by ITIS. Set to |
ask |
logical; should get_tsn be run in interactive mode?
If |
messages |
logical; should progress be printed? |
rows |
numeric; Any number from 1 to infinity. If the default NA, all
rows are considered. Note that this function still only gives back a tsn
class object with one to many identifiers. See
|
searchterm |
Deprecated, see |
... |
Ignored |
x |
Input to as.tsn |
check |
logical; Check if ID matches any existing on the DB, only
used in |
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_uid()
,
get_wiki()
,
get_wormsid()
## Not run: get_tsn("Quercus douglasii") get_tsn("Chironomus riparius") get_tsn(c("Chironomus riparius","Quercus douglasii")) splist <- c("annona cherimola", 'annona muricata', "quercus robur", "shorea robusta", "pandanus patina", "oryza sativa", "durio zibethinus") get_tsn(splist, messages=FALSE) # specify rows to limit choices available get_tsn('Arni') get_tsn('Arni', rows=1) get_tsn('Arni', rows=1:2) # When not found get_tsn("howdy") get_tsn(c("Chironomus riparius", "howdy")) # Using common names get_tsn("black bear", searchtype="common") # Convert a tsn without class information to a tsn class as.tsn(get_tsn("Quercus douglasii")) # already a tsn, returns the same as.tsn(get_tsn(c("Chironomus riparius","Pinus contorta"))) # same as.tsn(19322) # numeric as.tsn(c(19322,129313,506198)) # numeric vector, length > 1 as.tsn("19322") # character as.tsn(c("19322","129313","506198")) # character vector, length > 1 as.tsn(list("19322","129313","506198")) # list, either numeric or character ## dont check, much faster as.tsn("19322", check=FALSE) as.tsn(19322, check=FALSE) as.tsn(c("19322","129313","506198"), check=FALSE) as.tsn(list("19322","129313","506198"), check=FALSE) (out <- as.tsn(c(19322,129313,506198))) data.frame(out) as.tsn( data.frame(out) ) # Get all data back get_tsn_("Arni") get_tsn_("Arni", rows=1) get_tsn_("Arni", rows=1:2) get_tsn_(c("asdfadfasd","Pinus contorta"), rows=1:5) ## End(Not run)
## Not run: get_tsn("Quercus douglasii") get_tsn("Chironomus riparius") get_tsn(c("Chironomus riparius","Quercus douglasii")) splist <- c("annona cherimola", 'annona muricata', "quercus robur", "shorea robusta", "pandanus patina", "oryza sativa", "durio zibethinus") get_tsn(splist, messages=FALSE) # specify rows to limit choices available get_tsn('Arni') get_tsn('Arni', rows=1) get_tsn('Arni', rows=1:2) # When not found get_tsn("howdy") get_tsn(c("Chironomus riparius", "howdy")) # Using common names get_tsn("black bear", searchtype="common") # Convert a tsn without class information to a tsn class as.tsn(get_tsn("Quercus douglasii")) # already a tsn, returns the same as.tsn(get_tsn(c("Chironomus riparius","Pinus contorta"))) # same as.tsn(19322) # numeric as.tsn(c(19322,129313,506198)) # numeric vector, length > 1 as.tsn("19322") # character as.tsn(c("19322","129313","506198")) # character vector, length > 1 as.tsn(list("19322","129313","506198")) # list, either numeric or character ## dont check, much faster as.tsn("19322", check=FALSE) as.tsn(19322, check=FALSE) as.tsn(c("19322","129313","506198"), check=FALSE) as.tsn(list("19322","129313","506198"), check=FALSE) (out <- as.tsn(c(19322,129313,506198))) data.frame(out) as.tsn( data.frame(out) ) # Get all data back get_tsn_("Arni") get_tsn_("Arni", rows=1) get_tsn_("Arni", rows=1:2) get_tsn_(c("asdfadfasd","Pinus contorta"), rows=1:5) ## End(Not run)
Retrieve the Unique Identifier (UID) of a taxon from NCBI taxonomy browser.
get_uid( sci_com, ask = TRUE, messages = TRUE, rows = NA, modifier = NULL, rank_query = NULL, division_filter = NULL, rank_filter = NULL, key = NULL, sciname = NULL, ... ) as.uid(x, check = TRUE) ## S3 method for class 'uid' as.uid(x, check = TRUE) ## S3 method for class 'character' as.uid(x, check = TRUE) ## S3 method for class 'list' as.uid(x, check = TRUE) ## S3 method for class 'numeric' as.uid(x, check = TRUE) ## S3 method for class 'data.frame' as.uid(x, check = TRUE) ## S3 method for class 'uid' as.data.frame(x, ...) get_uid_(sci_com, messages = TRUE, rows = NA, key = NULL, sciname = NULL, ...)
get_uid( sci_com, ask = TRUE, messages = TRUE, rows = NA, modifier = NULL, rank_query = NULL, division_filter = NULL, rank_filter = NULL, key = NULL, sciname = NULL, ... ) as.uid(x, check = TRUE) ## S3 method for class 'uid' as.uid(x, check = TRUE) ## S3 method for class 'character' as.uid(x, check = TRUE) ## S3 method for class 'list' as.uid(x, check = TRUE) ## S3 method for class 'numeric' as.uid(x, check = TRUE) ## S3 method for class 'data.frame' as.uid(x, check = TRUE) ## S3 method for class 'uid' as.data.frame(x, ...) get_uid_(sci_com, messages = TRUE, rows = NA, key = NULL, sciname = NULL, ...)
sci_com |
character; scientific or common name. Or, a |
ask |
logical; should get_uid be run in interactive mode? If TRUE and more than one TSN is found for the species, the user is asked for input. If FALSE NA is returned for multiple matches. |
messages |
logical; If |
rows |
numeric; Any number from 1 to infinity. If the default NA, all
rows are considered. Note that this function still only gives back a uid
class object with one to many identifiers. See |
modifier |
(character) A modifier to the |
rank_query |
(character) A taxonomic rank name to modify the query sent
to NCBI. See rank_ref for possible options. Though note that
some data sources use atypical ranks, so inspect the data itself for
options. Optional. See |
division_filter |
(character) A division (aka phylum) name to filter
data after retrieved from NCBI. Optional. See |
rank_filter |
(character) A taxonomic rank name to filter data after
retrieved from NCBI. See rank_ref for possible options.
Though note that some data sources use atypical ranks, so inspect the data
itself for options. Optional. See |
key |
(character) NCBI Entrez API key. optional. See Details. |
sciname |
Deprecated, see |
... |
Ignored |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only used
in |
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
In case you run into errors due to your rate limit being exceeded, see
taxize_options()
, where you can set ncbi_sleep
.
The parameter rank_query
is used in the search sent
to NCBI, whereas rank_filter
filters data after it comes back. The
parameter modifier
adds modifiers to the name. For example,
modifier="Organism"
adds that to the name, giving e.g.,
Helianthus[Organism]
.
The parameters division_filter
and
rank_filter
are not used in the search to the data provider, but are
used in filtering the data down to a subset that is closer to the target
you want. For all these parameters, you can use regex strings since we use
grep()
internally to match. Filtering narrows down to the set
that matches your query, and removes the rest.
NCBI does funny things sometimes. E.g., if you search on Fringella morel, a slight misspelling of the genus name, and a non-existent epithet, NCBI gives back a morel fungal species. In addition, NCBI doesn't really do fuzzy searching very well, so if there is a slight mis-spelling in your names, you likely won't get what you are expecting. The lesson: clean your names before using this function. Other data sources are better about fuzzy matching.
See taxize-authentication for help on authentication
Note that even though you can't pass in your key to as.uid
functions,
we still use your Entrez API key if you have it saved as an R option
or environment variable.
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')
Eduard Szoecs, [email protected]
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_wiki()
,
get_wormsid()
## Not run: get_uid(c("Chironomus riparius", "Chaetopteryx")) get_uid(c("Chironomus riparius", "aaa vva")) # When not found get_uid("howdy") get_uid(c("Chironomus riparius", "howdy")) # Narrow down results to a division or rank, or both ## By modifying the query ### w/ modifiers to the name get_uid(sci_com = "Aratinga acuticauda", modifier = "Organism") get_uid(sci_com = "bear", modifier = "Common Name") ### w/ rank query get_uid(sci_com = "Pinus", rank_query = "genus") get_uid(sci_com = "Pinus", rank_query = "subgenus") ### division query doesn't really work, for unknown reasons, so not available ## By filtering the result ## Echinacea example ### Results w/o narrowing get_uid("Echinacea") ### w/ division get_uid(sci_com = "Echinacea", division_filter = "eudicots") get_uid(sci_com = "Echinacea", division_filter = "sea urchins") ## Satyrium example ### Results w/o narrowing get_uid(sci_com = "Satyrium") ### w/ division get_uid(sci_com = "Satyrium", division_filter = "monocots") get_uid(sci_com = "Satyrium", division_filter = "butterflies") ## Rank example get_uid(sci_com = "Pinus") get_uid(sci_com = "Pinus", rank_filter = "genus") get_uid(sci_com = "Pinus", rank_filter = "subgenus") # Fuzzy filter on any filtering fields ## uses grep on the inside get_uid("Satyrium", division_filter = "m") # specify rows to limit choices available get_uid('Dugesia') # user prompt needed get_uid('Dugesia', rows=1) # 2 choices, so returns only 1 row, so no choices get_uid('Dugesia', ask = FALSE) # returns NA for multiple matches # Go to a website with more info on the taxon res <- get_uid("Chironomus riparius") browseURL(attr(res, "uri")) # Convert a uid without class information to a uid class as.uid(get_uid("Chironomus riparius")) # already a uid, returns the same as.uid(get_uid(c("Chironomus riparius","Pinus contorta"))) # same as.uid(315567) # numeric as.uid(c(315567,3339,9696)) # numeric vector, length > 1 as.uid("315567") # character as.uid(c("315567","3339","9696")) # character vector, length > 1 as.uid(list("315567","3339","9696")) # list, either numeric or character ## dont check, much faster as.uid("315567", check=FALSE) as.uid(315567, check=FALSE) as.uid(c("315567","3339","9696"), check=FALSE) as.uid(list("315567","3339","9696"), check=FALSE) (out <- as.uid(c(315567,3339,9696))) data.frame(out) as.uid( data.frame(out) ) # Get all data back get_uid_("Puma concolor") get_uid_("Dugesia") get_uid_("Dugesia", rows=2) get_uid_("Dugesia", rows=1:2) get_uid_(c("asdfadfasd","Pinus contorta")) # use curl options get_uid("Quercus douglasii", verbose = TRUE) ## End(Not run)
## Not run: get_uid(c("Chironomus riparius", "Chaetopteryx")) get_uid(c("Chironomus riparius", "aaa vva")) # When not found get_uid("howdy") get_uid(c("Chironomus riparius", "howdy")) # Narrow down results to a division or rank, or both ## By modifying the query ### w/ modifiers to the name get_uid(sci_com = "Aratinga acuticauda", modifier = "Organism") get_uid(sci_com = "bear", modifier = "Common Name") ### w/ rank query get_uid(sci_com = "Pinus", rank_query = "genus") get_uid(sci_com = "Pinus", rank_query = "subgenus") ### division query doesn't really work, for unknown reasons, so not available ## By filtering the result ## Echinacea example ### Results w/o narrowing get_uid("Echinacea") ### w/ division get_uid(sci_com = "Echinacea", division_filter = "eudicots") get_uid(sci_com = "Echinacea", division_filter = "sea urchins") ## Satyrium example ### Results w/o narrowing get_uid(sci_com = "Satyrium") ### w/ division get_uid(sci_com = "Satyrium", division_filter = "monocots") get_uid(sci_com = "Satyrium", division_filter = "butterflies") ## Rank example get_uid(sci_com = "Pinus") get_uid(sci_com = "Pinus", rank_filter = "genus") get_uid(sci_com = "Pinus", rank_filter = "subgenus") # Fuzzy filter on any filtering fields ## uses grep on the inside get_uid("Satyrium", division_filter = "m") # specify rows to limit choices available get_uid('Dugesia') # user prompt needed get_uid('Dugesia', rows=1) # 2 choices, so returns only 1 row, so no choices get_uid('Dugesia', ask = FALSE) # returns NA for multiple matches # Go to a website with more info on the taxon res <- get_uid("Chironomus riparius") browseURL(attr(res, "uri")) # Convert a uid without class information to a uid class as.uid(get_uid("Chironomus riparius")) # already a uid, returns the same as.uid(get_uid(c("Chironomus riparius","Pinus contorta"))) # same as.uid(315567) # numeric as.uid(c(315567,3339,9696)) # numeric vector, length > 1 as.uid("315567") # character as.uid(c("315567","3339","9696")) # character vector, length > 1 as.uid(list("315567","3339","9696")) # list, either numeric or character ## dont check, much faster as.uid("315567", check=FALSE) as.uid(315567, check=FALSE) as.uid(c("315567","3339","9696"), check=FALSE) as.uid(list("315567","3339","9696"), check=FALSE) (out <- as.uid(c(315567,3339,9696))) data.frame(out) as.uid( data.frame(out) ) # Get all data back get_uid_("Puma concolor") get_uid_("Dugesia") get_uid_("Dugesia", rows=2) get_uid_("Dugesia", rows=1:2) get_uid_(c("asdfadfasd","Pinus contorta")) # use curl options get_uid("Quercus douglasii", verbose = TRUE) ## End(Not run)
Get the page name for a Wiki taxon
get_wiki( sci_com, wiki_site = "species", wiki = "en", ask = TRUE, messages = TRUE, limit = 100, rows = NA, x = NULL, ... ) as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'wiki' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'character' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'list' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'numeric' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'data.frame' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'wiki' as.data.frame(x, ...) get_wiki_( x, messages = TRUE, wiki_site = "species", wiki = "en", limit = 100, rows = NA, ... )
get_wiki( sci_com, wiki_site = "species", wiki = "en", ask = TRUE, messages = TRUE, limit = 100, rows = NA, x = NULL, ... ) as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'wiki' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'character' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'list' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'numeric' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'data.frame' as.wiki(x, check = TRUE, wiki_site = "species", wiki = "en") ## S3 method for class 'wiki' as.data.frame(x, ...) get_wiki_( x, messages = TRUE, wiki_site = "species", wiki = "en", limit = 100, rows = NA, ... )
sci_com |
(character) A vector of common or scientific names. Or, a
|
wiki_site |
(character) Wiki site. One of species (default), pedia, commons |
wiki |
(character) language. Default: en |
ask |
logical; should get_wiki be run in interactive mode?
If |
messages |
logical; should progress be printed? |
limit |
(integer) number of records to return |
rows |
numeric; Any number from 1 to infinity. If the default NA, all
rows are considered. Note that this function still only gives back a wiki
class object with one to many identifiers. See |
x |
For |
... |
Ignored |
check |
logical; Check if ID matches any existing on the DB, only
used in |
For wiki_site = "pedia"
, we use the english language site by
default. Set the wiki
parameter for a different language site.
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wormsid()
## Not run: get_wiki(sci_com = "Quercus douglasii") get_wiki(sci_com = "Quercu") get_wiki(sci_com = "Quercu", "pedia") get_wiki(sci_com = "Quercu", "commons") # diff. wikis with wikipedia get_wiki("Malus domestica", "pedia") get_wiki("Malus domestica", "pedia", "fr") # as coercion as.wiki("Malus_domestica") as.wiki("Malus_domestica", wiki_site = "commons") as.wiki("Malus_domestica", wiki_site = "pedia") as.wiki("Malus_domestica", wiki_site = "pedia", wiki = "fr") as.wiki("Malus_domestica", wiki_site = "pedia", wiki = "da") ## End(Not run)
## Not run: get_wiki(sci_com = "Quercus douglasii") get_wiki(sci_com = "Quercu") get_wiki(sci_com = "Quercu", "pedia") get_wiki(sci_com = "Quercu", "commons") # diff. wikis with wikipedia get_wiki("Malus domestica", "pedia") get_wiki("Malus domestica", "pedia", "fr") # as coercion as.wiki("Malus_domestica") as.wiki("Malus_domestica", wiki_site = "commons") as.wiki("Malus_domestica", wiki_site = "pedia") as.wiki("Malus_domestica", wiki_site = "pedia", wiki = "fr") as.wiki("Malus_domestica", wiki_site = "pedia", wiki = "da") ## End(Not run)
Retrieve Worms ID of a taxon from World Register of Marine Species (WORMS).
get_wormsid( sci_com, searchtype = "scientific", marine_only = TRUE, fuzzy = NULL, accepted = FALSE, ask = TRUE, messages = TRUE, rows = NA, query = NULL, ... ) as.wormsid(x, check = TRUE) ## S3 method for class 'wormsid' as.wormsid(x, check = TRUE) ## S3 method for class 'character' as.wormsid(x, check = TRUE) ## S3 method for class 'list' as.wormsid(x, check = TRUE) ## S3 method for class 'numeric' as.wormsid(x, check = TRUE) ## S3 method for class 'data.frame' as.wormsid(x, check = TRUE) ## S3 method for class 'wormsid' as.data.frame(x, ...) get_wormsid_( sci_com, messages = TRUE, searchtype = "scientific", marine_only = TRUE, fuzzy = NULL, accepted = TRUE, rows = NA, query = NULL, ... )
get_wormsid( sci_com, searchtype = "scientific", marine_only = TRUE, fuzzy = NULL, accepted = FALSE, ask = TRUE, messages = TRUE, rows = NA, query = NULL, ... ) as.wormsid(x, check = TRUE) ## S3 method for class 'wormsid' as.wormsid(x, check = TRUE) ## S3 method for class 'character' as.wormsid(x, check = TRUE) ## S3 method for class 'list' as.wormsid(x, check = TRUE) ## S3 method for class 'numeric' as.wormsid(x, check = TRUE) ## S3 method for class 'data.frame' as.wormsid(x, check = TRUE) ## S3 method for class 'wormsid' as.data.frame(x, ...) get_wormsid_( sci_com, messages = TRUE, searchtype = "scientific", marine_only = TRUE, fuzzy = NULL, accepted = TRUE, rows = NA, query = NULL, ... )
sci_com |
character; A vector of common or scientific names. Or, a
|
searchtype |
character; One of 'scientific' or 'common', or any unique abbreviation |
marine_only |
logical; marine only? default: |
fuzzy |
logical; fuzzy search. default: |
accepted |
logical; If TRUE, removes names that are not accepted valid
names by WORMS. Set to |
ask |
logical; should get_wormsid be run in interactive mode?
If |
messages |
logical; should progress be printed? |
rows |
numeric; Any number from 1 to infinity. If the default NaN, all
rows are considered. Note that this function still only gives back a wormsid
class object with one to many identifiers. See |
query |
Deprecated, see |
... |
Ignored |
x |
Input to |
check |
logical; Check if ID matches any existing on the DB, only
used in |
A vector of taxonomic identifiers as an S3 class.
If a taxon is not found an NA
is given. If more than one identifier
is found the function asks for user input if ask = TRUE
, otherwise
returns NA
. If ask=FALSE
and rows
does not equal
NA
, then a data.frame is given back, but not of the uid class, which
you can't pass on to other functions as you normally can.
See get_id_details
for further details including
attributes and exceptions
Other taxonomic-ids:
get_boldid()
,
get_eolid()
,
get_gbifid()
,
get_ids()
,
get_iucn()
,
get_natservid()
,
get_nbnid()
,
get_pow()
,
get_tolid()
,
get_tpsid()
,
get_tsn()
,
get_uid()
,
get_wiki()
## Not run: (x <- get_wormsid('Gadus morhua')) attributes(x) attr(x, "match") attr(x, "multiple_matches") attr(x, "pattern_match") attr(x, "uri") get_wormsid('Pomatomus saltatrix') get_wormsid(c("Gadus morhua", "Lichenopora neapolitana")) # marine_only get_wormsid("Apedinella", marine_only=TRUE) get_wormsid("Apedinella", marine_only=FALSE) # fuzzy ## searchtype="scientific": fuzzy is TRUE by default get_wormsid("Platypro", searchtype="scientific", fuzzy=TRUE) get_wormsid("Platypro", searchtype="scientific", fuzzy=FALSE) ## searchtype="common": fuzzy is FALSE by default get_wormsid("clam", searchtype="common", fuzzy=FALSE) get_wormsid("clam", searchtype="common", fuzzy=TRUE) # by common name get_wormsid("dolphin", 'common') get_wormsid("clam", 'common') # specify rows to limit choices available get_wormsid('Plat') get_wormsid('Plat', rows=1) get_wormsid('Plat', rows=1:2) # When not found get_wormsid("howdy") get_wormsid(c('Gadus morhua', "howdy")) # Convert a wormsid without class information to a wormsid class # already a wormsid, returns the same as.wormsid(get_wormsid('Gadus morhua')) # same as.wormsid(get_wormsid(c('Gadus morhua', 'Pomatomus saltatrix'))) # numeric as.wormsid(126436) # numeric vector, length > 1 as.wormsid(c(126436,151482)) # character as.wormsid("126436") # character vector, length > 1 as.wormsid(c("126436","151482")) # list, either numeric or character as.wormsid(list("126436","151482")) ## dont check, much faster as.wormsid("126436", check=FALSE) as.wormsid(126436, check=FALSE) as.wormsid(c("126436","151482"), check=FALSE) as.wormsid(list("126436","151482"), check=FALSE) (out <- as.wormsid(c(126436,151482))) data.frame(out) as.wormsid( data.frame(out) ) # Get all data back get_wormsid_("Plat") get_wormsid_("Plat", rows=1) get_wormsid_("Plat", rows=1:2) get_wormsid_("Plat", rows=1:75) # get_wormsid_(c("asdfadfasd","Plat"), rows=1:5) ## End(Not run)
## Not run: (x <- get_wormsid('Gadus morhua')) attributes(x) attr(x, "match") attr(x, "multiple_matches") attr(x, "pattern_match") attr(x, "uri") get_wormsid('Pomatomus saltatrix') get_wormsid(c("Gadus morhua", "Lichenopora neapolitana")) # marine_only get_wormsid("Apedinella", marine_only=TRUE) get_wormsid("Apedinella", marine_only=FALSE) # fuzzy ## searchtype="scientific": fuzzy is TRUE by default get_wormsid("Platypro", searchtype="scientific", fuzzy=TRUE) get_wormsid("Platypro", searchtype="scientific", fuzzy=FALSE) ## searchtype="common": fuzzy is FALSE by default get_wormsid("clam", searchtype="common", fuzzy=FALSE) get_wormsid("clam", searchtype="common", fuzzy=TRUE) # by common name get_wormsid("dolphin", 'common') get_wormsid("clam", 'common') # specify rows to limit choices available get_wormsid('Plat') get_wormsid('Plat', rows=1) get_wormsid('Plat', rows=1:2) # When not found get_wormsid("howdy") get_wormsid(c('Gadus morhua', "howdy")) # Convert a wormsid without class information to a wormsid class # already a wormsid, returns the same as.wormsid(get_wormsid('Gadus morhua')) # same as.wormsid(get_wormsid(c('Gadus morhua', 'Pomatomus saltatrix'))) # numeric as.wormsid(126436) # numeric vector, length > 1 as.wormsid(c(126436,151482)) # character as.wormsid("126436") # character vector, length > 1 as.wormsid(c("126436","151482")) # list, either numeric or character as.wormsid(list("126436","151482")) ## dont check, much faster as.wormsid("126436", check=FALSE) as.wormsid(126436, check=FALSE) as.wormsid(c("126436","151482"), check=FALSE) as.wormsid(list("126436","151482"), check=FALSE) (out <- as.wormsid(c(126436,151482))) data.frame(out) as.wormsid( data.frame(out) ) # Get all data back get_wormsid_("Plat") get_wormsid_("Plat", rows=1) get_wormsid_("Plat", rows=1:2) get_wormsid_("Plat", rows=1:75) # get_wormsid_(c("asdfadfasd","Plat"), rows=1:5) ## End(Not run)
Checks first to get key from your .Rprofile or .Renviron (or similar) file
getkey(x = NULL, service)
getkey(x = NULL, service)
x |
(character) An API key, defaults to |
service |
(character) The API data provider, used to match to default guest key (for Tropicos; there's no guest key for NCBI or IUCN, for which you have to get your own) |
## Not run: getkey(service="tropicos") getkey(service="iucn") getkey(service="entrez") ## End(Not run)
## Not run: getkey(service="tropicos") getkey(service="iucn") getkey(service="entrez") ## End(Not run)
Parse scientific names using Global Names Parser
gn_parse(names, ...)
gn_parse(names, ...)
names |
A vector of length 1 or more taxonomic names |
... |
Curl options passed on to crul::verb-GET |
A data.frame with results, the submitted names, and the parsed names with additional information.
http://gni.globalnames.org/
## Not run: gn_parse("Cyanistes caeruleus") gn_parse("Plantago minor") gn_parse("Plantago minor minor") gn_parse(c("Plantago minor minor","Helianthus annuus texanus")) # if > 20 names, uses an HTTP POST request x <- names_list("species", size = 30) gn_parse(x) # pass on curl options gn_parse("Cyanistes caeruleus", verbose = TRUE) ## End(Not run)
## Not run: gn_parse("Cyanistes caeruleus") gn_parse("Plantago minor") gn_parse("Plantago minor minor") gn_parse(c("Plantago minor minor","Helianthus annuus texanus")) # if > 20 names, uses an HTTP POST request x <- names_list("species", size = 30) gn_parse(x) # pass on curl options gn_parse("Cyanistes caeruleus", verbose = TRUE) ## End(Not run)
Uses the Global Names Index, see http://gni.globalnames.org/
gni_details(id, all_records = 1, ...)
gni_details(id, all_records = 1, ...)
id |
Name id. Required. |
all_records |
If all_records is 1, GNI returns all records from all repositories for the name string (takes 0, or 1 [default]). |
... |
Curl options passed on to crul::verb-GET |
Data.frame of results.
Scott Chamberlain
gnr_datasources()
, gni_search()
.
## Not run: gni_details(id = 17802847) # pass on curl options gni_details(id = 17802847, verbose = TRUE) ## End(Not run)
## Not run: gni_details(id = 17802847) # pass on curl options gni_details(id = 17802847, verbose = TRUE) ## End(Not run)
Parse scientific names using EOL's name parser.
gni_parse(names, ...)
gni_parse(names, ...)
names |
A vector of length 1 or more of taxonomic names |
... |
Curl options passed on to crul::verb-GET |
A data.frame with results, the submitted names, and the parsed names with additional information.
http://gni.globalnames.org/
## Not run: gni_parse("Cyanistes caeruleus") gni_parse("Plantago minor") gni_parse("Plantago minor minor") gni_parse(c("Plantago minor minor","Helianthus annuus texanus")) # pass on curl options gni_parse("Cyanistes caeruleus", verbose = TRUE) ## End(Not run)
## Not run: gni_parse("Cyanistes caeruleus") gni_parse("Plantago minor") gni_parse("Plantago minor minor") gni_parse(c("Plantago minor minor","Helianthus annuus texanus")) # pass on curl options gni_parse("Cyanistes caeruleus", verbose = TRUE) ## End(Not run)
Uses the Global Names Index, see http://gni.globalnames.org
gni_search( sci, per_page = NULL, page = NULL, justtotal = FALSE, parse_names = FALSE, search_term = NULL, ... )
gni_search( sci, per_page = NULL, page = NULL, justtotal = FALSE, parse_names = FALSE, search_term = NULL, ... )
sci |
(character) required. Name pattern you want to search for. WARNING: Does not work for common names. Search term may include following options (Note: can, uni, gen, sp, ssp, au, yr work only for parsed names)
|
per_page |
Number of items per one page (numbers larger than 1000 will be decreased to 1000) (default is 30). |
page |
Page number you want to see (default is 1). |
justtotal |
Return only the total results found. |
parse_names |
If |
search_term |
Deprecated, see |
... |
Curl options passed on to crul::verb-GET |
Note that you can use fuzzy searching, e.g., by attaching an asterisk to the end of a search term. See the first two examples below
data.frame of results.
Scott Chamberlain
http://gni.globalnames.org/ https://github.com/dimus/gni/wiki/api
gnr_datasources()
, gni_search()
## Not run: gni_search(sci = "ani*") gni_search(sci = "ama*", per_page = 3, page = 21) gni_search(sci = "animalia", per_page = 8, page = 1) gni_search(sci = "animalia", per_page = 8, page = 1, justtotal=TRUE) gni_search(sci = "Cyanistes caeruleus", parse_names=TRUE) # pass on curl options gni_search(sci = "ani*", verbose = TRUE) ## End(Not run)
## Not run: gni_search(sci = "ani*") gni_search(sci = "ama*", per_page = 3, page = 21) gni_search(sci = "animalia", per_page = 8, page = 1) gni_search(sci = "animalia", per_page = 8, page = 1, justtotal=TRUE) gni_search(sci = "Cyanistes caeruleus", parse_names=TRUE) # pass on curl options gni_search(sci = "ani*", verbose = TRUE) ## End(Not run)
Retrieve data sources used in the Global Names Resolver
gnr_datasources(..., todf)
gnr_datasources(..., todf)
... |
Curl options passed on to crul::HttpClient |
todf |
defunct, always get a data.frame back now |
data.frame/tibble
https://resolver.globalnames.org/data_sources
## Not run: # all data sources gnr_datasources() # give me the id for EOL out <- gnr_datasources() out[out$title == "EOL", "id"] # Fuzzy search for sources with the word zoo out <- gnr_datasources() out[agrep("zoo", out$title, ignore.case = TRUE), ] ## End(Not run)
## Not run: # all data sources gnr_datasources() # give me the id for EOL out <- gnr_datasources() out[out$title == "EOL", "id"] # Fuzzy search for sources with the word zoo out <- gnr_datasources() out[agrep("zoo", out$title, ignore.case = TRUE), ] ## End(Not run)
See section Age of datasets in the Global Names Resolver
gnr_resolve( sci, data_source_ids = NULL, resolve_once = FALSE, with_context = FALSE, canonical = FALSE, highestscore = TRUE, best_match_only = FALSE, preferred_data_sources = NULL, with_canonical_ranks = FALSE, http = "get", cap_first = TRUE, fields = "minimal", names = NULL, ... )
gnr_resolve( sci, data_source_ids = NULL, resolve_once = FALSE, with_context = FALSE, canonical = FALSE, highestscore = TRUE, best_match_only = FALSE, preferred_data_sources = NULL, with_canonical_ranks = FALSE, http = "get", cap_first = TRUE, fields = "minimal", names = NULL, ... )
sci |
character; taxonomic names to be resolved. Doesn't work for vernacular/common names. |
data_source_ids |
character; IDs to specify what data source
is searched. See |
resolve_once |
logical; Find the first available match instead of
matches across all data sources with all possible renderings of a name.
When |
with_context |
logical; Reduce the likelihood of matches to taxonomic
homonyms. When |
canonical |
logical; If |
highestscore |
logical; Return those names with the highest score for each searched name? Defunct |
best_match_only |
(logical) If |
preferred_data_sources |
(character) A vector of one or more data source IDs. |
with_canonical_ranks |
(logical) Returns names with infraspecific
ranks, if present. If |
http |
The HTTP method to use, one of "get" or "post". Default: "get".
Use |
cap_first |
(logical) For each name, fix so that the first name part is
capitalized, while others are not. This web service is sensitive to
capitalization, so you'll get different results depending on capitalization.
First name capitalized is likely what you'll want and is the default.
If |
fields |
(character) One of minimal (default) or all. Minimal gives back just four fields, whereas all gives all fields back. |
names |
Deprecated, see |
... |
Curl options passed on to crul::HttpClient |
A data.frame with one attribute not_known
: a character
vector of taxa unknown to the Global Names Index. Access like
attr(output, "not_known")
, or attributes(output)$not_known
.
Columns of the output data.frame:
user_supplied_name (character) - the name you passed in to the
names
parameter, unchanged.
submitted_name (character) - the actual name submitted to the GNR service
data_source_id (integer/numeric) - data source ID
data_source_title (character) - data source name
gni_uuid (character) - Global Names Index UUID (aka identifier)
matched_name (character) - the matched name in the GNR service
matched_name2 (character) - returned if canonical=TRUE
, in
which case matched_name is not returned
classification_path (character) - names of the taxonomic
classification tree, with names separated by pipes (|
)
classification_path_ranks (character) - ranks of the taxonomic
classification tree, with names separated by pipes (|
)
classification_path_ids (character) - identifiers of the taxonomic
classification tree, with names separated by pipes (|
)
taxon_id (character) - taxon identifier
edit_distance (integer/numeric) - edit distance
imported_at (character) - date imported
match_type (integer/numeric) - match type
match_value (character) - description of match type
prescore (character) - pre score
score (numeric) - score
local_id (character) - local identifier
url (character) - URL for taxon
global_id (character) - global identifier
current_taxon_id (character) - current taxon id
current_name_string (character) - current name string
Note that names (i.e. rows) are dropped that are NA, are zero length strings, are not character vectors, or are not found by the API.
IMPORTANT: Datasets used in the Global Names Resolver vary in how recently
they've been updated. See the updated_at
field in the
output of gnr_datasources()
for dates when each dataset
was last updated.
If preferred_data_sources
is used, only the preferred data
is returned - if it has any results.
Scott Chamberlain
http://gnrd.globalnames.org/api http://gnrd.globalnames.org/
## Not run: gnr_resolve(sci = c("Helianthus annuus", "Homo sapiens")) gnr_resolve(sci = c("Asteraceae", "Plantae")) # Using data source 12 (Encyclopedia of Life) sources <- gnr_datasources() sources eol <- sources$id[sources$title == 'EOL'] gnr_resolve(names=c("Helianthos annuus","Homo sapians"), data_source_ids=eol) # Two species in the NE Brazil catalogue sps <- c('Justicia brasiliana','Schinopsis brasiliensis') gnr_resolve(sci = sps, data_source_ids = 145) # Best match only, compare the two gnr_resolve(sci = "Helianthus annuus", best_match_only = FALSE) gnr_resolve(sci = "Helianthus annuus", best_match_only = TRUE) # Preferred data source gnr_resolve(sci = "Helianthus annuus", preferred_data_sources = c(3,4)) # Return canonical names - default is canonical=FALSE head(gnr_resolve(sci = "Helianthus annuus")) head(gnr_resolve(sci = "Helianthus annuus", canonical=TRUE)) # Return canonical names with authority stripped but # ranks still present gnr_resolve("Scorzonera hispanica L. subsp. asphodeloides Wallr.") ## vs. gnr_resolve("Scorzonera hispanica L. subsp. asphodeloides Wallr.", with_canonical_ranks = TRUE) ## End(Not run)
## Not run: gnr_resolve(sci = c("Helianthus annuus", "Homo sapiens")) gnr_resolve(sci = c("Asteraceae", "Plantae")) # Using data source 12 (Encyclopedia of Life) sources <- gnr_datasources() sources eol <- sources$id[sources$title == 'EOL'] gnr_resolve(names=c("Helianthos annuus","Homo sapians"), data_source_ids=eol) # Two species in the NE Brazil catalogue sps <- c('Justicia brasiliana','Schinopsis brasiliensis') gnr_resolve(sci = sps, data_source_ids = 145) # Best match only, compare the two gnr_resolve(sci = "Helianthus annuus", best_match_only = FALSE) gnr_resolve(sci = "Helianthus annuus", best_match_only = TRUE) # Preferred data source gnr_resolve(sci = "Helianthus annuus", preferred_data_sources = c(3,4)) # Return canonical names - default is canonical=FALSE head(gnr_resolve(sci = "Helianthus annuus")) head(gnr_resolve(sci = "Helianthus annuus", canonical=TRUE)) # Return canonical names with authority stripped but # ranks still present gnr_resolve("Scorzonera hispanica L. subsp. asphodeloides Wallr.") ## vs. gnr_resolve("Scorzonera hispanica L. subsp. asphodeloides Wallr.", with_canonical_ranks = TRUE) ## End(Not run)
Taxonomic IDs to taxonomic names
id2name(id, db = NULL, x = NULL, ...) ## Default S3 method: id2name(id, db = NULL, x = NULL, ...) ## S3 method for class 'tolid' id2name(id, ...) ## S3 method for class 'tsn' id2name(id, ...) ## S3 method for class 'uid' id2name(id, ...) ## S3 method for class 'wormsid' id2name(id, ...) ## S3 method for class 'gbifid' id2name(id, ...) ## S3 method for class 'boldid' id2name(id, ...)
id2name(id, db = NULL, x = NULL, ...) ## Default S3 method: id2name(id, db = NULL, x = NULL, ...) ## S3 method for class 'tolid' id2name(id, ...) ## S3 method for class 'tsn' id2name(id, ...) ## S3 method for class 'uid' id2name(id, ...) ## S3 method for class 'wormsid' id2name(id, ...) ## S3 method for class 'gbifid' id2name(id, ...) ## S3 method for class 'boldid' id2name(id, ...)
id |
vector of taxonomic IDs (character or numeric) |
db |
(character) database to query. One or more of |
x |
Deprecated, see |
... |
Further args passed on to |
A named list of data.frames, named by the input taxonomic ids
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: # ITIS id2name(19322, db = "itis") # TOL id2name(515698, db = "tol") # get NCBI ID and pass to classification() x <- id2name(515698, db = "tol") classification(as.uid(x[[1]]$tax_sources_ncbi)) # NCBI id2name(315567, db = "ncbi") id2name(3339, db = "ncbi") id2name(9696, db = "ncbi") id2name(c(9695, 9696), db = "ncbi") # WORMS id2name(105706, db = "worms") # GBIF id2name(2441176, db = "gbif") # BOLD id2name(88899, db = "bold") ## End(Not run)
## Not run: # ITIS id2name(19322, db = "itis") # TOL id2name(515698, db = "tol") # get NCBI ID and pass to classification() x <- id2name(515698, db = "tol") classification(as.uid(x[[1]]$tax_sources_ncbi)) # NCBI id2name(315567, db = "ncbi") id2name(3339, db = "ncbi") id2name(9696, db = "ncbi") id2name(c(9695, 9696), db = "ncbi") # WORMS id2name(105706, db = "worms") # GBIF id2name(2441176, db = "gbif") # BOLD id2name(88899, db = "bold") ## End(Not run)
ION - Index to Organism Names
ion(x, ...)
ion(x, ...)
x |
An LSID number. Required. |
... |
Curl options passed on to crul::verb-GET |
A data.frame
http://www.organismnames.com
## Not run: ion(155166) ion(298678) ion(4796748) # ursus americanus ion(1280626) # puma concolor ## End(Not run)
## Not run: ion(155166) ion(298678) ion(4796748) # ursus americanus ion(1280626) # puma concolor ## End(Not run)
iPlant name resolution
iplant_resolve(sci, retrieve = "all", query = NULL, ...)
iplant_resolve(sci, retrieve = "all", query = NULL, ...)
sci |
Vector of one or more taxonomic names (no common names) |
retrieve |
Specifies whether to retrieve all matches for the names submitted. One of 'best' (retrieves only the single best match for each name submitted) or 'all' (retrieves all matches) |
query |
Deprecated, see |
... |
Curl options passed on to crul::verb-GET |
A data.frame
## Not run: iplant_resolve(sci=c("Helianthus annuus", "Homo sapiens")) iplant_resolve("Helianthusss") iplant_resolve("Pooa") iplant_resolve("Helianthusss", verbose = TRUE) ## End(Not run)
## Not run: iplant_resolve(sci=c("Helianthus annuus", "Homo sapiens")) iplant_resolve("Helianthusss") iplant_resolve("Pooa") iplant_resolve("Helianthusss", verbose = TRUE) ## End(Not run)
Note: This data source is also provided in the Global Names Index (GNI) (http://gni.globalnames.org/data_sources). The interface to the data is different among the two services though.
ipni_search( family = NULL, infrafamily = NULL, genus = NULL, infragenus = NULL, species = NULL, infraspecies = NULL, publicationtitle = NULL, authorabbrev = NULL, includepublicationauthors = NULL, includebasionymauthors = NULL, geounit = NULL, addedsince = NULL, modifiedsince = NULL, isapnirecord = NULL, isgcirecord = NULL, isikrecord = NULL, ranktoreturn = NULL, output = "minimal", ... )
ipni_search( family = NULL, infrafamily = NULL, genus = NULL, infragenus = NULL, species = NULL, infraspecies = NULL, publicationtitle = NULL, authorabbrev = NULL, includepublicationauthors = NULL, includebasionymauthors = NULL, geounit = NULL, addedsince = NULL, modifiedsince = NULL, isapnirecord = NULL, isgcirecord = NULL, isikrecord = NULL, ranktoreturn = NULL, output = "minimal", ... )
family |
Family name to search on (Optional) |
infrafamily |
Infrafamilial name to search on (Optional) |
genus |
Genus name to search on (Optional) |
infragenus |
Infrageneric name to search on (Optional) |
species |
Species name to search on (Optional) - Note, this is the epithet, not the full genus - epithet name combination. |
infraspecies |
Infraspecies name to search on (Optional) |
publicationtitle |
Publication name or abbreviation to search on. Again, replace any spaces with a '+' (e.g. 'J.+Bot.') (Optional) |
authorabbrev |
Author standard form to search on (publishing author, basionym author or both - see below) (Optional) |
includepublicationauthors |
TRUE (default) to include the taxon author in the search or FALSE to exclude it |
includebasionymauthors |
TRUE (default) to include the basionum author in the search or FALSE to exclude it |
geounit |
Country name or other geographical unit to search on (see the help pages for more information and warnings about the use of this option) (Optional) |
addedsince |
Date to search on in the format 'yyyy-mm-dd', e.g. 2005-08-01 for all records added since the first of August, 2005. (see the help pages for more information and warnings about the use of this option) (Optional. If supplied must be in format YYYY-MM-DD and must be greater than or equal to 1984-01-01.) |
modifiedsince |
Date to search on in the format 'yyyy-mm-dd', e.g. 2005-08-01 for all records edited since the first of August, 2005. (See the help pages for more information about the use of this option) (Optional. If supplied must be in format YYYY-MM-DD and must be greater than or equal to 1993-01-01.) |
isapnirecord |
FALSE (default) to exclude records from the Australian Plant Name Index |
isgcirecord |
FALSE (default) to exclude records from the Gray Cards Index |
isikrecord |
FALSE (default) to exclude records from the Index Kewensis |
ranktoreturn |
One of a few options to choose the ranks returned. See details. |
output |
One of minimal (default), classic, short, or extended |
... |
Curl options passed on to crul::verb-GET (Optional). Default: returns all ranks. |
ranktoreturn
options:
"all" - all records
"fam" - family records
"infrafam" - infrafamilial records
"gen" - generic records
"infragen" - infrageneric records
"spec" - species records
"infraspec" - infraspecific records
a tibble (data.frame)
https://web.archive.org/web/20190501132148/http://www.ipni.org/link_to_ipni.html
## Not run: ipni_search(genus='Brintonia', isapnirecord=TRUE, isgcirecord=TRUE, isikrecord=TRUE) ipni_search(genus='Ceanothus') ipni_search(genus='Pinus', species='contorta') # Different output formats ipni_search(genus='Ceanothus') ipni_search(genus='Ceanothus', output='short') ipni_search(genus='Ceanothus', output='extended') ## End(Not run)
## Not run: ipni_search(genus='Brintonia', isapnirecord=TRUE, isgcirecord=TRUE, isikrecord=TRUE) ipni_search(genus='Ceanothus') ipni_search(genus='Pinus', species='contorta') # Different output formats ipni_search(genus='Ceanothus') ipni_search(genus='Ceanothus', output='short') ipni_search(genus='Ceanothus', output='extended') ## End(Not run)
Retrieve accepted TSN and name
itis_acceptname(searchtsn, ...)
itis_acceptname(searchtsn, ...)
searchtsn |
One or more TSN for a taxon (numeric/integer) |
... |
Curl options passed on tocrul::verb-GET |
data.frame with with row number equal to input vector length, and with three columns:
submittedtsn (numeric) - The submitted TSN
acceptedname (character) - The accepted name - if the submitted TSN
is the accepted TSN, then this is NA_character_
because ITIS does
not return a name along with the TSN if it's an accepted name. We could
make an extra HTTP request to ITIS, but that means additional time.
acceptedtsn (numeric) - The accepted TSN
author (character) - taxonomic authority
## Not run: # TSN accepted - good name itis_acceptname(searchtsn = 208527) # TSN not accepted - input TSN is old itis_acceptname(searchtsn = 504239) # many accepted names ids <- c(18161, 18162, 18163, 18164, 18165, 18166, 46173, 46174, 46178, 46181, 46186, 46193, 46196, 46197, 46200, 46201, 46204, 46207, 46867, 46868) itis_acceptname(searchtsn = ids) # many unaccepted names ids <- c(39087, 46208, 46973, 46976, 46978, 46980, 47295, 47445, 47448, 47512, 47515, 47527, 47546, 47622, 47783, 47786, 47787, 47788, 47835, 47839) itis_acceptname(searchtsn = ids) # many: mix of accepted and unaccepted names ids <- c(18161, 18162, 47527, 47546, 47622, 46200) itis_acceptname(searchtsn = ids) ## End(Not run)
## Not run: # TSN accepted - good name itis_acceptname(searchtsn = 208527) # TSN not accepted - input TSN is old itis_acceptname(searchtsn = 504239) # many accepted names ids <- c(18161, 18162, 18163, 18164, 18165, 18166, 46173, 46174, 46178, 46181, 46186, 46193, 46196, 46197, 46200, 46201, 46204, 46207, 46867, 46868) itis_acceptname(searchtsn = ids) # many unaccepted names ids <- c(39087, 46208, 46973, 46976, 46978, 46980, 47295, 47445, 47448, 47512, 47515, 47527, 47546, 47622, 47783, 47786, 47787, 47788, 47835, 47839) itis_acceptname(searchtsn = ids) # many: mix of accepted and unaccepted names ids <- c(18161, 18162, 47527, 47546, 47622, 46200) itis_acceptname(searchtsn = ids) ## End(Not run)
Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.
itis_downstream(id, downto, intermediate = FALSE, tsns = NULL, ...)
itis_downstream(id, downto, intermediate = FALSE, tsns = NULL, ...)
id |
A taxonomic serial number. |
downto |
The taxonomic level you want to go down to. See examples below.
The taxonomic level IS case sensitive, and you do have to spell it
correctly. See |
intermediate |
(logical) If TRUE, return a list of length two with target taxon rank names, with additional list of data.frame's of intermediate taxonomic groups. Default: FALSE |
tsns |
Deprecated, see |
... |
Further args passed on to |
Data.frame of taxonomic information downstream to family from e.g.,
Order, Class, etc., or if intermediated=TRUE
, list of length two,
with target taxon rank names, and intermediate names.
## Not run: ## the plant class Bangiophyceae, tsn 846509 itis_downstream(id = 846509, downto="genus") itis_downstream(id = 846509, downto="genus", intermediate=TRUE) # get families downstream from Acridoidea itis_downstream(id = 650497, "family") ## here, intermediate leads to the same result as the target itis_downstream(id = 650497, "family", intermediate=TRUE) # get species downstream from Ursus itis_downstream(id = 180541, "species") # get orders down from the Division Rhodophyta (red algae) itis_downstream(id = 660046, "order") itis_downstream(id = 660046, "order", intermediate=TRUE) # get tribes down from the family Apidae itis_downstream(id = 154394, downto="tribe") itis_downstream(id = 154394, downto="tribe", intermediate=TRUE) ## End(Not run)
## Not run: ## the plant class Bangiophyceae, tsn 846509 itis_downstream(id = 846509, downto="genus") itis_downstream(id = 846509, downto="genus", intermediate=TRUE) # get families downstream from Acridoidea itis_downstream(id = 650497, "family") ## here, intermediate leads to the same result as the target itis_downstream(id = 650497, "family", intermediate=TRUE) # get species downstream from Ursus itis_downstream(id = 180541, "species") # get orders down from the Division Rhodophyta (red algae) itis_downstream(id = 660046, "order") itis_downstream(id = 660046, "order", intermediate=TRUE) # get tribes down from the family Apidae itis_downstream(id = 154394, downto="tribe") itis_downstream(id = 154394, downto="tribe", intermediate=TRUE) ## End(Not run)
Get full ITIS record for one or more ITIS TSN's or lsid's.
itis_getrecord(values, by = "tsn", ...)
itis_getrecord(values, by = "tsn", ...)
values |
(character) One or more TSN's (taxonomic serial number) or lsid's for a taxonomic group |
by |
(character) By "tsn" (default) or "lsid" |
... |
Further arguments passed on to ritis::full_record |
You can only enter values in tsn parameter or lsid, not both.
## Not run: # by TSN itis_getrecord(202385) itis_getrecord(c(202385,70340)) # by lsid itis_getrecord("urn:lsid:itis.gov:itis_tsn:202385", "lsid") ## End(Not run)
## Not run: # by TSN itis_getrecord(202385) itis_getrecord(c(202385,70340)) # by lsid itis_getrecord("urn:lsid:itis.gov:itis_tsn:202385", "lsid") ## End(Not run)
Get hierarchies from TSN values, full, upstream only, or immediate downstream only
itis_hierarchy(tsn, what = "full", ...)
itis_hierarchy(tsn, what = "full", ...)
tsn |
One or more TSN's (taxonomic serial number). Required. |
what |
One of full (full hierarchy), up (immediate upstream), or down (immediate downstream) |
... |
Further arguments passed on to |
Note that itis_downstream()
gets taxa downstream to a
particular rank, while this function only gets immediate names downstream.
## Not run: # Get full hierarchy itis_hierarchy(tsn=180543) # Get hierarchy upstream itis_hierarchy(tsn=180543, "up") # Get hierarchy downstream itis_hierarchy(tsn=180543, "down") # Many tsn's itis_hierarchy(tsn=c(180543,41074,36616)) ## End(Not run)
## Not run: # Get full hierarchy itis_hierarchy(tsn=180543) # Get hierarchy upstream itis_hierarchy(tsn=180543, "up") # Get hierarchy downstream itis_hierarchy(tsn=180543, "down") # Many tsn's itis_hierarchy(tsn=c(180543,41074,36616)) ## End(Not run)
Get kingdom names
itis_kingdomnames(tsn = NULL, ...)
itis_kingdomnames(tsn = NULL, ...)
tsn |
One or more TSN's (taxonomic serial number) |
... |
Further arguments passed on to getkingdomnamefromtsn |
## Not run: itis_kingdomnames(202385) itis_kingdomnames(tsn=c(202385,183833,180543)) ## End(Not run)
## Not run: itis_kingdomnames(202385) itis_kingdomnames(tsn=c(202385,183833,180543)) ## End(Not run)
Get TSN from LSID
itis_lsid(lsid = NULL, what = "tsn", ...)
itis_lsid(lsid = NULL, what = "tsn", ...)
lsid |
One or more lsid's |
what |
What to retrieve. One of tsn, record, or fullrecord |
... |
Further arguments passed on to |
## Not run: # Get TSN itis_lsid("urn:lsid:itis.gov:itis_tsn:180543") itis_lsid(lsid=c("urn:lsid:itis.gov:itis_tsn:180543","urn:lsid:itis.gov:itis_tsn:28726")) # Get partial record itis_lsid("urn:lsid:itis.gov:itis_tsn:180543", "record") # Get full record itis_lsid("urn:lsid:itis.gov:itis_tsn:180543", "fullrecord") # An invalid lsid (a tsn actually) itis_lsid(202385) ## End(Not run)
## Not run: # Get TSN itis_lsid("urn:lsid:itis.gov:itis_tsn:180543") itis_lsid(lsid=c("urn:lsid:itis.gov:itis_tsn:180543","urn:lsid:itis.gov:itis_tsn:28726")) # Get partial record itis_lsid("urn:lsid:itis.gov:itis_tsn:180543", "record") # Get full record itis_lsid("urn:lsid:itis.gov:itis_tsn:180543", "fullrecord") # An invalid lsid (a tsn actually) itis_lsid(202385) ## End(Not run)
Get taxonomic names for a given taxonomic name query.
itis_name(query = NULL, get = NULL)
itis_name(query = NULL, get = NULL)
query |
TSN number (taxonomic serial number). |
get |
The rank of the taxonomic name to get. |
Taxonomic name for the searched taxon.
## Not run: itis_name(query="Helianthus annuus", get="family") ## End(Not run)
## Not run: itis_name(query="Helianthus annuus", get="family") ## End(Not run)
Get jurisdiction data, i.e., native or not native in a region.
itis_native(tsn = NULL, what = "bytsn", ...)
itis_native(tsn = NULL, what = "bytsn", ...)
tsn |
One or more TSN's (taxonomic serial number) |
what |
One of bytsn, values, or originvalues |
... |
Further arguments passed on to
|
## Not run: # Get values itis_native(what="values") # Get origin values itis_native(what="originvalues") # Get values by tsn itis_native(tsn=180543) itis_native(tsn=c(180543,41074,36616)) ## End(Not run)
## Not run: # Get values itis_native(what="values") # Get origin values itis_native(what="originvalues") # Get values by tsn itis_native(tsn=180543) itis_native(tsn=c(180543,41074,36616)) ## End(Not run)
Get references related to a ITIS TSN.
itis_refs(tsn, ...)
itis_refs(tsn, ...)
tsn |
One or more TSN's (taxonomic serial number) for a taxonomic group (numeric) |
... |
Further arguments passed on to getpublicationsfromtsn |
## Not run: itis_refs(202385) itis_refs(c(202385, 70340)) ## End(Not run)
## Not run: itis_refs(202385) itis_refs(c(202385, 70340)) ## End(Not run)
Retrieve taxonomic rank name from given TSN.
itis_taxrank(query = NULL, ...)
itis_taxrank(query = NULL, ...)
query |
TSN for a taxonomic group (numeric). If query is left as default
(NULL), you get all possible rank names, and their TSN's (using function
|
... |
Further arguments passed on to |
You can print messages by setting verbose=FALSE
.
Taxonomic rank names or data.frame of all ranks.
## Not run: # All ranks itis_taxrank() # A single TSN itis_taxrank(query=202385) # Many TSN's itis_taxrank(query=c(202385,183833,180543)) ## End(Not run)
## Not run: # All ranks itis_taxrank() # A single TSN itis_taxrank(query=202385) # Many TSN's itis_taxrank(query=c(202385,183833,180543)) ## End(Not run)
Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.
itis_terms(query, what = "both", ...)
itis_terms(query, what = "both", ...)
query |
One or more common or scientific names, or partial names |
what |
One of both (search common and scientific names), common (search just common names), or scientific (search just scientific names) |
... |
Further arguments passed on to |
## Not run: # Get terms searching both common and scientific names itis_terms(query='bear') # Get terms searching just common names itis_terms(query='tarweed', "common") # Get terms searching just scientific names itis_terms(query='Poa annua', "scientific") ## End(Not run)
## Not run: # Get terms searching both common and scientific names itis_terms(query='bear') # Get terms searching just common names itis_terms(query='tarweed', "common") # Get terms searching just scientific names itis_terms(query='Poa annua', "scientific") ## End(Not run)
Get any matching IUCN species names
iucn_getname(name, verbose = TRUE, ...)
iucn_getname(name, verbose = TRUE, ...)
name |
character; taxon name |
verbose |
logical; should messages be printed? |
... |
Further arguments passed on to |
Beware: IUCN functions can give back incorrect data. This isn't our fault. We do our best to get you the correct data quickly, but sometimes IUCN gives back the wrong data, and sometimes Global Names gives back the wrong data. We will fix these as soon as possible. In the meantime, just make sure that the data you get back is correct.
Character vector of names that matched in IUCN
## Not run: iucn_getname(name = "Cyanistes caeruleus") iucn_getname(name = "Panthera uncia") # not found in global names # iucn_getname(name = "Abronia pinsapo") # not found in IUCN search iucn_getname(name = "Acacia allenii") ## End(Not run)
## Not run: iucn_getname(name = "Cyanistes caeruleus") iucn_getname(name = "Panthera uncia") # not found in global names # iucn_getname(name = "Abronia pinsapo") # not found in IUCN search iucn_getname(name = "Acacia allenii") ## End(Not run)
Get an ID for a IUCN listed taxon
iucn_id(sciname, key = NULL, ...)
iucn_id(sciname, key = NULL, ...)
sciname |
character; Scientific name. Should be cleand and in the
format |
key |
(character) required. you IUCN Redlist API key. See rredlist::rredlist-package for help on authenticating with IUCN Redlist |
... |
Curl options passed on to crul::HttpClient |
A named list (names are input taxa names) of one or more IUCN IDs. Taxa that aren't found are silently dropped.
Scott Chamberlain,
## Not run: iucn_id("Branta canadensis") iucn_id("Branta bernicla") iucn_id("Panthera uncia") iucn_id("Lynx lynx") # many names iucn_id(c("Panthera uncia", "Lynx lynx")) # many names, some not found iucn_id(c("Panthera uncia", "Lynx lynx", "foo bar", "hello world")) # a name not found iucn_id("Foo bar") ## End(Not run)
## Not run: iucn_id("Branta canadensis") iucn_id("Branta bernicla") iucn_id("Panthera uncia") iucn_id("Lynx lynx") # many names iucn_id(c("Panthera uncia", "Lynx lynx")) # many names, some not found iucn_id(c("Panthera uncia", "Lynx lynx", "foo bar", "hello world")) # a name not found iucn_id("Foo bar") ## End(Not run)
iucn
-class.Extractor functions for iucn
-class.
iucn_status(x, ...)
iucn_status(x, ...)
x |
an |
... |
Currently not used |
A character vector with the status.
## Not run: ia <- iucn_summary(c("Panthera uncia", "Lynx lynx")) iucn_status(ia) ## End(Not run)
## Not run: ia <- iucn_summary(c("Panthera uncia", "Lynx lynx")) iucn_status(ia) ## End(Not run)
Get a summary from the IUCN Red List (https://www.iucnredlist.org/).
iucn_summary(x, distr_detail = FALSE, key = NULL, ...)
iucn_summary(x, distr_detail = FALSE, key = NULL, ...)
x |
character; Scientific name. Should be cleaned and in the
format |
distr_detail |
logical; If |
key |
a Redlist API key, get one from
https://apiv3.iucnredlist.org/api/v3/token Required for
|
... |
curl options passed on to crul::verb-GET |
Beware: IUCN functions can give back incorrect data. This isn't our fault. We do our best to get you the correct data quickly, but sometimes IUCN gives back the wrong data, and sometimes Global Names gives back the wrong data. We will fix these as soon as possible. In the meantime, just make sure that the data you get back is correct.
iucn_summary
has a default method that errors when anything's
passed in that's not character
or iucn
class - a
iucn_summary.character
method for when you pass in taxon names -
and a iucn_summary.iucn
method so you can pass in iucn class objects
as output from get_iucn()
or as.iucn()
. If you
already have IUCN IDs, coerce them to iucn
class via
as.iucn(..., check = FALSE)
A list (for every species one entry) of lists with the following items:
status
Red List Category.
history
History of status, if available.
distr
Geographic distribution, if available.
trend
Trend of population size, if available.
iucn_summary
uses the new Redlist API for searching for a IUCN ID, so we
use the rl_search()
function internally. This function
requires an API key. Get the key at https://apiv3.iucnredlist.org/api/v3/token,
and pass it to the key
parameter, or store in your .Renviron
file like
IUCN_REDLIST_KEY=yourkey
or in your .Rprofile
file like
options(iucn_redlist_key="yourkey")
. We strongly encourage you to not pass
the key in the function call but rather store it in one of those two files.
This key will also set you up to use the rredlist package.
Not all entries (history, distr, trend) are available for every species
and NA is returned.
iucn_status()
is an extractor function to easily extract
status into a vector.
Eduard Szoecs, [email protected]
Philippe Marchand, [email protected]
Scott Chamberlain,
## Not run: # if you send a taxon name, an IUCN API key is required ## here, the key is being detected from a .Rprofile file ## or .Renviron file, See "Redlist Authentication" above iucn_summary("Lutra lutra") ia <- iucn_summary(c("Panthera uncia", "Lynx lynx")) ia <- iucn_summary(c("Panthera uncia", "Lynx lynx", "aaa")) iucn_summary("Muntiacus rooseveltorum/truongsonensis") iucn_summary(c("Muntiacus rooseveltorum/truongsonensis", "Lynx lynx")) ## get detailed distribution iac <- iucn_summary(x="Ara chloropterus", distr_detail = TRUE) iac[[1]]$distr # If you pass in an IUCN ID, you don't need to pass in a Redlist API Key # extract status iucn_status(iac) ## End(Not run)
## Not run: # if you send a taxon name, an IUCN API key is required ## here, the key is being detected from a .Rprofile file ## or .Renviron file, See "Redlist Authentication" above iucn_summary("Lutra lutra") ia <- iucn_summary(c("Panthera uncia", "Lynx lynx")) ia <- iucn_summary(c("Panthera uncia", "Lynx lynx", "aaa")) iucn_summary("Muntiacus rooseveltorum/truongsonensis") iucn_summary(c("Muntiacus rooseveltorum/truongsonensis", "Lynx lynx")) ## get detailed distribution iac <- iucn_summary(x="Ara chloropterus", distr_detail = TRUE) iac[[1]]$distr # If you pass in an IUCN ID, you don't need to pass in a Redlist API Key # extract status iucn_status(iac) ## End(Not run)
Sets up authentication to diverse providers by providing the user a detailed prompt.
use_tropicos() use_entrez() use_iucn()
use_tropicos() use_entrez() use_iucn()
Key helpers
use_tropicos()
Browses to Tropicos API key request URL and provides instruction on how to store the key. After filling the form you will get the key soon, but not immediately.
use_entrez()
Browse NCBI Entrez to help make an API key request and provides instruction on how to store the key. There's no direct URL to request a key, one first needs to log in or register and then to generate a key from one's account.
Note that NCBI Entrez doesn't require that you use an API key, but you should get higher rate limit with a key, so do get one.
use_iucn()
Browse IUCN Red List API key request URL and provides instruction on how
to store the key. This function wraps rredlist::rl_use_iucn()
from the rredlist
package. After filling the form you will get
the key soon, but not immediately.
Retrieve the lowest common taxon and rank for a given taxon name or ID
lowest_common(...) ## Default S3 method: lowest_common( sci_id, db = NULL, rows = NA, class_list = NULL, low_rank = NULL, x = NULL, ... ) ## S3 method for class 'uid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'tsn' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'gbifid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'tolid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...)
lowest_common(...) ## Default S3 method: lowest_common( sci_id, db = NULL, rows = NA, class_list = NULL, low_rank = NULL, x = NULL, ... ) ## S3 method for class 'uid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'tsn' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'gbifid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'tolid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...)
... |
Other arguments passed to |
sci_id |
Vector of taxa names (character) or id (character or numeric) to query. |
db |
character; database to query. either |
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 of any of the acceptable classes: tsn, gbifid, tolid. NCBI has a method for this function but rows doesn't work. |
class_list |
(list) A list of classifications, as returned from
|
low_rank |
(character) taxonomic rank to return, of length 1 |
x |
Deprecated, see |
NA when no match, or a data.frame with columns
name
rank
id
See taxize-authentication for help on authentication
Jimmy O'Donnell [email protected] Scott Chamberlain
## Not run: id <- c("9031", "9823", "9606", "9470") id_class <- classification(id, db = 'ncbi') lowest_common(id[2:4], db = "ncbi") lowest_common(id[2:4], db = "ncbi", low_rank = 'class') lowest_common(id[2:4], db = "ncbi", low_rank = 'family') lowest_common(id[2:4], class_list = id_class) lowest_common(id[2:4], class_list = id_class, low_rank = 'class') lowest_common(id[2:4], class_list = id_class, low_rank = 'family') # TOL taxa <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") (cls <- classification(taxa, db = "tol")) lowest_common(taxa, db = "tol", class_list = cls) lowest_common(get_tolid(taxa), class_list = cls) xx <- get_tolid(taxa) lowest_common(xx, class_list = cls) spp <- c("Sus scrofa", "Homo sapiens", "Nycticebus coucang") lowest_common(spp, db = "ncbi") lowest_common(get_uid(spp)) lowest_common(spp, db = "itis") lowest_common(get_tsn(spp)) gbifid <- c("2704179", "3119195") lowest_common(gbifid, db = "gbif") spp <- c("Poa annua", "Helianthus annuus") lowest_common(spp, db = "gbif") lowest_common(get_gbifid(spp)) cool_orchid <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") orchid_ncbi <- get_uid(cool_orchid) orchid_gbif <- get_gbifid(cool_orchid) cool_orchids2 <- c("Domingoa haematochila", "Gymnadenia conopsea", "Masdevallia coccinea") orchid_itis <- get_tsn(cool_orchids2) orchid_hier_ncbi <- classification(orchid_ncbi, db = 'ncbi') orchid_hier_gbif <- classification(orchid_gbif, db = 'gbif') orchid_hier_itis <- classification(orchid_itis, db = 'itis') lowest_common(orchid_ncbi, low_rank = 'class') lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi, low_rank = 'class') lowest_common(orchid_gbif, low_rank = 'class') lowest_common(orchid_gbif, orchid_hier_gbif, low_rank = 'class') lowest_common(get_uid(cool_orchid), low_rank = 'class') lowest_common(get_uid(cool_orchid), low_rank = 'family') lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi, low_rank = 'subfamily') lowest_common(orchid_gbif, class_list = orchid_hier_gbif, low_rank = 'subfamily') lowest_common(orchid_itis, class_list = orchid_hier_itis, low_rank = 'class') ## Pass in sci. names nms <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") lowest_common(x = nms, db = "ncbi") lowest_common(x = nms, db = "gbif") # lowest_common(x = nms, db = "itis") ## NAs due to taxon not found, stops with error message # lowest_common(orchid_itis, db = "itis") # lowest_common(get_tsn(cool_orchid)) ## End(Not run)
## Not run: id <- c("9031", "9823", "9606", "9470") id_class <- classification(id, db = 'ncbi') lowest_common(id[2:4], db = "ncbi") lowest_common(id[2:4], db = "ncbi", low_rank = 'class') lowest_common(id[2:4], db = "ncbi", low_rank = 'family') lowest_common(id[2:4], class_list = id_class) lowest_common(id[2:4], class_list = id_class, low_rank = 'class') lowest_common(id[2:4], class_list = id_class, low_rank = 'family') # TOL taxa <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") (cls <- classification(taxa, db = "tol")) lowest_common(taxa, db = "tol", class_list = cls) lowest_common(get_tolid(taxa), class_list = cls) xx <- get_tolid(taxa) lowest_common(xx, class_list = cls) spp <- c("Sus scrofa", "Homo sapiens", "Nycticebus coucang") lowest_common(spp, db = "ncbi") lowest_common(get_uid(spp)) lowest_common(spp, db = "itis") lowest_common(get_tsn(spp)) gbifid <- c("2704179", "3119195") lowest_common(gbifid, db = "gbif") spp <- c("Poa annua", "Helianthus annuus") lowest_common(spp, db = "gbif") lowest_common(get_gbifid(spp)) cool_orchid <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") orchid_ncbi <- get_uid(cool_orchid) orchid_gbif <- get_gbifid(cool_orchid) cool_orchids2 <- c("Domingoa haematochila", "Gymnadenia conopsea", "Masdevallia coccinea") orchid_itis <- get_tsn(cool_orchids2) orchid_hier_ncbi <- classification(orchid_ncbi, db = 'ncbi') orchid_hier_gbif <- classification(orchid_gbif, db = 'gbif') orchid_hier_itis <- classification(orchid_itis, db = 'itis') lowest_common(orchid_ncbi, low_rank = 'class') lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi, low_rank = 'class') lowest_common(orchid_gbif, low_rank = 'class') lowest_common(orchid_gbif, orchid_hier_gbif, low_rank = 'class') lowest_common(get_uid(cool_orchid), low_rank = 'class') lowest_common(get_uid(cool_orchid), low_rank = 'family') lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi, low_rank = 'subfamily') lowest_common(orchid_gbif, class_list = orchid_hier_gbif, low_rank = 'subfamily') lowest_common(orchid_itis, class_list = orchid_hier_itis, low_rank = 'class') ## Pass in sci. names nms <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") lowest_common(x = nms, db = "ncbi") lowest_common(x = nms, db = "gbif") # lowest_common(x = nms, db = "itis") ## NAs due to taxon not found, stops with error message # lowest_common(orchid_itis, db = "itis") # lowest_common(get_tsn(cool_orchid)) ## End(Not run)
Family and order names come from the APG plant names list. Genus and species names come from Theplantlist.org.
names_list(rank = "genus", size = 10)
names_list(rank = "genus", size = 10)
rank |
(character) Taxonomic rank, one of species, genus (default), family, order |
size |
(integer/numeric) Number of names to get. Maximum depends on the rank |
character vector of taxonomic names
Scott Chamberlain
names_list() names_list('species') names_list('genus') names_list('family') names_list('order') names_list('order', 2) names_list('order', 15) # You can get a lot of genus or species names if you want nrow(theplantlist) names_list('genus', 500)
names_list() names_list('species') names_list('genus') names_list('family') names_list('order') names_list('order', 2) names_list('order', 15) # You can get a lot of genus or species names if you want nrow(theplantlist) names_list('genus', 500)
Search UK National Biodiversity Network database for taxonomic classification
nbn_classification(id, ...)
nbn_classification(id, ...)
id |
(character) An NBN identifier. |
... |
Further args passed on to crul::verb-GET |
A data.frame
Scott Chamberlain,
https://api.nbnatlas.org/
Other nbn:
get_nbnid()
,
nbn_search()
,
nbn_synonyms()
## Not run: nbn_classification(id="NHMSYS0000376773") # get id first, then pass to this fxn id <- get_nbnid("Zootoca vivipara", rec_only = TRUE, rank = "Species") nbn_classification(id) nbn_classification(id="NHMSYS0000502940", verbose = TRUE) ## End(Not run)
## Not run: nbn_classification(id="NHMSYS0000376773") # get id first, then pass to this fxn id <- get_nbnid("Zootoca vivipara", rec_only = TRUE, rank = "Species") nbn_classification(id) nbn_classification(id="NHMSYS0000502940", verbose = TRUE) ## End(Not run)
Search UK National Biodiversity Network
nbn_search( sci_com, fq = NULL, order = NULL, sort = NULL, start = 0, rows = 25, facets = NULL, q = NULL, ... )
nbn_search( sci_com, fq = NULL, order = NULL, sort = NULL, start = 0, rows = 25, facets = NULL, q = NULL, ... )
sci_com |
(character) The query terms(s), a scientific or common name |
fq |
(character) Filters to be applied to the original query. These are additional params of the form fq=INDEXEDFIELD:VALUE e.g. fq=rank:kingdom. See https://species-ws.nbnatlas.org/indexFields for all the fields that are queryable. |
order |
(character) Supports "asc" or "desc" |
sort |
(character) The indexed field to sort by |
start |
(integer) Record offset, to enable paging |
rows |
(integer) Number of records to return |
facets |
(list) Comma separated list of the fields to create facets on e.g. facets=basis_of_record. |
q |
Deprecated, see |
... |
Further args passed on to crul::HttpClient. |
a list with slots for metadata (meta
) with list of response
attributes, and data (data
) with a data.frame of results
Scott Chamberlain,
https://api.nbnatlas.org/
Other nbn:
get_nbnid()
,
nbn_classification()
,
nbn_synonyms()
## Not run: x <- nbn_search(sci_com = "Vulpes") x$meta$totalRecords x$meta$pageSize x$meta$urlParameters x$meta$queryTitle head(x$data) nbn_search(sci_com = "blackbird", start = 4) # debug curl stuff nbn_search(sci_com = "blackbird", verbose = TRUE) ## End(Not run)
## Not run: x <- nbn_search(sci_com = "Vulpes") x$meta$totalRecords x$meta$pageSize x$meta$urlParameters x$meta$queryTitle head(x$data) nbn_search(sci_com = "blackbird", start = 4) # debug curl stuff nbn_search(sci_com = "blackbird", verbose = TRUE) ## End(Not run)
Return all synonyms for a taxon name with a given id from NBN
nbn_synonyms(id, ...)
nbn_synonyms(id, ...)
id |
the taxon identifier code |
... |
Further args passed on to crul::verb-GET |
A data.frame
https://api.nbnatlas.org/
Other nbn:
get_nbnid()
,
nbn_classification()
,
nbn_search()
## Not run: nbn_synonyms(id = 'NHMSYS0001501147') nbn_synonyms(id = 'NHMSYS0000456036') # none nbn_synonyms(id = 'NHMSYS0000502940') ## End(Not run)
## Not run: nbn_synonyms(id = 'NHMSYS0001501147') nbn_synonyms(id = 'NHMSYS0000456036') # none nbn_synonyms(id = 'NHMSYS0000502940') ## End(Not run)
Search the NCBI Taxonomy database for uids of children of taxa. Taxa can be referenced by name or uid. Referencing by name is faster
In a few cases, different taxa have the same name (e.g. Satyrium; see examples). If one of these are searched for then the children of both taxa will be returned. This can be avoided by using a uid instead of the name or specifying an ancestor. If an ancestor is provided, only children of both the taxon and its ancestor are returned. This will only fail if there are two taxa with the same name and the same specified ancestor.
ncbi_children( name = NULL, id = NULL, start = 0, max_return = 1000, ancestor = NULL, out_type = c("summary", "uid"), ambiguous = FALSE, key = NULL, ... )
ncbi_children( name = NULL, id = NULL, start = 0, max_return = 1000, ancestor = NULL, out_type = c("summary", "uid"), ambiguous = FALSE, key = NULL, ... )
name |
( |
id |
( |
start |
The first record to return. If omitted, the results are returned from the first record (start=0). |
max_return |
( |
ancestor |
( |
out_type |
(character) Currently either
|
ambiguous |
|
key |
(character) NCBI Entrez API key. optional. See Details. |
... |
Curl options passed on to crul::HttpClient |
The output type depends on the value of the out_type
parameter. Taxa that cannot be found will result in NA
s and a lack
of children results in an empty data structure.
See taxize-authentication()
for help on authentication.
We strongly recommend getting an API key
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')
In case you run into errors due to your rate limit being exceeded, see
taxize_options()
, where you can set ncbi_sleep
.
Zachary Foster [email protected]
ncbi_get_taxon_summary()
, children()
## Not run: ncbi_children(name="Satyrium") #Satyrium is the name of two different genera ncbi_children(name="Satyrium", ancestor="Eumaeini") # A genus of butterflies ncbi_children(name="Satyrium", ancestor="Orchidaceae") # A genus of orchids ncbi_children(id="266948") #"266948" is the uid for the butterfly genus ncbi_children(id="62858") #"62858" is the uid for the orchid genus # use curl options ncbi_children(name="Satyrium", ancestor="Eumaeini", verbose = TRUE) ## End(Not run)
## Not run: ncbi_children(name="Satyrium") #Satyrium is the name of two different genera ncbi_children(name="Satyrium", ancestor="Eumaeini") # A genus of butterflies ncbi_children(name="Satyrium", ancestor="Orchidaceae") # A genus of orchids ncbi_children(id="266948") #"266948" is the uid for the butterfly genus ncbi_children(id="62858") #"62858" is the uid for the orchid genus # use curl options ncbi_children(name="Satyrium", ancestor="Eumaeini", verbose = TRUE) ## End(Not run)
Retrieve all taxa names downstream in hierarchy for NCBI
ncbi_downstream(id, downto, intermediate = FALSE, ...)
ncbi_downstream(id, downto, intermediate = FALSE, ...)
id |
(numeric/integer) An NCBI taxonomic identifier |
downto |
The taxonomic level you want to go down to. See examples below.
The taxonomic level IS case sensitive, and you do have to spell it
correctly. See |
intermediate |
(logical) If |
... |
Further args passed on to |
Data.frame of taxonomic information downstream to family from e.g.,
Order, Class, etc., or if intermediate=TRUE
, list of length two,
with target taxon rank names, and intermediate names.
A sticky point with NCBI is that they can have designation for taxonomic rank of "No Rank". So we have no way of programatically knowing what to do with that taxon. Of course one can manually look at a name and perhaps know what it is, or look it up on the web - but we can't do anything programatically. So, no rank things will sometimes be missing.
See taxize-authentication()
for help on authentication.
We strongly recommend getting an API key
Scott Chamberlain
## Not run: ## genus Apis ncbi_downstream(id = 7459, downto="species") ## get intermediate taxa as a separate object ncbi_downstream(id = 7459, downto="species", intermediate = TRUE) ## Lepidoptera ncbi_downstream(id = 7088, downto="superfamily") ## families in the ferns (Moniliformopses) (id <- get_uid("Moniliformopses")) ncbi_downstream(id = id, downto = "order") ## End(Not run)
## Not run: ## genus Apis ncbi_downstream(id = 7459, downto="species") ## get intermediate taxa as a separate object ncbi_downstream(id = 7459, downto="species", intermediate = TRUE) ## Lepidoptera ncbi_downstream(id = 7088, downto="superfamily") ## families in the ferns (Moniliformopses) (id <- get_uid("Moniliformopses")) ncbi_downstream(id = id, downto = "order") ## End(Not run)
Downloads summary taxon information from the NCBI taxonomy databases for a set of taxonomy UIDs using eutils esummary.
ncbi_get_taxon_summary(id, key = NULL, ...)
ncbi_get_taxon_summary(id, key = NULL, ...)
id |
(character) NCBI taxonomy uids to retrieve information for. See Details. |
key |
(character) NCBI Entrez API key. optional. See Details. |
... |
Curl options passed on to crul::verb-GET |
If your input vector or list of NCBI IDs is longer than about
2500 characters (use nchar(paste(ids, collapse = "+"))
), split
the list up into chunks since at about that number of characters you
will run into the HTTP 414 error "Request-URI Too Long".
A data.frame
with the following columns:
uid
The uid queried for
name
The name of the taxon; a binomial name if the taxon is of rank species
rank
The taxonomic rank (e.g. 'Genus')
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')
See taxize-authentication for help on authentication. We strongly recommend getting an API key
Zachary Foster [email protected]
## Not run: ncbi_get_taxon_summary(c(1430660, 4751)) # use curl options ncbi_get_taxon_summary(c(1430660, 4751), verbose = TRUE) ## End(Not run)
## Not run: ncbi_get_taxon_summary(c(1430660, 4751)) # use curl options ncbi_get_taxon_summary(c(1430660, 4751), verbose = TRUE) ## End(Not run)
Ping an API used in taxize to see if it's working.
col_ping(what = "status", ...) eol_ping(what = "status", ...) itis_ping(what = "status", ...) ncbi_ping(what = "status", key = NULL, ...) tropicos_ping(what = "status", ...) nbn_ping(what = "status", ...) gbif_ping(what = "status", ...) bold_ping(what = "status", ...) ipni_ping(what = "status", ...) vascan_ping(what = "status", ...) fg_ping(what = "status", ...)
col_ping(what = "status", ...) eol_ping(what = "status", ...) itis_ping(what = "status", ...) ncbi_ping(what = "status", key = NULL, ...) tropicos_ping(what = "status", ...) nbn_ping(what = "status", ...) gbif_ping(what = "status", ...) bold_ping(what = "status", ...) ipni_ping(what = "status", ...) vascan_ping(what = "status", ...) fg_ping(what = "status", ...)
what |
(character) One of status (default), content, or an HTTP status
code. If status, we just check that the HTTP status code is 200, or similar
signifying the service is up. If content, we do a simple, quick check to
determine if returned content matches what's expected. If an HTTP status
code, it must match an appropriate code. See |
... |
Curl options passed on to crul::verb-GET |
key |
(character) NCBI Entrez API key. optional. See |
For ITIS, see ritis::description, which provides number of scientific and common names in a character string.
A logical, TRUE or FALSE
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: col_ping() col_ping("content") col_ping(200) col_ping("200") col_ping(204) itis_ping() eol_ping() ncbi_ping() tropicos_ping() nbn_ping() gbif_ping() gbif_ping(200) bold_ping() bold_ping(200) bold_ping("content") ipni_ping() ipni_ping(200) ipni_ping("content") vascan_ping() vascan_ping(200) vascan_ping("content") # curl options vascan_ping(verbose = TRUE) eol_ping(500, verbose = TRUE) ## End(Not run)
## Not run: col_ping() col_ping("content") col_ping(200) col_ping("200") col_ping(204) itis_ping() eol_ping() ncbi_ping() tropicos_ping() nbn_ping() gbif_ping() gbif_ping(200) bold_ping() bold_ping(200) bold_ping("content") ipni_ping() ipni_ping(200) ipni_ping("content") vascan_ping() vascan_ping(200) vascan_ping("content") # curl options vascan_ping(verbose = TRUE) eol_ping(500, verbose = TRUE) ## End(Not run)
These names are from http://www.theplantlist.org, and are a randomly chosen subset of genera names for the purpose of having some names to play with for examples in this package.
A vector of length 793
http://www.theplantlist.org
Search for taxonomy data from Plantminer.com
plantminer(plants, from = "tpl", messages = TRUE, ...)
plantminer(plants, from = "tpl", messages = TRUE, ...)
plants |
(character) Vector of plant species names. Required. |
from |
(character) One of tpl (for theplantlist.com data), or
flora (for Brazilian Flora Checklist). Required. Default: |
messages |
(logical) informative messages or not. Default: |
... |
curl options passed on to crul::HttpClient |
data.frame of results.
you used to need an API key for Plantminer; it's no longer needed
## Not run: # A single taxon plantminer("Ocotea pulchella") # Many taxa plants <- c("Myrcia lingua", "Myrcia bella", "Ocotea pulchella", "Miconia", "Coffea arabica var. amarella", "Bleh") plantminer(plants) # By deafult, tpl is used, for Theplantlist data, # toggle the from parameter here plantminer("Ocotea pulchella", from = "flora") ## End(Not run)
## Not run: # A single taxon plantminer("Ocotea pulchella") # Many taxa plants <- c("Myrcia lingua", "Myrcia bella", "Ocotea pulchella", "Miconia", "Coffea arabica var. amarella", "Bleh") plantminer(plants) # By deafult, tpl is used, for Theplantlist data, # toggle the from parameter here plantminer("Ocotea pulchella", from = "flora") ## End(Not run)
These names are from http://www.theplantlist.org, and are a randomly chosen subset of names of the form genus/specific epithet for the purpose of having some names to play with for examples in this package.
A vector of length 1182
http://www.theplantlist.org
Lookup taxa in Kew's Plants of the World
pow_lookup(id, include = NULL, ...)
pow_lookup(id, include = NULL, ...)
id |
(character) taxon id. required |
include |
(character) vector of additional fields to include in results. options include 'distribution' and 'descriptions'. optional |
... |
Further args passed on to crul::HttpClient. |
Other pow:
get_pow()
,
pow_search()
,
pow_synonyms()
## Not run: pow_lookup(id = 'urn:lsid:ipni.org:names:320035-2') pow_lookup(id = 'urn:lsid:ipni.org:names:320035-2', include = "distribution") pow_lookup(id = 'urn:lsid:ipni.org:names:320035-2', include = c("distribution", "descriptions")) ## End(Not run)
## Not run: pow_lookup(id = 'urn:lsid:ipni.org:names:320035-2') pow_lookup(id = 'urn:lsid:ipni.org:names:320035-2', include = "distribution") pow_lookup(id = 'urn:lsid:ipni.org:names:320035-2', include = c("distribution", "descriptions")) ## End(Not run)
Search Kew's Plants of the World
pow_search(sci_com, limit = 100, cursor = "*", sort = NULL, q = NULL, ...)
pow_search(sci_com, limit = 100, cursor = "*", sort = NULL, q = NULL, ...)
sci_com |
(character) query terms, scientific or common name |
limit |
(integer) Number of records to return. default: 100 |
cursor |
(character) cursor string |
sort |
(character) The field to sort by and sort order separted with
underscore, e.g., |
q |
Deprecated, see |
... |
Further args passed on to crul::HttpClient. |
a list with slots for metadata (meta
) with list of response
attributes, and data (data
) with a data.frame of results
Scott Chamberlain,
http://powo.science.kew.org/
Other pow:
get_pow()
,
pow_lookup()
,
pow_synonyms()
## Not run: x <- pow_search(sci_com = "Quercus") x$meta x$meta$totalResults x$meta$perPage x$meta$totalPages x$meta$page x$meta$cursor head(x$data) # pagination pow_search(sci_com = "sunflower", limit = 2) # debug curl stuff invisible(pow_search(sci_com = "Helianthus annuus", verbose = TRUE)) # sort desc <- pow_search(sci_com = "Helianthus", sort = "name_desc") desc$data$name asc <- pow_search(sci_com = "Helianthus", sort = "name_asc") asc$data$name ## End(Not run)
## Not run: x <- pow_search(sci_com = "Quercus") x$meta x$meta$totalResults x$meta$perPage x$meta$totalPages x$meta$page x$meta$cursor head(x$data) # pagination pow_search(sci_com = "sunflower", limit = 2) # debug curl stuff invisible(pow_search(sci_com = "Helianthus annuus", verbose = TRUE)) # sort desc <- pow_search(sci_com = "Helianthus", sort = "name_desc") desc$data$name asc <- pow_search(sci_com = "Helianthus", sort = "name_asc") asc$data$name ## End(Not run)
Lookup synonyms in Kew's Plants of the World
pow_synonyms(id, ...)
pow_synonyms(id, ...)
id |
(character) taxon id. required |
... |
Further args passed on to |
Other pow:
get_pow()
,
pow_lookup()
,
pow_search()
## Not run: pow_synonyms(id = 'urn:lsid:ipni.org:names:320035-2') pow_synonyms(id = 'urn:lsid:ipni.org:names:358881-1') pow_synonyms(id = 'urn:lsid:ipni.org:names:359855-1') ## End(Not run)
## Not run: pow_synonyms(id = 'urn:lsid:ipni.org:names:320035-2') pow_synonyms(id = 'urn:lsid:ipni.org:names:358881-1') pow_synonyms(id = 'urn:lsid:ipni.org:names:359855-1') ## End(Not run)
data.frame of 46 rows, with 2 columns:
rankid - a numeric rank id, consecutive
ranks - a comma separated vector of names that are considered equal to one another within the row
We use this data.frame to do data sorting/filtering based on the ordering of ranks.
Please let us know if there is a rank that occurs from one of the data
sources taxize that we don't have in rank_ref
dataset.
Let us know if you disagree with the ordering of ranks.
Note that rankid
280 are essentially "genetic variants"; placed just above
'unspecified' to denote they're not without rank, but they're not
really taxonomic ranks either. As far as I know there's no way
to delineate among these "genetic variant" types.
Same as rank_ref
but specifically for WoRMS, where section/subsection
ranks are put between family/order rather than between species/genus.
Aggregate data by given taxonomic rank
rankagg(data = NULL, datacol = NULL, rank = NULL, fxn = "sum")
rankagg(data = NULL, datacol = NULL, rank = NULL, fxn = "sum")
data |
A data.frame. Column headers must have capitalized ranks (e.g., Genus, Tribe, etc.) (data.frame) |
datacol |
The data column (character) |
rank |
Taxonomic rank to aggregate by (character) |
fxn |
Arithmetic function or vector or functions (character) |
if (require(vegan)) { data(dune.taxon, dune, package='vegan') dat <- dune.taxon dat$abundance <- colSums(dune) rankagg(data=dat, datacol="abundance", rank="Genus") rankagg(data=dat, "abundance", rank="Family") rankagg(data=dat, "abundance", rank="Genus", fxn="mean") rankagg(data=dat, "abundance", rank="Subclass") rankagg(data=dat, "abundance", rank="Subclass", fxn="sd") }
if (require(vegan)) { data(dune.taxon, dune, package='vegan') dat <- dune.taxon dat$abundance <- colSums(dune) rankagg(data=dat, datacol="abundance", rank="Genus") rankagg(data=dat, "abundance", rank="Family") rankagg(data=dat, "abundance", rank="Genus", fxn="mean") rankagg(data=dat, "abundance", rank="Subclass") rankagg(data=dat, "abundance", rank="Subclass", fxn="sd") }
Resolve names from iPlant's name resolver, and the Global Names Resolver (GNR)
resolve(sci, db = "gnr", query = NULL, ...)
resolve(sci, db = "gnr", query = NULL, ...)
sci |
Vector of one or more taxonomic names (common names not supported) |
db |
Source to check names against. One of iplant or gnr.
Default: gnr. Note that each taxonomic data source has their own
identifiers, so that if you provide the wrong |
query |
Deprecated, see |
... |
Curl options passed on to crul::verb-GET or crul::verb-POST. In addition, further named args passed on to each respective function. See examples |
A list with length equal to length of the db parameter (number of sources requested), with each element being a data.frame or list with results from that source.
## Not run: resolve(sci=c("Helianthus annuus", "Homo sapiens")) resolve(sci="Quercus keloggii", db='gnr') resolve(sci=c("Helianthus annuus", "Homo sapiens"), db=c('iplant', 'gnr')) resolve(sci="Quercus keloggii", db=c('iplant', 'gnr')) # pass in options specific to each source resolve("Helianthus annuus", db = 'gnr', preferred_data_sources = c(3, 4)) resolve("Helianthus annuus", db = 'iplant', retrieve = 'best') identical( resolve("Helianthus annuus", db = 'iplant', retrieve = 'best')$iplant, iplant_resolve("Helianthus annuus", retrieve = 'best') ) # pass in curl options resolve(sci="Qercuss", db = "iplant", verbose = TRUE) ## End(Not run)
## Not run: resolve(sci=c("Helianthus annuus", "Homo sapiens")) resolve(sci="Quercus keloggii", db='gnr') resolve(sci=c("Helianthus annuus", "Homo sapiens"), db=c('iplant', 'gnr')) resolve(sci="Quercus keloggii", db=c('iplant', 'gnr')) # pass in options specific to each source resolve("Helianthus annuus", db = 'gnr', preferred_data_sources = c(3, 4)) resolve("Helianthus annuus", db = 'iplant', retrieve = 'best') identical( resolve("Helianthus annuus", db = 'iplant', retrieve = 'best')$iplant, iplant_resolve("Helianthus annuus", retrieve = 'best') ) # pass in curl options resolve(sci="Qercuss", db = "iplant", verbose = TRUE) ## End(Not run)
Get common names from scientific names.
sci2comm(...) ## Default S3 method: sci2comm(sci, db = "ncbi", simplify = TRUE, scinames = NULL, ...) ## S3 method for class 'uid' sci2comm(id, ...) ## S3 method for class 'tsn' sci2comm(id, simplify = TRUE, ...) ## S3 method for class 'wormsid' sci2comm(id, simplify = TRUE, ...) ## S3 method for class 'iucn' sci2comm(id, simplify = TRUE, ...)
sci2comm(...) ## Default S3 method: sci2comm(sci, db = "ncbi", simplify = TRUE, scinames = NULL, ...) ## S3 method for class 'uid' sci2comm(id, ...) ## S3 method for class 'tsn' sci2comm(id, simplify = TRUE, ...) ## S3 method for class 'wormsid' sci2comm(id, simplify = TRUE, ...) ## S3 method for class 'iucn' sci2comm(id, simplify = TRUE, ...)
... |
Further arguments passed on to functions |
sci |
character; One or more scientific names or partial names. |
db |
character; Data source, one of |
simplify |
(logical) If TRUE, simplify output to a vector of names.
If FALSE, return variable formats from different sources, usually a
data.frame. Only applies to eol and itis. Specify |
scinames |
Deprecated, see |
id |
character; identifiers, as returned by |
List of character vectors, named by input taxon name,
or taxon ID. character(0)
on no match
See taxize-authentication for help on authentication
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')
Scott Chamberlain
## Not run: sci2comm(sci='Helianthus annuus') sci2comm(sci='Helianthus annuus', db='eol') sci2comm(sci=c('Helianthus annuus', 'Poa annua')) sci2comm(sci='Puma concolor', db='ncbi') sci2comm('Gadus morhua', db='worms') sci2comm('Pomatomus saltatrix', db='worms') sci2comm('Loxodonta africana', db='iucn') # Passing id in, works for sources: itis and ncbi, not eol sci2comm(get_uid('Helianthus annuus')) sci2comm(get_wormsid('Gadus morhua')) sci2comm(get_iucn('Loxodonta africana')) # Don't simplify returned sci2comm(get_iucn('Loxodonta africana'), simplify=FALSE) # Use curl options sci2comm('Helianthus annuus', db="ncbi", verbose = TRUE) ## End(Not run)
## Not run: sci2comm(sci='Helianthus annuus') sci2comm(sci='Helianthus annuus', db='eol') sci2comm(sci=c('Helianthus annuus', 'Poa annua')) sci2comm(sci='Puma concolor', db='ncbi') sci2comm('Gadus morhua', db='worms') sci2comm('Pomatomus saltatrix', db='worms') sci2comm('Loxodonta africana', db='iucn') # Passing id in, works for sources: itis and ncbi, not eol sci2comm(get_uid('Helianthus annuus')) sci2comm(get_wormsid('Gadus morhua')) sci2comm(get_iucn('Loxodonta africana')) # Don't simplify returned sci2comm(get_iucn('Loxodonta africana'), simplify=FALSE) # Use curl options sci2comm('Helianthus annuus', db="ncbi", verbose = TRUE) ## End(Not run)
Uses the Global Names Recognition and Discovery service, see http://gnrd.globalnames.org/
Note: this function sometimes gives data back and sometimes not. The API that this function is extremely buggy.
scrapenames( url = NULL, file = NULL, text = NULL, engine = NULL, unique = NULL, verbatim = NULL, detect_language = NULL, all_data_sources = NULL, data_source_ids = NULL, return_content = FALSE, ... )
scrapenames( url = NULL, file = NULL, text = NULL, engine = NULL, unique = NULL, verbatim = NULL, detect_language = NULL, all_data_sources = NULL, data_source_ids = NULL, return_content = FALSE, ... )
url |
An encoded URL for a web page, PDF, Microsoft Office document, or image file, see examples |
file |
When using multipart/form-data as the content-type, a file may be sent. This should be a path to your file on your machine. |
text |
Type: string. Text content; best used with a POST request, see examples |
engine |
(optional) (integer) Default: 0. Either 1 for TaxonFinder, 2 for NetiNeti, or 0 for both. If absent, both engines are used. |
unique |
(optional) (logical) If |
verbatim |
(optional) Type: boolean, If |
detect_language |
(optional) Type: boolean, When |
all_data_sources |
(optional) Type: boolean. Resolve found names against all available Data Sources. |
data_source_ids |
(optional) Type: string. Pipe separated list of data source ids to resolve found names against. See list of Data Sources http://resolver.globalnames.org/data_sources |
return_content |
(logical) return OCR'ed text. returns text
string in |
... |
Further args passed to crul::verb-GET |
One of url, file, or text must be specified - and only one of them.
A list of length two, first is metadata, second is the data as a data.frame.
Scott Chamberlain
## Not run: # Get data from a website using its URL scrapenames('https://en.wikipedia.org/wiki/Spider') scrapenames('https://en.wikipedia.org/wiki/Animal') scrapenames('https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0095068') scrapenames('https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080498') scrapenames('http://ucjeps.berkeley.edu/cgi-bin/get_JM_treatment.pl?CARYOPHYLLACEAE') # Scrape names from a pdf at a URL url <- 'https://journals.plos.org/plosone/article/file?id= 10.1371/journal.pone.0058268&type=printable' scrapenames(url = sub('\n', '', url)) # With arguments scrapenames(url = 'https://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf', unique=TRUE) scrapenames(url = 'https://en.wikipedia.org/wiki/Spider', data_source_ids=c(1, 169)) # Get data from a file speciesfile <- system.file("examples", "species.txt", package = "taxize") scrapenames(file = speciesfile) nms <- paste0(names_list("species"), collapse="\n") file <- tempfile(fileext = ".txt") writeLines(nms, file) scrapenames(file = file) # Get data from text string scrapenames(text='A spider named Pardosa moesta Banks, 1892') # return OCR content scrapenames(url='https://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf', return_content = TRUE) ## End(Not run)
## Not run: # Get data from a website using its URL scrapenames('https://en.wikipedia.org/wiki/Spider') scrapenames('https://en.wikipedia.org/wiki/Animal') scrapenames('https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0095068') scrapenames('https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080498') scrapenames('http://ucjeps.berkeley.edu/cgi-bin/get_JM_treatment.pl?CARYOPHYLLACEAE') # Scrape names from a pdf at a URL url <- 'https://journals.plos.org/plosone/article/file?id= 10.1371/journal.pone.0058268&type=printable' scrapenames(url = sub('\n', '', url)) # With arguments scrapenames(url = 'https://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf', unique=TRUE) scrapenames(url = 'https://en.wikipedia.org/wiki/Spider', data_source_ids=c(1, 169)) # Get data from a file speciesfile <- system.file("examples", "species.txt", package = "taxize") scrapenames(file = speciesfile) nms <- paste0(names_list("species"), collapse="\n") file <- tempfile(fileext = ".txt") writeLines(nms, file) scrapenames(file = file) # Get data from text string scrapenames(text='A spider named Pardosa moesta Banks, 1892') # return OCR content scrapenames(url='https://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf', return_content = TRUE) ## End(Not run)
These names have been compiled from Species Plantarum by Carl Linnaeus originally published in 1753. It is the first work to consistently apply binomial names and was the starting point for the naming of plants. The book lists every species of plant known at the time, classified into genera. The dataset provides a useful reference point to see how taxonomic names have changed since their inception. The names were transcribed by Robert W. Kiger.
A data frame with 5940 rows and 3 variables:
genus First part of the binomial species name for each species within the genus
epithet specific epithet or second part of the binomial species name for each species
page_number The following abbreviations sometimes are used in the page_number field.
"add." refers to addenda that appear on the unnumbered last page of the index in volume two.
"err." refers to the unnumbered page of errata that appears following the index in volume two.
"canc." following a page number indicates that the binomial appeared on the cancelled version of that page and does not appear on its replacement (as in the 1957-1959 facsimile edition.
Carl Linnaeus
Hunt Institute for Botanical Documentation
Linnaeus, C. 1753. Species Plantarum. 2 vols. Salvius, Stockholm. [Facsimile edition, 1957-1959, Ray Society, London.]
Get HTTP status codes
status_codes()
status_codes()
status_codes()
status_codes()
Retrieve synonyms from various sources given input taxonomic names or identifiers
synonyms(...) ## Default S3 method: synonyms(sci_id, db = NULL, rows = NA, x = NULL, ...) ## S3 method for class 'tsn' synonyms(id, ...) ## S3 method for class 'tpsid' synonyms(id, ...) ## S3 method for class 'nbnid' synonyms(id, ...) ## S3 method for class 'wormsid' synonyms(id, ...) ## S3 method for class 'iucn' synonyms(id, ...) ## S3 method for class 'pow' synonyms(id, ...) ## S3 method for class 'ids' synonyms(id, ...) synonyms_df(x)
synonyms(...) ## Default S3 method: synonyms(sci_id, db = NULL, rows = NA, x = NULL, ...) ## S3 method for class 'tsn' synonyms(id, ...) ## S3 method for class 'tpsid' synonyms(id, ...) ## S3 method for class 'nbnid' synonyms(id, ...) ## S3 method for class 'wormsid' synonyms(id, ...) ## S3 method for class 'iucn' synonyms(id, ...) ## S3 method for class 'pow' synonyms(id, ...) ## S3 method for class 'ids' synonyms(id, ...) synonyms_df(x)
... |
Other passed arguments to internal functions |
sci_id |
Vector of taxa names (character) or IDs (character or numeric) |
db |
character; database to query. either |
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 of any of the acceptable classes: tsn, tpsid, nbnid, ids. |
x |
For |
id |
character; identifiers, returned by |
If IDs are supplied directly (not from the get_*()
functions)
you must specify the type of ID.
For db = "itis"
you can pass in a parameter accepted
to
toggle whether only accepted names are used accepted = TRUE
, or if
all are used accepted = FALSE
. The default is accepted = FALSE
Note that IUCN requires an API key. See rredlist::rredlist-package for help on authentiating with IUCN Redlist
A named list of results with three types of output in each slot:
if the name was not found: NA_character_
if the name was found but no synonyms found, an empty data.frame (0 rows)
if the name was found, and synonyms found, a data.frames with the synonyms - the column names vary by data source
get_tsn()
get_tpsid()
get_nbnid()
get_wormsid()
get_iucn()
get_pow()
## Not run: # Plug in taxon IDs synonyms(183327, db="itis") synonyms("25509881", db="tropicos") synonyms("NBNSYS0000004629", db='nbn') synonyms(105706, db='worms') synonyms(12392, db='iucn') synonyms('urn:lsid:ipni.org:names:358881-1', db='pow') # Plug in taxon names directly synonyms("Pinus contorta", db="itis") synonyms("Puma concolor", db="itis") synonyms(c("Poa annua",'Pinus contorta','Puma concolor'), db="itis") synonyms("Poa annua", db="tropicos") synonyms("Pinus contorta", db="tropicos") synonyms(c("Poa annua",'Pinus contorta'), db="tropicos") synonyms("Pinus sylvestris", db='nbn') synonyms('Pomatomus', db='worms') synonyms('Pomatomus saltatrix', db='worms') synonyms('Lithocarpus mindanaensis', db='pow') synonyms('Poa annua', db='pow') synonyms(c('Poa annua', 'Pinus contorta', 'foo bar'), db='pow') # not accepted names, with ITIS ## looks for whether the name given is an accepted name, ## and if not, uses the accepted name to look for synonyms synonyms("Acer drummondii", db="itis") synonyms("Spinus pinus", db="itis") # Use get_* methods synonyms(get_tsn("Poa annua")) synonyms(get_tpsid("Poa annua")) synonyms(get_nbnid("Carcharodon carcharias")) synonyms(get_iucn('Loxodonta africana')) synonyms(get_pow('Lithocarpus mindanaensis')) # Pass many ids from class "ids" out <- get_ids(names="Poa annua", db = c('itis','tropicos')) synonyms(out) # Use the rows parameter to select certain rows synonyms("Poa annua", db='tropicos', rows=1) synonyms("Poa annua", db='tropicos', rows=1:3) synonyms("Pinus sylvestris", db='nbn', rows=1:3) # Use curl options synonyms("Poa annua", db='tropicos', rows=1, verbose = TRUE) synonyms("Poa annua", db='itis', rows=1, verbose = TRUE) # combine many outputs together x <- synonyms(c("Osmia bicornis", "Osmia rufa", "Osmia"), db = "itis") synonyms_df(x) ## note here how Pinus contorta is dropped due to no synonyms found synonyms_df(x) ## note here that ids are taxon identifiers b/c you start with them x <- synonyms(c(25509881, 13100094), db="tropicos") synonyms_df(x) ## NBN x <- synonyms(c('Aglais io', 'Usnea hirta', 'Arctostaphylos uva-ursi'), db="nbn") synonyms_df(x) ## End(Not run)
## Not run: # Plug in taxon IDs synonyms(183327, db="itis") synonyms("25509881", db="tropicos") synonyms("NBNSYS0000004629", db='nbn') synonyms(105706, db='worms') synonyms(12392, db='iucn') synonyms('urn:lsid:ipni.org:names:358881-1', db='pow') # Plug in taxon names directly synonyms("Pinus contorta", db="itis") synonyms("Puma concolor", db="itis") synonyms(c("Poa annua",'Pinus contorta','Puma concolor'), db="itis") synonyms("Poa annua", db="tropicos") synonyms("Pinus contorta", db="tropicos") synonyms(c("Poa annua",'Pinus contorta'), db="tropicos") synonyms("Pinus sylvestris", db='nbn') synonyms('Pomatomus', db='worms') synonyms('Pomatomus saltatrix', db='worms') synonyms('Lithocarpus mindanaensis', db='pow') synonyms('Poa annua', db='pow') synonyms(c('Poa annua', 'Pinus contorta', 'foo bar'), db='pow') # not accepted names, with ITIS ## looks for whether the name given is an accepted name, ## and if not, uses the accepted name to look for synonyms synonyms("Acer drummondii", db="itis") synonyms("Spinus pinus", db="itis") # Use get_* methods synonyms(get_tsn("Poa annua")) synonyms(get_tpsid("Poa annua")) synonyms(get_nbnid("Carcharodon carcharias")) synonyms(get_iucn('Loxodonta africana')) synonyms(get_pow('Lithocarpus mindanaensis')) # Pass many ids from class "ids" out <- get_ids(names="Poa annua", db = c('itis','tropicos')) synonyms(out) # Use the rows parameter to select certain rows synonyms("Poa annua", db='tropicos', rows=1) synonyms("Poa annua", db='tropicos', rows=1:3) synonyms("Pinus sylvestris", db='nbn', rows=1:3) # Use curl options synonyms("Poa annua", db='tropicos', rows=1, verbose = TRUE) synonyms("Poa annua", db='itis', rows=1, verbose = TRUE) # combine many outputs together x <- synonyms(c("Osmia bicornis", "Osmia rufa", "Osmia"), db = "itis") synonyms_df(x) ## note here how Pinus contorta is dropped due to no synonyms found synonyms_df(x) ## note here that ids are taxon identifiers b/c you start with them x <- synonyms(c(25509881, 13100094), db="tropicos") synonyms_df(x) ## NBN x <- synonyms(c('Aglais io', 'Usnea hirta', 'Arctostaphylos uva-ursi'), db="nbn") synonyms_df(x) ## End(Not run)
Aggregate species data to given taxonomic rank
tax_agg(x, rank, db = "ncbi", messages = FALSE, ...) ## S3 method for class 'tax_agg' print(x, ...)
tax_agg(x, rank, db = "ncbi", messages = FALSE, ...) ## S3 method for class 'tax_agg' print(x, ...)
x |
Community data matrix. Taxa in columns, samples in rows. |
rank |
character; Taxonomic rank to aggregate by. |
db |
character; taxonomic API to use, 'ncbi, 'itis' or both, see
|
messages |
(logical) If FALSE (Default) suppress messages |
... |
tax_agg
aggregates (sum) taxa to a specific taxonomic level.
If a taxon is not found in the database (ITIS or NCBI) or the supplied taxon
is on higher taxonomic level this taxon is not aggregated.
A list of class tax_agg
with the following items:
x
Community data matrix with aggregated data.
by
A lookup-table showing which taxa were aggregated.
n_pre
Number of taxa before aggregation.
rank
Rank at which taxa have been aggregated.
## Not run: if (requireNamespace("vegan", quietly = TRUE)) { # use dune dataset data(dune, package='vegan') species <- c("Achillea millefolium", "Agrostis stolonifera", "Aira praecox", "Alopecurus geniculatus", "Anthoxanthum odoratum", "Bellis perennis", "Bromus hordeaceus", "Chenopodium album", "Cirsium arvense", "Comarum palustre", "Eleocharis palustris", "Elymus repens", "Empetrum nigrum", "Hypochaeris radicata", "Juncus articulatus", "Juncus bufonius", "Lolium perenne", "Plantago lanceolata", "Poa pratensis", "Poa trivialis", "Ranunculus flammula", "Rumex acetosa", "Sagina procumbens", "Salix repens", "Scorzoneroides autumnalis", "Trifolium pratense", "Trifolium repens", "Vicia lathyroides", "Brachythecium rutabulum", "Calliergonella cuspidata") colnames(dune) <- species # aggregate sample to families (agg <- tax_agg(dune, rank = 'family', db = 'ncbi')) # extract aggregated community data matrix for further usage agg$x # check which taxa have been aggregated agg$by } # A use case where there are different taxonomic levels in the same dataset spnames <- c('Puma','Ursus americanus','Ursidae') df <- data.frame(c(1,2,3), c(11,12,13), c(1,4,50)) names(df) <- spnames out <- tax_agg(x=df, rank = 'family', db='itis') out$x # You can input a matrix too mat <- matrix(c(1,2,3, 11,12,13), nrow = 2, ncol = 3, dimnames=list(NULL, c('Puma concolor','Ursus americanus','Ailuropoda melanoleuca'))) tax_agg(mat, rank = 'family', db='itis') ## End(Not run)
## Not run: if (requireNamespace("vegan", quietly = TRUE)) { # use dune dataset data(dune, package='vegan') species <- c("Achillea millefolium", "Agrostis stolonifera", "Aira praecox", "Alopecurus geniculatus", "Anthoxanthum odoratum", "Bellis perennis", "Bromus hordeaceus", "Chenopodium album", "Cirsium arvense", "Comarum palustre", "Eleocharis palustris", "Elymus repens", "Empetrum nigrum", "Hypochaeris radicata", "Juncus articulatus", "Juncus bufonius", "Lolium perenne", "Plantago lanceolata", "Poa pratensis", "Poa trivialis", "Ranunculus flammula", "Rumex acetosa", "Sagina procumbens", "Salix repens", "Scorzoneroides autumnalis", "Trifolium pratense", "Trifolium repens", "Vicia lathyroides", "Brachythecium rutabulum", "Calliergonella cuspidata") colnames(dune) <- species # aggregate sample to families (agg <- tax_agg(dune, rank = 'family', db = 'ncbi')) # extract aggregated community data matrix for further usage agg$x # check which taxa have been aggregated agg$by } # A use case where there are different taxonomic levels in the same dataset spnames <- c('Puma','Ursus americanus','Ursidae') df <- data.frame(c(1,2,3), c(11,12,13), c(1,4,50)) names(df) <- spnames out <- tax_agg(x=df, rank = 'family', db='itis') out$x # You can input a matrix too mat <- matrix(c(1,2,3, 11,12,13), nrow = 2, ncol = 3, dimnames=list(NULL, c('Puma concolor','Ursus americanus','Ailuropoda melanoleuca'))) tax_agg(mat, rank = 'family', db='itis') ## End(Not run)
Get taxonomic names for a given rank
tax_name( sci, get, db = "itis", pref = "ncbi", messages = TRUE, query = NULL, ... )
tax_name( sci, get, db = "itis", pref = "ncbi", messages = TRUE, query = NULL, ... )
sci |
(character) Vector of taxonomic names to query. required. |
get |
(character) The ranks of the taxonomic name to get, see rank_ref. required. |
db |
(character) The database to search from: 'itis', 'ncbi' or 'both'. If 'both' both NCBI and ITIS will be queried. Result will be the union of both. If using ncbi, we recommend getting an API key; see taxize-authentication |
pref |
(character) If db = 'both', sets the preference for the union. Either 'ncbi' (default) or 'itis'. Currently not implemented. |
messages |
(logical) If |
query |
Deprecated, see |
... |
A data.frame with one column for every queried rank, in addition to a column for db and queried term.
See taxize-authentication for help on authentication
While tax_rank()
returns the actual rank of a
taxon, tax_name()
searches and returns any specified rank
higher in taxonomy.
## Not run: # A case where itis and ncbi use the same names tax_name(sci = "Helianthus annuus", get = "family", db = "itis") tax_name(sci = "Helianthus annuus", get = "family", db = "ncbi") tax_name(sci = "Helianthus annuus", get = c("genus","family","order"), db = "ncbi") # Case where itis and ncbi use different names tax_name(sci = "Helianthus annuus", get = "kingdom", db = "itis") tax_name(sci = "Helianthus annuus", get = "kingdom", db = "ncbi") # multiple rank arguments tax_name(sci = c("Helianthus annuus","Baetis rhodani"), get = c("genus", "kingdom"), db = "ncbi") tax_name(sci = c("Helianthus annuus","Baetis rhodani"), get = c("genus", "kingdom"), db = "itis") # query both sources tax_name(sci=c("Helianthus annuus", 'Baetis rhodani'), get=c("genus", "kingdom"), db="both") ## End(Not run)
## Not run: # A case where itis and ncbi use the same names tax_name(sci = "Helianthus annuus", get = "family", db = "itis") tax_name(sci = "Helianthus annuus", get = "family", db = "ncbi") tax_name(sci = "Helianthus annuus", get = c("genus","family","order"), db = "ncbi") # Case where itis and ncbi use different names tax_name(sci = "Helianthus annuus", get = "kingdom", db = "itis") tax_name(sci = "Helianthus annuus", get = "kingdom", db = "ncbi") # multiple rank arguments tax_name(sci = c("Helianthus annuus","Baetis rhodani"), get = c("genus", "kingdom"), db = "ncbi") tax_name(sci = c("Helianthus annuus","Baetis rhodani"), get = c("genus", "kingdom"), db = "itis") # query both sources tax_name(sci=c("Helianthus annuus", 'Baetis rhodani'), get=c("genus", "kingdom"), db="both") ## End(Not run)
Get rank for a given taxonomic name.
tax_rank(sci_id, db = NULL, rows = NA, x = NULL, ...)
tax_rank(sci_id, db = NULL, rows = NA, x = NULL, ...)
sci_id |
(character) Vector of one or more taxon names (character) or
IDs (character or numeric) to query. Or objects returned from |
db |
(character) database to query. either |
rows |
numeric; Any number from 1 to infinity. If the default NA,
all rows are considered. passed down to |
x |
Deprecated, see |
... |
Additional arguments to |
A named list of character vectors with ranks (all lower-cased)
While tax_name()
returns the name of a specified
rank, tax_rank()
returns the actual rank of the taxon.
## Not run: tax_rank("Helianthus annuus", db = "itis") tax_rank("Helianthus annuus", db = "natserv") tax_rank(get_tsn("Helianthus annuus")) tax_rank(c("Helianthus", "Pinus", "Poa"), db = "itis") tax_rank(get_boldid("Helianthus annuus")) tax_rank("421377", db = "bold") tax_rank(421377, db = "bold") tax_rank(c("Plantae", "Helianthus annuus", "Puma", "Homo sapiens"), db = 'itis') tax_rank(c("Helianthus annuus", "Quercus", "Fabaceae"), db = 'tropicos') tax_rank(names_list("species"), db = 'gbif') tax_rank(names_list("family"), db = 'gbif') tax_rank(c("Gadus morhua", "Lichenopora neapolitana"), db = "worms") ## End(Not run)
## Not run: tax_rank("Helianthus annuus", db = "itis") tax_rank("Helianthus annuus", db = "natserv") tax_rank(get_tsn("Helianthus annuus")) tax_rank(c("Helianthus", "Pinus", "Poa"), db = "itis") tax_rank(get_boldid("Helianthus annuus")) tax_rank("421377", db = "bold") tax_rank(421377, db = "bold") tax_rank(c("Plantae", "Helianthus annuus", "Puma", "Homo sapiens"), db = 'itis') tax_rank(c("Helianthus annuus", "Quercus", "Fabaceae"), db = 'tropicos') tax_rank(names_list("species"), db = 'gbif') tax_rank(names_list("family"), db = 'gbif') tax_rank(c("Gadus morhua", "Lichenopora neapolitana"), db = "worms") ## End(Not run)
Capitalize the first letter of a character string.
taxize_capwords(s, strict = FALSE, onlyfirst = FALSE)
taxize_capwords(s, strict = FALSE, onlyfirst = FALSE)
s |
A character string |
strict |
Should the algorithm be strict about capitalizing. Defaults to FALSE. |
onlyfirst |
Capitalize only first word, lowercase all others. Useful for taxonomic names. |
taxize_capwords(c("using AIC for model selection")) taxize_capwords(c("using AIC for model selection"), strict=TRUE)
taxize_capwords(c("using AIC for model selection")) taxize_capwords(c("using AIC for model selection"), strict=TRUE)
Get citations and licenses for data sources used in taxize
taxize_cite(fxn = "itis", what = "citation")
taxize_cite(fxn = "itis", what = "citation")
fxn |
Function to search on. A special case is the package name 'taxize' that will give the citations for the package. |
what |
One of citation (default), license, or both. |
taxize_cite(fxn='eol_search') taxize_cite(fxn='itis_hierarchy') taxize_cite(fxn='tp_classification') taxize_cite(fxn='gbif_ping') taxize_cite(fxn='plantminer') taxize_cite(fxn='get_natservid_') taxize_cite(fxn='as.natservid') taxize_cite(fxn='get_wormsid') taxize_cite(fxn='as.wormsid') # Functions that use many data sources taxize_cite(fxn='synonyms') taxize_cite(fxn='classification') # Get the taxize citation taxize_cite(fxn='taxize') # Get license information taxize_cite(fxn='taxize', "license")
taxize_cite(fxn='eol_search') taxize_cite(fxn='itis_hierarchy') taxize_cite(fxn='tp_classification') taxize_cite(fxn='gbif_ping') taxize_cite(fxn='plantminer') taxize_cite(fxn='get_natservid_') taxize_cite(fxn='as.natservid') taxize_cite(fxn='get_wormsid') taxize_cite(fxn='as.wormsid') # Functions that use many data sources taxize_cite(fxn='synonyms') taxize_cite(fxn='classification') # Get the taxize citation taxize_cite(fxn='taxize') # Get license information taxize_cite(fxn='taxize', "license")
taxize options
taxize_options(taxon_state_messages = NULL, ncbi_sleep = NULL, quiet = FALSE)
taxize_options(taxon_state_messages = NULL, ncbi_sleep = NULL, quiet = FALSE)
taxon_state_messages |
(logical) suppress messages? default: |
ncbi_sleep |
(numeric/integer) number of seconds to sleep between
NCBI ENTREZ http requests. applies to the functions: |
quiet |
(logical) quiet informational output from this function.
default: |
## Not run: taxize_options() taxize_options(FALSE) taxize_options(TRUE) taxize_options(ncbi_sleep = 0.4) taxize_options(taxon_state_messages = TRUE, ncbi_sleep = 0.4) ## End(Not run)
## Not run: taxize_options() taxize_options(FALSE) taxize_options(TRUE) taxize_options(ncbi_sleep = 0.4) taxize_options(taxon_state_messages = TRUE, ncbi_sleep = 0.4) ## End(Not run)
Help on authentication
An API is an Application Programming Interface. The term "API" can be used for lots of scenarios, but in this case we're talking about web APIs, or APIs (interfaces) to web resources. taxize interacts with remote databases on the web via their APIs. You don't need to worry about the details of how that all works; just know that some of them require authentication and some do not.
For those APIs that require authentication, the way that's typically done is through API keys: alphanumeric strings of variable lengths that are supplied with a request to an API.
taxize won't get these keys for you; rather, you have to
go get a key for each service, but we do provide information on how
to get those keys. See key_helpers()
for help on how to
obtain keys for this package.
You can store API keys as R options in your .Rprofile
file, or
as environment variables in either your .Renviron
file or
.bash_profile
file, o.zshrc
file (if you use oh-my-zsh) or
similar. See Startup for help on R options and environment
variables.
Save your API keys with the following names:
Tropicos: R option or env var as 'TROPICOS_KEY'
IUCN: R option or env var as 'IUCN_REDLIST_KEY'
ENTREZ: R option or env var as 'ENTREZ_KEY'
If you save in .Renviron it looks like: ENTREZ_KEY=somekey
If you save in a .bash_profile, .zshrc, or similar file it looks like:
export ENTREZ_KEY=somekey
If you save in a .Rprofile it looks like: options(ENTREZ_KEY = "somekey")
Remember to restart your R session (and to start a new shell window/tab if you're using the shell) to take advantage of the new R options or environment variables.
We strongly recommend using environment variables (https://en.wikipedia.org/wiki/Environment_variable) over R options because environment variables are widely used across programming languages, operating systems, and computing environments; whereas R options are specific to R.
Note that NCBI Entrez doesn't require that you use an API key, but you do get a higher rate limit with a key (more requests per time period), from 3 to 10 requests per second, so do get one.
The following functions are now defunct (no longer available):
All COL functions are defunct: as.colid,
col_children,
col_classification,
col_downstream,
col_search,
get_colid,
get_colid_,
as.data.frame.colid,
children.colid,
classification.colid,
downstream.colid,
id2name.colid,
lowest_common.colid,
synonyms.colid,
upstream.colid'
col_classification()
: Seeclassification()
tp_classification()
: Seeclassification()
eol_hierarchy()
: Seeclassification()
eol_invasive()
: See eol
in the originr package.
use_eol()
: EOL no longer requires an API key
tpl_search()
: Use the Taxonstand functions TPL
or TPLck
directly.
get_seqs()
: This function changed name toncbi_getbyname()
()].
get_genes()
: This function changed name toncbi_getbyid()
()].
get_genes_avail()
: This function changed name toncbi_search()
()].
ncbi_getbyname()
: See ncbi_byname
in the traits package.
ncbi_getbyid()
: See ncbi_byid
in the traits package.
ncbi_search()
: See ncbi_searcher
in the traits package.
gisd_isinvasive()
: See gisd
in the originr package.
ubio_classification()
: The uBio web services was down for quite a while, is
now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.
ubio_classification_search()
: The uBio web services was down for quite
a while, is now (as of 2016-05-09) back up, but we don't trust that it will stay up
and available.
ubio_id()
: The uBio web services was down for quite a while, is
now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.
ubio_ping()
: The uBio web services was down for quite a while, is
now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.
ubio_search()
: The uBio web services was down for quite a while, is
now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.
ubio_synonyms()
: The uBio web services was down for quite a while, is
now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.
get_ubioid()
: The uBio web services are apparently down indefinitely.
phylomatic_tree()
: This function is defunct. See
phylomatic
in the package brranching
phylomatic_format()
: This function is defunct. See
phylomatic_names
in the package brranching
iucn_summary_id()
: This function is defunct. Use iucn_summary()
eubon()
: This function is defunct. Use eubon_search()
tnrs()
: This function is defunct. Was too unreliable
tnrs_sources()
: This function is defunct. Was too unreliable
Information on standardized parameters across the package
sci
: scientific name
com
: common name
id
: name identifier
sci_com
: scientific name or common name
sci_id
: scientific name or name identifier
We were going to standardize parameter names for cases in which
a parameter accepts either of three options: scientific name,
common name, or name identifier. However, there was no clear
parameter name we could use for this case, so we've left
parameter names as they are for the two cases (get_ids()
and
vascan_search()
)
get_*
function callLast taxon state object from a get_*
function call
taxon_last() taxon_clear()
taxon_last() taxon_clear()
taxon_last()
: get the last taxon_state
object in use
taxon_clear()
: clear any data from last taxon_state
object
The taxon_state
object is an R6 object that holds data and methods
used for keeping track of results gathered within a get_*
function.
You shouldn't create taxon_state
R6 objects yourself.
Behaviors to be aware of:
If a taxon_state
object is not passed you don't need to worry about
a previously run get_*
function interfering with another get_*
function call - you have to explicitly pass a taxon_state
object
to use taxon_state
The passed in taxon_state
object must have a $class
matching that of
the get_*
function being called. For example, you can only pass a
taxon_state
with $class
of gbifid
to get_gbifid()
, and so on.
If you run taxon_clear()
while a get*
function is running, you may
lose track of any state known to this package before it was cleared
See the internal method progressor for information on how we control messages
in get*
functions
taxon_last()
returns an object of class taxon_state
, the last
one used, else NULL
if none found. taxon_clear()
clears the saved state
## Not run: spp <- names_list("species", 3) res <- get_gbifid(spp) z <- taxon_last() z z$taxa_remaining() z$taxa_completed() z$count # active binding; no parens needed # cleanup taxon_clear() ## End(Not run)
## Not run: spp <- names_list("species", 3) res <- get_gbifid(spp) z <- taxon_last() z z$taxa_remaining() z$taxa_completed() z$count # active binding; no parens needed # cleanup taxon_clear() ## End(Not run)
These names are from http://www.theplantlist.org, and are from
version 1.1 of their data. This data is used in the function
names_list()
. This is a randomly selected subset of the ~350K
accepted species names in Theplantlist.
A data frame with 10,000 rows and 3 variables:
family
family name
genus
genus name
species
specific epithet name
http://www.theplantlist.org
Resolve names using Open Tree of Life (OTL) resolver
tol_resolve( names = NULL, context_name = NULL, do_approximate_matching = TRUE, ids = NULL, include_suppressed = FALSE, ... )
tol_resolve( names = NULL, context_name = NULL, do_approximate_matching = TRUE, ids = NULL, include_suppressed = FALSE, ... )
names |
(character) taxon names to be queried |
context_name |
name of the taxonomic context to be searched
(length-one character vector). Must match (case sensitive) one
of the values returned by |
do_approximate_matching |
(logical) A logical indicating whether or not
to perform approximate string (a.k.a. “fuzzy”) matching. Using |
ids |
An array of OTL ids to use for identifying names. These will be assigned to each name in the names array. If ids is provided, then ids and names must be identical in length. |
include_suppressed |
(logical) Ordinarily, some quasi-taxa, such as
incertae sedis buckets and other non-OTUs, are suppressed from TNRS
results. If this parameter is true, these quasi-taxa are allowed as
possible TNRS results. Default: |
... |
Curl options passed on to |
A data frame summarizing the results of the query. The
original query output is appended as an attribute to the
returned object (and can be obtained using
attr(object, "original_response")
).
Francois Michonneau [email protected] Scott Chamberlain
https://github.com/OpenTreeOfLife/germinator/wiki/TNRS-API-v3#match_names
## Not run: tol_resolve(names=c("echinodermata", "xenacoelomorpha", "chordata", "hemichordata")) tol_resolve(c("Hyla", "Salmo", "Diadema", "Nautilus")) tol_resolve(c("Hyla", "Salmo", "Diadema", "Nautilus"), context_name = "Animals") turducken_spp <- c("Meleagris gallopavo", "Anas platyrhynchos", "Gallus gallus") tol_resolve(turducken_spp, context_name="Animals") ## End(Not run)
## Not run: tol_resolve(names=c("echinodermata", "xenacoelomorpha", "chordata", "hemichordata")) tol_resolve(c("Hyla", "Salmo", "Diadema", "Nautilus")) tol_resolve(c("Hyla", "Salmo", "Diadema", "Nautilus"), context_name = "Animals") turducken_spp <- c("Meleagris gallopavo", "Anas platyrhynchos", "Gallus gallus") tol_resolve(turducken_spp, context_name="Animals") ## End(Not run)
Return all accepted names for a taxon name with a given id.
tp_accnames(id, key = NULL, ...)
tp_accnames(id, key = NULL, ...)
id |
the taxon identifier code |
key |
Your Tropicos API key; See taxize-authentication for help on authentication |
... |
Curl options passed on to crul::verb-GET |
List or dataframe.
## Not run: tp_accnames(id = 25503923) tp_accnames(id = 25538750) # No accepted names found tp_accnames(id = 25509881) ## End(Not run)
## Not run: tp_accnames(id = 25503923) tp_accnames(id = 25538750) # No accepted names found tp_accnames(id = 25509881) ## End(Not run)
Return all distribution records for for a taxon name with a given id.
tp_dist(id, key = NULL, ...)
tp_dist(id, key = NULL, ...)
id |
the taxon identifier code |
key |
Your Tropicos API key; See taxize-authentication for help on authentication |
... |
Curl options passed on to crul::HttpClient |
List of two data.frame's, one named "location", and one "reference".
http://services.tropicos.org/help?method=GetNameDistributionsXml
## Not run: # Query using a taxon name Id out <- tp_dist(id = 25509881) ## just location data head(out[['location']]) ## just reference data head(out[['reference']]) ## End(Not run)
## Not run: # Query using a taxon name Id out <- tp_dist(id = 25509881) ## just location data head(out[['location']]) ## just reference data head(out[['reference']]) ## End(Not run)
Return all reference records for for a taxon name with a given id.
tp_refs(id, key = NULL, ...)
tp_refs(id, key = NULL, ...)
id |
the taxon identifier code |
key |
Your Tropicos API key; See taxize-authentication for help on authentication |
... |
Curl options passed on to crul::HttpClient |
List or dataframe.
## Not run: tp_refs(id = 25509881) ## End(Not run)
## Not run: tp_refs(id = 25509881) ## End(Not run)
Search Tropicos by scientific name, common name, or Tropicos ID.
tp_search( sci = NULL, com = NULL, nameid = NULL, orderby = NULL, sortorder = NULL, pagesize = NULL, startrow = NULL, type = NULL, key = NULL, name = NULL, commonname = NULL, ... )
tp_search( sci = NULL, com = NULL, nameid = NULL, orderby = NULL, sortorder = NULL, pagesize = NULL, startrow = NULL, type = NULL, key = NULL, name = NULL, commonname = NULL, ... )
sci |
A scientific name, e.g., "poa annua". See Details. |
com |
A common name, e.g., "annual blue grass" |
nameid |
Your search string. e.g., "25509881" |
orderby |
Your search string. e.g., "1" |
sortorder |
Your search string. e.g., "ascending" |
pagesize |
Your search string. e.g., "100" |
startrow |
Your search string. e.g., "1" |
type |
Type of search, "wildcard" (default) will add a wildcard to the end of your search string. "exact" will use your search string exactly. |
key |
Your Tropicos API key; See taxize-authentication for help on authentication |
name |
Deprecated, see |
commonname |
Deprecated, see |
... |
Further args passed on to crul::HttpClient |
More details on the name
parameter: Tropicos will fail
if you include a period (.
) in your name string, e.g., var.
,
so we replace periods before the request is made to the Tropicos web service.
In addition, Tropicos for some reason doesn't want to see sub-specific rank
names like var
/subsp
, so remove those from your query.
List or dataframe.
http://services.tropicos.org/help?method=SearchNameXml
## Not run: tp_search(sci = 'Poa annua') tp_search(sci = 'Poa annua subsp. annua') tp_search(sci = 'Poa annua var. annua') tp_search(sci = 'Poa annua var annua') tp_search(sci = 'Poa annua annua') ## End(Not run)
## Not run: tp_search(sci = 'Poa annua') tp_search(sci = 'Poa annua subsp. annua') tp_search(sci = 'Poa annua var. annua') tp_search(sci = 'Poa annua var annua') tp_search(sci = 'Poa annua annua') ## End(Not run)
Return summary data a taxon name with a given id.
tp_summary(id, key = NULL, ...)
tp_summary(id, key = NULL, ...)
id |
the taxon identifier code |
key |
Your Tropicos API key; See taxize-authentication for help on authentication |
... |
Curl options passed on to crul::verb-GET |
A data.frame.
## Not run: tp_summary(id = 25509881) tp_summary(id = 2700851) tp_summary(id = 24900183) ## End(Not run)
## Not run: tp_summary(id = 25509881) tp_summary(id = 2700851) tp_summary(id = 24900183) ## End(Not run)
Return all synonyms for a taxon name with a given id.
tp_synonyms(id, key = NULL, ...)
tp_synonyms(id, key = NULL, ...)
id |
the taxon identifier code |
key |
Your Tropicos API key; See taxize-authentication for help on authentication |
... |
Curl options passed on to crul::HttpClient |
List or dataframe.
## Not run: tp_synonyms(id = 25509881) ## End(Not run)
## Not run: tp_synonyms(id = 25509881) ## End(Not run)
Get The Plant List families.
tpl_families(...)
tpl_families(...)
... |
(list) Curl options passed on to crul::verb-GET |
Requires an internet connection in order to connect to <www.theplantlist.org>.
Returns a data.frame
including the names of all families
indexed by The Plant List, and the major groups into which they fall
(i.e. Angiosperms, Gymnosperms, Bryophytes and Pteridophytes).
John Baumgartner ([email protected])
## Not run: # Get a data.frame of plant families, with the group name # (Angiosperms, etc.) head(tpl_families()) ## End(Not run)
## Not run: # Get a data.frame of plant families, with the group name # (Angiosperms, etc.) head(tpl_families()) ## End(Not run)
Get The Plant List csv files.
tpl_get(x, family = NULL, ...)
tpl_get(x, family = NULL, ...)
x |
Directory to write csv files to. |
family |
If you want just one, or >1 family, but not all, list them in a vector. |
... |
(list) Curl options passed on to crul::verb-GET |
Throws a warning if you already have a directory of the one provided, but still works. Writes to your home directory, change x as needed.
Returns nothing to console, except a message and progress bar. Writes csv files to x.
John Baumgartner [email protected]
The Plant List http://www.theplantlist.org
## Not run: # Get a few families dir <- file.path(tempdir(), "abc") tpl_get(dir, family = c("Platanaceae","Winteraceae")) readLines(file.path(dir, "Platanaceae.csv"), n = 5) # You can now get Gymnosperms as well dir1 <- file.path(tempdir(), "def") tpl_get(dir1, family = c("Pinaceae","Taxaceae")) # You can get mosses too! dir2 <- file.path(tempdir(), "ghi") tpl_get(dir2, family = "Echinodiaceae") # Get all families ## Beware, will take a while ## dir3 <- file.path(tempdir(), "jkl") ## tpl_get("dir3) ## End(Not run)
## Not run: # Get a few families dir <- file.path(tempdir(), "abc") tpl_get(dir, family = c("Platanaceae","Winteraceae")) readLines(file.path(dir, "Platanaceae.csv"), n = 5) # You can now get Gymnosperms as well dir1 <- file.path(tempdir(), "def") tpl_get(dir1, family = c("Pinaceae","Taxaceae")) # You can get mosses too! dir2 <- file.path(tempdir(), "ghi") tpl_get(dir2, family = "Echinodiaceae") # Get all families ## Beware, will take a while ## dir3 <- file.path(tempdir(), "jkl") ## tpl_get("dir3) ## End(Not run)
THIS FUNCTION IS DEFUNCT.
tpl_search()
tpl_search()
This function uses a while loop to continually collect taxa up to the
taxonomic rank that you specify in the upto
parameter. You can get data
from ITIS (itis) only currently. There is no method exposed by itis
for getting taxa at a specific taxonomic rank, so we do it ourselves inside
the function.
upstream(...) ## Default S3 method: upstream(sci_id, db = NULL, upto = NULL, rows = NA, x = NULL, ...) ## S3 method for class 'tsn' upstream(sci_id, db = NULL, upto = NULL, ...) ## S3 method for class 'ids' upstream(sci_id, db = NULL, upto = NULL, ...)
upstream(...) ## Default S3 method: upstream(sci_id, db = NULL, upto = NULL, rows = NA, x = NULL, ...) ## S3 method for class 'tsn' upstream(sci_id, db = NULL, upto = NULL, ...) ## S3 method for class 'ids' upstream(sci_id, db = NULL, upto = NULL, ...)
... |
Further args passed on to |
sci_id |
Vector of taxa names (character) or IDs (character or numeric) to query. |
db |
character; database to query. One or both of |
upto |
What taxonomic rank to go down to. One of: 'superkingdom', 'kingdom', 'subkingdom','infrakingdom','phylum','division','subphylum', 'subdivision','infradivision', 'superclass','class','subclass','infraclass', 'superorder','order','suborder','infraorder','superfamily','family', 'subfamily','tribe','subtribe','genus','subgenus', 'section','subsection', 'species','subspecies','variety','form','subvariety','race', 'stirp', 'morph','aberration','subform', or 'unspecified' |
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 of any of the acceptable classes: tsn. |
x |
Deprecated, see |
A named list of data.frames with the upstream names of every supplied taxa. You get an NA if there was no match in the database.
## Not run: upstream('Pinus contorta', db = 'itis', upto = 'genus') ## End(Not run)
## Not run: upstream('Pinus contorta', db = 'itis', upto = 'genus') ## End(Not run)
Search the CANADENSYS Vascan API.
vascan_search(q, format = "json", raw = FALSE, ...)
vascan_search(q, format = "json", raw = FALSE, ...)
q |
(character) Can be a scientific name, a vernacular name or a VASCAN taxon identifier (e.g. 861) |
format |
(character) One of json (default) or xml. |
raw |
(logical) If TRUE, raw json or xml returned, if FALSE, parsed data returned. |
... |
(list) Further args passed on to crul::verb-GET |
Note that we lowercase all outputs in data.frame's, but when a list is given back, we don't touch the list names.
json, xml or a list.
Scott Chamberlain
API docs https://data.canadensys.net/vascan/api
## Not run: vascan_search(q = "Helianthus annuus") vascan_search(q = "Helianthus annuus", raw=TRUE) vascan_search(q = c("Helianthus annuus", "Crataegus dodgei"), raw=TRUE) # format type ## json c <- vascan_search(q = "Helianthus annuus", format="json", raw=TRUE) library("jsonlite") fromJSON(c, FALSE) ## xml d <- vascan_search(q = "Helianthus annuus", format="xml", raw=TRUE) library("xml2") xml2::read_xml(d) # lots of names, in this case 50 splist <- names_list(rank='species', size=50) vascan_search(q = splist) # Curl options invisible(vascan_search(q = "Helianthus annuus", verbose = TRUE)) ## End(Not run)
## Not run: vascan_search(q = "Helianthus annuus") vascan_search(q = "Helianthus annuus", raw=TRUE) vascan_search(q = c("Helianthus annuus", "Crataegus dodgei"), raw=TRUE) # format type ## json c <- vascan_search(q = "Helianthus annuus", format="json", raw=TRUE) library("jsonlite") fromJSON(c, FALSE) ## xml d <- vascan_search(q = "Helianthus annuus", format="xml", raw=TRUE) library("xml2") xml2::read_xml(d) # lots of names, in this case 50 splist <- names_list(rank='species', size=50) vascan_search(q = splist) # Curl options invisible(vascan_search(q = "Helianthus annuus", verbose = TRUE)) ## End(Not run)
Retrieve all taxa names downstream in hierarchy for WORMS
worms_downstream(id, downto, intermediate = FALSE, start = 1, ...)
worms_downstream(id, downto, intermediate = FALSE, start = 1, ...)
id |
(integer) One or more AphiaID's |
downto |
(character) The taxonomic level you want to go down to. See examples below. The taxonomic level IS case sensitive, and you do have to spell it correctly. See rank_ref_zoo for spelling. |
intermediate |
(logical) If |
start |
(integer) Record number to start at |
... |
crul options passed on to |
data.frame of taxonomic information downstream to family from e.g.,
Order, Class, etc., or if intermediated=TRUE
, list of length two,
with target taxon rank names, and intermediate names.
## Not run: ## the genus Gadus worms_downstream(id = 125732, downto="species") worms_downstream(id = 125732, downto="species", intermediate=TRUE) worms_downstream(id = 51, downto="class") worms_downstream(id = 51, downto="subclass", intermediate=TRUE) worms_downstream(id = 105, downto="subclass") # marine_only parameter worms_downstream(545470, downto = "species") worms_downstream(545470, downto = "species", marine_only = FALSE) ## End(Not run)
## Not run: ## the genus Gadus worms_downstream(id = 125732, downto="species") worms_downstream(id = 125732, downto="species", intermediate=TRUE) worms_downstream(id = 51, downto="class") worms_downstream(id = 51, downto="subclass", intermediate=TRUE) worms_downstream(id = 105, downto="subclass") # marine_only parameter worms_downstream(545470, downto = "species") worms_downstream(545470, downto = "species", marine_only = FALSE) ## End(Not run)
Created using worrms::wm_ranks_id(-1)
on 2020-02-11.
A data frame with 216 rows and 2 variables:
id
: rank id
rank
: rank name
Present in taxize in the case where WORMS does not return rank names - with this dataset we can fill in rank information as long as rank ids are returned