Taxonomic Information from Around the Web

Description

This package interacts with a suite of web 'APIs' for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.

About

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.

Currently supported APIs

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

Catalogue of Life (COL)

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+

Author(s)

Scott Chamberlain

Eduard Szoecs eduardszoecs@gmail.com

Zachary Foster zacharyfoster1989@gmail.com

Carl Boettiger cboettig@gmail.com

Karthik Ram karthik@ropensci.org

Ignasi Bartomeus nacho.bartomeus@gmail.com

John Baumgartner johnbb@student.unimelb.edu.au

James O'Donnell jodonnellbio@gmail.com

Get APG names

Description

Generic names and their replacements from the Angiosperm Phylogeny Group III system of flowering plant classification.

Usage

apgOrders(...)

apgFamilies(...)

Arguments

References

http://www.mobot.org/MOBOT/research/APweb/

Examples

## Not run: 
head(apgOrders())
head(apgFamilies())

## End(Not run)

MOBOT family names

Description

Family names and their replacements from the Angiosperm Phylogeny Website system of flowering plant classification.

Format

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

Details

This dataset is from Version 14, incorporated on 2020-06-03, generated using apgFamilies()

(update script in inst/ignore/apg_script.R)

Source

http://www.mobot.org/MOBOT/research/APweb/

Lookup in the APGIII taxonomy and replace family names

Description

Lookup in the APGIII taxonomy and replace family names

Usage

apg_lookup(taxa, rank = "family")

Arguments

Details

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/)

Value

A APGIII family or order name, the original name if the name is the same as APG has, or NA if no match found

Examples

# 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")

MOBOT order names

Description

Order names and their replacements from the Angiosperm Phylogeny Website system of flowering plant classification.

Format

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

Details

This dataset is from Version 14, incorporated on 2020-06-03, generated using apgOrders()

(update script in inst/ignore/apg_script.R)

Source

http://www.mobot.org/MOBOT/research/APweb/

Barcode of Life taxonomic children

Description

BEWARE: this function scrapes data from 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

Usage

bold_children(id, ...)

Arguments

Value

list of data.frame's

Examples

## Not run: 
# Osmia (genus): 253 children
bold_children(id = 4940)
# Momotus (genus): 3 children
bold_children(id = 88899)
# Momotus aequatorialis (species): no children
bold_children(id = 115130)
# Osmia sp1 (species): no children
bold_children(id = 293378)
# Arthropoda (phylum): 27 children
bold_children(id = 82)
# Psocodea (order): 51 children
bold_children(id = 737139)
# Megachilinae (subfamily): 2 groups (tribes: 3, genera: 60)
bold_children(id = 4962)
# Stelis (species): 78 taxa
bold_children(id = 4952)

## End(Not run)

Retrieve all taxa names downstream in hierarchy for BOLD

Description

Retrieve all taxa names downstream in hierarchy for BOLD

Usage

bold_downstream(id, downto, intermediate = FALSE, ...)

Arguments

Details

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

Value

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.

Examples

## 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

Description

Search Barcode of Life for taxonomic IDs

Usage

bold_search(
  sci = NULL,
  id = NULL,
  fuzzy = FALSE,
  dataTypes = "basic",
  includeTree = FALSE,
  response = FALSE,
  name = NULL,
  ...
)

Arguments

Details

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.

Value

A list of data.frame's.

References

http://www.boldsystems.org/index.php/resources/api

Examples

## 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)

Search BOLD for taxonomy data by BOLD ID.

Description

Search BOLD for taxonomy data by BOLD ID.

Usage

bold_tax_id(
  id,
  dataTypes = "basic",
  includeTree = FALSE,
  response = FALSE,
  ...
)

Search BOLD for taxonomy data by BOLD ID.

Description

Search BOLD for taxonomy data by BOLD ID.

Usage

bold_tax_id2(
  id,
  dataTypes = "basic",
  includeTree = FALSE,
  response = FALSE,
  ...
)

Retrieve immediate children taxa for a given taxon name or ID.

Description

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.

Usage

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, ...)

Arguments

Value

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.

ncbi

note that with db = "ncbi", we set ambiguous = TRUE; that is, children taxa with words like "unclassified", "unknown", "uncultured", "sp." are NOT removed

bold

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

Examples

## 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)

Convert a list of classifications to a tree.

Description

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.

Usage

class2tree(input, varstep = TRUE, check = TRUE, remove_shared = FALSE, ...)

## S3 method for class 'classtree'
plot(x, ...)

## S3 method for class 'classtree'
print(x, ...)

Arguments

Details

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.

Value

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.

Examples

## 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.

Description

Retrieve the taxonomic hierarchy for a given taxon ID.

Usage

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(...)

Arguments

Details

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

Value

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

Lots of results

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.

Authentication

See taxize-authentication

EOL

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?

NCBI Rate limits

In case you run into NCBI errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

HTTP version for NCBI requests

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 Also

get_tsn(), get_uid(), get_eolid(), get_tpsid(), get_gbifid(), get_wormsid(), get_natservid(), get_boldid(), get_wiki(), get_pow()

Examples

## 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)

COL defunct functions

Description

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

Usage

as.colid(...)

col_children(...)

col_classification(...)

col_downstream(...)

col_search(...)

get_colid(...)

get_colid_(...)

Arguments

Get scientific names from common names.

Description

Get scientific names from common names.

Usage

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, ...)

Arguments

Details

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.

Value

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

Authentication

See taxize-authentication for help on authentication

HTTP version for NCBI requests

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')

Rate limits

In case you run into errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

Author(s)

Scott Chamberlain

See Also

sci2comm()

Examples

## 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)

Retrieve the downstream taxa for a given taxon name or ID.

Description

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.

Usage

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, ...)

Arguments

Value

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.

Authentication

See taxize-authentication for help on authentication

bold

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

Examples

## 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

Description

Given the identifier for a data object, return all metadata about the object

Usage

eol_dataobjects(id, taxonomy = TRUE, language = NULL, ...)

Arguments

Details

It's possible to return JSON or XML with the EOL API. However, this function only returns JSON for now.

Value

A list, optionally with a data.frame if taxonomy=TRUE

Examples

## Not run: 
eol_dataobjects(id = 7561533)

# curl options
eol_dataobjects(id = 7561533, verbose = TRUE)

## End(Not run)

Retrieve the taxonomic hierarchy from given EOL taxonID.

Description

THIS FUNCTION IS DEFUNCT.

Usage

eol_hierarchy(...)

Search for presence of taxonomic names in EOL invasive species databases.

Description

THIS FUNCTION IS DEFUNCT.

Usage

eol_invasive(...)

Search for pages in EOL database using a taxonconceptID.

Description

Search for pages in EOL database using a taxonconceptID.

Usage

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,
  ...
)

Arguments

Details

It's possible to return JSON or XML with the EOL API. However, this function only returns JSON for now.

Value

JSON list object, or data.frame.

Examples

## 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.

Description

Search for terms in EOL database.

Usage

eol_search(
  sci,
  page = 1,
  exact = NULL,
  filter_tid = NULL,
  filter_heid = NULL,
  filter_by_string = NULL,
  cache_ttl = NULL,
  terms = NULL,
  ...
)

Arguments

Details

It's possible to return JSON or XML with the EOL API. However, this function only returns JSON for now.

Value

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

Examples

## Not run: 
eol_search(sci='Homo')
eol_search(sci='Salix', verbose = TRUE)
eol_search(sci='Ursus americanus')
eol_search('Pinus contorta')

## End(Not run)

DEFUNCT

Description

DEFUNCT

Usage

eubon(...)

EUBON capabilities

Description

EUBON capabilities

Usage

eubon_capabilities(...)

Arguments

References

https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html

See Also

Other eubon-methods: eubon_children(), eubon_hierarchy(), eubon_search()

Examples

## Not run: 
eubon_capabilities()

## End(Not run)

EUBON children

Description

EUBON children

Usage

eubon_children(id, providers = NULL, timeout = 0, ...)

Arguments

Value

a data.frame or an empty list if no results found

Note

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

References

https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html

See Also

Other eubon-methods: eubon_capabilities(), eubon_hierarchy(), eubon_search()

Examples

## Not run: 
x <- eubon_children(id = "urn:lsid:marinespecies.org:taxname:126141",
  providers = 'worms')
head(x)

## End(Not run)

EUBON hierarchy

Description

EUBON hierarchy

Usage

eubon_hierarchy(id, providers = "pesi", timeout = 0, ...)

Arguments

Note

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

References

https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html

See Also

Other eubon-methods: eubon_capabilities(), eubon_children(), eubon_search()

Examples

## 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

Description

EUBON taxonomy search

Usage

eubon_search(
  query,
  providers = "pesi",
  searchMode = "scientificNameExact",
  addSynonymy = FALSE,
  addParentTaxon = FALSE,
  timeout = 0,
  dedup = NULL,
  limit = 20,
  page = 1,
  ...
)

Arguments

References

https://cybertaxonomy.eu/eu-bon/utis/1.3/doc.html

See Also

Other eubon-methods: eubon_capabilities(), eubon_children(), eubon_hierarchy()

Examples

## 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)

Index Fungorum

Description

Search for taxonomic names in Index Fungorum

Usage

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, ...)

Arguments

Value

A data.frame, or NULL if no results

References

http://www.indexfungorum.org/, API docs: http://www.indexfungorum.org/ixfwebservice/fungus.asmx

Examples

## 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

Description

Retrieve all taxonomic names downstream in hierarchy for GBIF

Usage

gbif_downstream(
  id,
  downto,
  intermediate = FALSE,
  limit = 100,
  start = NULL,
  key = NULL,
  ...
)

Arguments

Details

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

Value

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.

Author(s)

Scott Chamberlain

Examples

## 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)

Lookup details for specific names in all taxonomies in GBIF.

Description

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.

Usage

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,
  ...
)

Arguments

Value

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)

References

https://www.gbif.org/developer/summary

Parse taxon names using the GBIF name parser.

Description

Parse taxon names using the GBIF name parser.

Usage

gbif_parse(scientificname, ...)

Arguments

Value

A data.frame containing fields extracted from parsed taxon names. Fields returned are the union of fields extracted from all species names in scientificname.

Author(s)

John Baumgartner johnbb@student.unimelb.edu.au

References

https://www.gbif.org/tools/name-parser/about

See Also

gni_parse(), gna_parse()

Examples

## 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

Description

Get NCBI taxonomy UID from GenBankID

Usage

genbank2uid(id, batch_size = 100, key = NULL, ...)

Arguments

Details

See https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html for help on why there are two identifiers, and the difference between them.

Value

one or more NCBI taxonomic IDs

Authentication

See taxize-authentication for help on authentication. We recommend getting an API key.

HTTP version

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')

Rate limits

In case you run into errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

Examples

## 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.

Description

Get the BOLD (Barcode of Life) code for a search term.

Usage

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,
  ...
)

Arguments

Value

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

Filtering

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.

See Also

classification()

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()

Examples

## 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)

Get the EOL ID from Encyclopedia of Life from taxonomic names.

Description

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.

Usage

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, ...)

Arguments

Details

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.

Value

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

Filtering

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.

Author(s)

Scott Chamberlain

See Also

classification()

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()

Examples

## 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.

Description

Get the GBIF backbone taxon ID from taxonomic names.

Usage

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
)

Arguments

Details

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.

Value

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

method parameter

"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.

Filtering

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.

Author(s)

Scott Chamberlain,

See Also

classification()

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()

Examples

## 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)

Retrieve gene sequences from NCBI by accession number.

Description

THIS FUNCTION IS DEFUNCT.

Usage

get_genes(...)

Retrieve gene sequences from NCBI by accession number.

Description

THIS FUNCTION IS DEFUNCT.

Usage

get_genes_avail(...)

Details on ⁠get_*()⁠ functions

Description

Including outputs from ⁠get_*()⁠ functions, as well as their attributes, and all exception behaviors.

Details

This document applies to the following functions:

• get_boldid()

• get_eolid()

• get_gbifid()

• get_ids()

• get_iucn()

• get_natservid()

• get_nbnid()

• get_tolid()

• get_tpsid()

• get_tsn()

• get_ubioid()

• get_uid()

• get_wiki()

• get_wormsid()

attributes

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

exceptions

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.

Retrieve taxonomic identifiers for a given taxon name.

Description

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.

Usage

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,
  ...
)

Arguments

Value

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).

Authentication

See taxize-authentication for help on authentication

Note

There is a timeout of 1/3 seconds between queries to NCBI.

See Also

classification()

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()

Examples

## 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

Description

Get a IUCN Redlist taxon

Usage

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, ...)

Arguments

Details

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.

Value

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.

See Also

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()

Examples

## Not run: 
get_iucn("Branta canadensis")
get_iucn("Branta bernicla")
get_iucn("Panthera uncia")


## End(Not run)

Get a IUCN Redlist taxon data

Description

Used to get IUCN data for other functions to use.

Usage

get_iucn_data(names_or_ids, messages = TRUE, key = NULL, latest = FALSE, ...)

Arguments

Get NatureServe taxonomic ID for a taxon name

Description

Get NatureServe taxonomic ID for a taxon name

Usage

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,
  ...
)

Arguments

Value

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

Note

Authentication no longer required

See Also

classification()

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()

Examples

## 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.

Description

Get the UK National Biodiversity Network ID from taxonomic names.

Usage

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,
  ...
)

Arguments

Value

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

Author(s)

Scott Chamberlain,

References

https://api.nbnatlas.org/

See Also

classification()

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()

Examples

## 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

Description

Get Kew's Plants of the World code for a taxon

Usage

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, ...)

Arguments

Value

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

Filtering

The parameters family_filter anrank_filterer 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.

Rate-limits

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.

See Also

classification()

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()

Examples

## 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 gene sequences from NCBI by accession number.

Description

THIS FUNCTION IS DEFUNCT.

Usage

get_seqs(...)

Get the OTT id for a search term

Description

Retrieve the Open Tree of Life Taxonomy (OTT) id of a taxon from OpenTreeOfLife

Usage

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)

Arguments

Value

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

See Also

classification()

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()

Examples

## 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.

Description

Get the NameID codes from Tropicos for taxonomic names.

Usage

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, ...)

Arguments

Value

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

Filtering

The parameters family anranknk 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.

Author(s)

Scott Chamberlain,

See Also

classification()

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()

Examples

## 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)

Get the TSN code for a search term.

Description

Retrieve the taxonomic serial numbers (TSN) of a taxon from ITIS.

Usage

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,
  ...
)

Arguments

Value

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

See Also

classification()

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()

Examples

## 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)

Get the uBio id for a search term

Description

THIS FUNCTION IS DEFUNCT.

Usage

get_ubioid(...)

as.ubioid(...)

get_ubioid_(...)

Get the UID codes from NCBI for taxonomic names.

Description

Retrieve the Unique Identifier (UID) of a taxon from NCBI taxonomy browser.

Usage

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, ...)

Arguments

Value

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

Rate limits

In case you run into errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

Querying

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].

Filtering

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.

Beware

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.

Authentication

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.

HTTP version

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')

Author(s)

Eduard Szoecs, eduardszoecs@gmail.com

See Also

classification()

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()

Examples

## 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

Description

Get the page name for a Wiki taxon

Usage

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,
  ...
)

Arguments

Details

For wiki_site = "pedia" , we use the english language site by default. Set the wiki parameter for a different language site.

Value

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

See Also

classification()

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()

Examples

## 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)

Get Worms ID for a taxon name

Description

Retrieve Worms ID of a taxon from World Register of Marine Species (WORMS).

Usage

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,
  ...
)

Arguments

Value

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

See Also

classification()

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()

Examples

## 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)

## End(Not run)

Function to get API key.

Description

Checks first to get key from your .Rprofile or .Renviron (or similar) file

Usage

getkey(x = NULL, service)

Arguments

Examples

## Not run: 
getkey(service="tropicos")
getkey(service="iucn")
getkey(service="entrez")

## End(Not run)

Check invasive species status for a set of species from GISD database

Description

THIS FUNCTION IS DEFUNCT.

Usage

gisd_isinvasive(...)

Get metadata about GNA data sources

Description

Downloads metadata about Global Names Architecture (GNA) data sources available to be used in other GNA functions.

Usage

gna_data_sources(output_type = "table", ...)

Arguments

Author(s)

Zachary S.L. Foster

Examples

## Not run: 

gna_data_sources()

## End(Not run)

Parse scientific names using Global Names Parser

Description

Parse scientific names using Global Names Parser

Usage

gna_parse(names, ...)

Arguments

Value

A data.frame with results, the submitted names, and the parsed names with additional information.

References

http://gni.globalnames.org/

See Also

gbif_parse(), gni_parse()

Examples

## Not run: 
gna_parse("Cyanistes caeruleus")
gna_parse("Plantago minor")
gna_parse("Plantago minor minor")
gna_parse(c("Plantago minor minor","Helianthus annuus texanus"))

# if > 20 names, uses an HTTP POST request
x <- names_list("species", size = 30)
gna_parse(x)

# pass on curl options
gna_parse("Cyanistes caeruleus", verbose = TRUE)

## End(Not run)

Search for taxonomic names using the Global Names Architecture

Description

Uses the Global Names Index, see http://gni.globalnames.org

Usage

gna_search(sci, justtotal = FALSE, parse_names = FALSE, ...)

Arguments

Value

data.frame of results.

Author(s)

Scott Chamberlain, Zachary Foster

References

http://gni.globalnames.org/ https://apidoc.globalnames.org/gnames

See Also

gnr_datasources(), gna_search()

Examples

## Not run: 
gna_search('n:B. bubo ds:1,2 au:Linn. y:1700-')

## End(Not run)

Verify a list of scientific names against biodiversity data-sources.

Description

This service parses incoming names, executes exact or fuzzy matching as required, and returns the best-scored result. Optionally, it can also return matches from data-sources selected by a user.

Usage

gna_verifier(
  names,
  data_sources = c(1, 12),
  all_matches = FALSE,
  capitalize = FALSE,
  species_group = FALSE,
  fuzzy_uninomial = FALSE,
  stats = FALSE,
  main_taxon_threshold = 0.5,
  output_type = "table",
  ...
)

Arguments

Value

Depends on the value of the output_type option

Author(s)

Zachary S.L. Foster

Examples

## Not run: 
gna_verifier(c("Helianthus annuus", "Homo saapiens"))
gna_verifier(c("Helianthus annuus", "Homo saapiens"), all_matches = TRUE)

## End(Not run)

Search for taxonomic name details using the Global Names Index

Description

Uses the Global Names Index, see http://gni.globalnames.org/

Usage

gni_details(id, all_records = 1, ...)

Arguments

Value

Data.frame of results.

Author(s)

Scott Chamberlain

See Also

gnr_datasources(), gna_search().

Examples

## 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.

Description

THIS FUNCTION IS DEFUNCT.

Usage

gni_parse(names, ...)

Search for taxonomic names using the Global Names Index

Description

THIS FUNCTION IS DEFUNCT.

Usage

gni_seach(names, ...)

Global Names Resolver Data Sources

Description

Retrieve data sources used in the Global Names Resolver

Usage

gnr_datasources(..., todf)

Arguments

Value

data.frame/tibble

References

https://resolver.globalnames.org/data_sources

See Also

gnr_resolve(), gna_search()

Examples

## 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)

Resolve names using Global Names Resolver

Description

NOTE: this function is depreciated and will be removed in a future version. The service this function interacts with is no longer maintained and has been replaced by GNA Verifier, which can be used with the gna_verifier() function.

Usage

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,
  ...
)

Arguments

Details

See section Age of datasets in the Global Names Resolver

Value

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.

Age of datasets in the Global Names Resolver

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.

preferred_data_sources

If preferred_data_sources is used, only the preferred data is returned - if it has any results.

Author(s)

Scott Chamberlain

References

http://gnrd.globalnames.org/api http://gnrd.globalnames.org/

See Also

gnr_datasources()

Examples

## 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

Description

Taxonomic IDs to taxonomic names

Usage

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, ...)

Arguments

Value

A named list of data.frames, named by the input taxonomic ids

HTTP version for NCBI requests

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')

Examples

## 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

Description

ION - Index to Organism Names

Usage

ion(x, ...)

Arguments

Value

A data.frame

References

http://www.organismnames.com

Examples

## Not run: 
ion(155166)
ion(298678)
ion(4796748) # ursus americanus
ion(1280626) # puma concolor

## End(Not run)

iPlant name resolution

Description

iPlant name resolution

Usage

iplant_resolve(sci, retrieve = "all", query = NULL, ...)

Arguments

Value

A data.frame

Examples

## Not run: 
iplant_resolve(sci=c("Helianthus annuus", "Homo sapiens"))
iplant_resolve("Helianthusss")
iplant_resolve("Pooa")
iplant_resolve("Helianthusss", verbose = TRUE)

## End(Not run)

Search for names in the International Plant Names Index (IPNI).

Description

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.

Usage

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",
  ...
)

Arguments

Details

ranktoreturn options:

• "all" - all records

• "fam" - family records

• "infrafam" - infrafamilial records

• "gen" - generic records

• "infragen" - infrageneric records

• "spec" - species records

• "infraspec" - infraspecific records

Value

a tibble (data.frame)

References

https://web.archive.org/web/20190501132148/http://www.ipni.org/link_to_ipni.html

Examples

## 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

Description

Retrieve accepted TSN and name

Usage

itis_acceptname(searchtsn, ...)

Arguments

Value

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

Examples

## 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.

Description

Retrieve all taxa names or TSNs downstream in hierarchy from given TSN.

Usage

itis_downstream(id, downto, intermediate = FALSE, tsns = NULL, ...)

Arguments

Value

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.

Examples

## 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.

Description

Get full ITIS record for one or more ITIS TSN's or lsid's.

Usage

itis_getrecord(values, by = "tsn", ...)

Arguments

Details

You can only enter values in tsn parameter or lsid, not both.

Examples

## 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)

ITIS hierarchy

Description

Get hierarchies from TSN values, full, upstream only, or immediate downstream only

Usage

itis_hierarchy(tsn, what = "full", ...)

Arguments

Details

Note that itis_downstream() gets taxa downstream to a particular rank, while this function only gets immediate names downstream.

See Also

itis_downstream()

Examples

## 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

Description

Get kingdom names

Usage

itis_kingdomnames(tsn = NULL, ...)

Arguments

Examples

## Not run: 
itis_kingdomnames(202385)
itis_kingdomnames(tsn=c(202385,183833,180543))

## End(Not run)

Get TSN from LSID

Description

Get TSN from LSID

Usage

itis_lsid(lsid = NULL, what = "tsn", ...)

Arguments

Examples

## 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.

Description

Get taxonomic names for a given taxonomic name query.

Usage

itis_name(query = NULL, get = NULL)

Arguments

Value

Taxonomic name for the searched taxon.

Examples

## Not run: 
itis_name(query="Helianthus annuus", get="family")

## End(Not run)

Get jurisdiction data, i.e., native or not native in a region.

Description

Get jurisdiction data, i.e., native or not native in a region.

Usage

itis_native(tsn = NULL, what = "bytsn", ...)

Arguments

Examples

## 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.

Description

Get references related to a ITIS TSN.

Usage

itis_refs(tsn, ...)

Arguments

Examples

## Not run: 
itis_refs(202385)
itis_refs(c(202385, 70340))

## End(Not run)

Retrieve taxonomic rank name from given TSN.

Description

Retrieve taxonomic rank name from given TSN.

Usage

itis_taxrank(query = NULL, ...)

Arguments

Details

You can print messages by setting verbose=FALSE.

Value

Taxonomic rank names or data.frame of all ranks.

Examples

## 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.

Description

Get ITIS terms, i.e., tsn's, authors, common names, and scientific names.

Usage

itis_terms(query, what = "both", ...)

Arguments

Examples

## 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

Description

Get any matching IUCN species names

Usage

iucn_getname(name, verbose = TRUE, ...)

Arguments

Details

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.

Value

Character vector of names that matched in IUCN

See Also

iucn_summary() iucn_status()

Examples

## Not run: 
iucn_getname(name = "Cyanistes caeruleus")
iucn_getname(name = "Panthera uncia")

# not found in IUCN search
iucn_getname(name = "Acacia allenii")

## End(Not run)

Get an ID for a IUCN listed taxon

Description

Get an ID for a IUCN listed taxon

Usage

iucn_id(sciname, key = NULL, ...)

Arguments

Value

A named list (names are input taxa names) of one or more IUCN IDs. Taxa that aren't found are silently dropped.

Author(s)

Scott Chamberlain,

Examples

## 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", "Gorilla gorilla gorilla"))

# a name not found
iucn_id("Foo bar")

## End(Not run)

Extractor functions for iucn-class.

Description

Extractor functions for iucn-class.

Usage

iucn_status(x, ...)

Arguments

Value

A character vector with the status.

See Also

iucn_summary()

Examples

## Not run: 
ia <- iucn_summary(c("Panthera uncia", "Lynx lynx"))
iucn_status(ia)
## End(Not run)

Get a summary from the IUCN Red List

Description

Get a summary from the IUCN Red List (https://www.iucnredlist.org/).

Usage

iucn_summary(x, distr_detail = FALSE, key = NULL, ...)

Arguments

Details

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)

Value

A list (for every species one entry) of data returned by rredlist::rl_species_latest().

Redlist Authentication

iucn_summary uses the new Redlist API for searching for a IUCN ID, so we use the rredlist::rl_species() 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.

Note

Not all data types are available for every species and NA is returned. iucn_status() is an extractor function to easily extract status into a vector.

Author(s)

Eduard Szoecs, eduardszoecs@gmail.com

Philippe Marchand, marchand.philippe@gmail.com

Scott Chamberlain,

Zachary S.L. Foster

See Also

iucn_status()

Examples

## 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)

Helpers to set up authentication for the different providers.

Description

Sets up authentication to diverse providers by providing the user a detailed prompt.

Usage

use_tropicos()

use_entrez()

use_iucn()

Details

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.

See Also

taxize-authentication

Print a subset of a character vector

Description

Prints the start and end values for a character vector. The number of values printed depend on the width of the screen by default.

Usage

limited_print(
  chars,
  prefix = "",
  max_chars = getOption("width") - nchar(prefix) - 5,
  type = "message"
)

Arguments

Value

NULL

Retrieve the lowest common taxon and rank for a given taxon name or ID

Description

Retrieve the lowest common taxon and rank for a given taxon name or ID

Usage

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, ...)

Arguments

Value

NA when no match, or a data.frame with columns

• name

• rank

• id

Authentication

See taxize-authentication for help on authentication

Author(s)

Jimmy O'Donnell jodonnellbio@gmail.com Scott Chamberlain

Examples

## 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")

## End(Not run)

Get a random vector of species names.

Description

Family and order names come from the APG plant names list. Genus and species names come from Theplantlist.org.

Usage

names_list(rank = "genus", size = 10)

Arguments

Value

character vector of taxonomic names

Author(s)

Scott Chamberlain

Examples

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

Description

Search UK National Biodiversity Network database for taxonomic classification

Usage

nbn_classification(id, ...)

Arguments

Value

A data.frame

Author(s)

Scott Chamberlain,

References

https://api.nbnatlas.org/

See Also

Other nbn: get_nbnid(), nbn_search(), nbn_synonyms()

Examples

## 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

Description

Search UK National Biodiversity Network

Usage

nbn_search(
  sci_com,
  fq = NULL,
  order = NULL,
  sort = NULL,
  start = 0,
  rows = 25,
  facets = NULL,
  q = NULL,
  ...
)

Arguments

Value

a list with slots for metadata (meta) with list of response attributes, and data (data) with a data.frame of results

Author(s)

Scott Chamberlain,

References

https://api.nbnatlas.org/

See Also

Other nbn: get_nbnid(), nbn_classification(), nbn_synonyms()

Examples

## 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

Description

Return all synonyms for a taxon name with a given id from NBN

Usage

nbn_synonyms(id, ...)

Arguments

Value

A data.frame

References

https://api.nbnatlas.org/

See Also

Other nbn: get_nbnid(), nbn_classification(), nbn_search()

Examples

## Not run: 
nbn_synonyms(id = 'NHMSYS0001501147')
nbn_synonyms(id = 'NHMSYS0000456036')

# none
nbn_synonyms(id = 'NHMSYS0000502940')

## End(Not run)

Search NCBI for children of a taxon

Description

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.

Usage

ncbi_children(
  name = NULL,
  id = NULL,
  start = 0,
  max_return = 1000,
  ancestor = NULL,
  out_type = c("summary", "uid"),
  ambiguous = FALSE,
  key = NULL,
  ...
)

Arguments

Value

The output type depends on the value of the out_type parameter. Taxa that cannot be found will result in NAs and a lack of children results in an empty data structure.

Authentication

See taxize-authentication() for help on authentication. We strongly recommend getting an API key

HTTP version

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')

Rate limits

In case you run into errors due to your rate limit being exceeded, see taxize_options(), where you can set ncbi_sleep.

Author(s)

Zachary Foster zacharyfoster1989@gmail.com

See Also

ncbi_get_taxon_summary(), children()

Examples

## 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

Description

Retrieve all taxa names downstream in hierarchy for NCBI

Usage

ncbi_downstream(id, downto, intermediate = FALSE, ...)

Arguments

Value

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.

No Rank

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.

Authentication

See taxize-authentication() for help on authentication. We strongly recommend getting an API key

Author(s)

Scott Chamberlain

Examples

## 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)

NCBI taxon information from uids

Description

Downloads summary taxon information from the NCBI taxonomy databases for a set of taxonomy UIDs using eutils esummary.

Usage

ncbi_get_taxon_summary(id, key = NULL, ...)

Arguments

Details

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".

Value

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')

HTTP version

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')

Authentication

See taxize-authentication for help on authentication. We strongly recommend getting an API key

Author(s)

Zachary Foster zacharyfoster1989@Sgmail.com

Examples

## Not run: 
ncbi_get_taxon_summary(c(1430660, 4751))

# use curl options
ncbi_get_taxon_summary(c(1430660, 4751), verbose = TRUE)

## End(Not run)

Retrieve gene sequences from NCBI by accession number.

Description

THIS FUNCTION IS DEFUNCT.

Usage

ncbi_getbyid(...)

Author(s)

Scott Chamberlain

Retrieve gene sequences from NCBI by taxon name and gene names.

Description

THIS FUNCTION IS DEFUNCT.

Usage

ncbi_getbyname(...)

Author(s)

Scott Chamberlain

Search for gene sequences available for taxa from NCBI.

Description

THIS FUNCTION IS DEFUNCT.

Usage

ncbi_search(...)

Get family names to make Phylomatic input object, and output input string to Phylomatic for use in the function phylomatic_tree.

Description

THIS FUNCTION IS DEFUNCT.

Usage

phylomatic_format(...)

Arguments

Query Phylomatic for a phylogenetic tree.

Description

THIS FUNCTION IS DEFUNCT.

Usage

phylomatic_tree(...)

Arguments

Ping an API used in taxize to see if it's working.

Description

Ping an API used in taxize to see if it's working.

Usage

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", ...)

Arguments

Details

For ITIS, see ritis::description, which provides number of scientific and common names in a character string.

Value

A logical, TRUE or FALSE

HTTP version for NCBI requests

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')

Examples

## 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)

Vector of plant genus names from ThePlantList

Description

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.

Format

A vector of length 793

Source

http://www.theplantlist.org

Search for taxonomy data from Plantminer.com

Description

Search for taxonomy data from Plantminer.com

Usage

plantminer(plants, from = "tpl", messages = TRUE, ...)

Arguments

Value

data.frame of results.

Note

you used to need an API key for Plantminer; it's no longer needed

Examples

## 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)

Vector of plant species (genus - specific epithet) names from ThePlantList

Description

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.

Format

A vector of length 1182

Source

http://www.theplantlist.org

Lookup taxa in Kew's Plants of the World

Description

Lookup taxa in Kew's Plants of the World

Usage

pow_lookup(id, include = NULL, ...)

Arguments

See Also

Other pow: get_pow(), pow_search(), pow_synonyms()

Examples

## 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

Description

Search Kew's Plants of the World

Usage

pow_search(sci_com, limit = 100, cursor = "*", sort = NULL, q = NULL, ...)

Arguments

Value

a list with slots for metadata (meta) with list of response attributes, and data (data) with a data.frame of results

Author(s)

Scott Chamberlain,

References

https://powo.science.kew.org/

See Also

Other pow: get_pow(), pow_lookup(), pow_synonyms()

Examples

## 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

Description

Lookup synonyms in Kew's Plants of the World

Usage

pow_synonyms(id, ...)

Arguments

See Also

Other pow: get_pow(), pow_lookup(), pow_search()

Examples

## 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)

methods for preparing/printing info for prompts for ⁠get_*⁠ functions

Description

methods for preparing/printing info for prompts for ⁠get_*⁠ functions

methods for preparing/printing info for prompts for ⁠get_*⁠ functions

Public fields

Active bindings

Methods

Public methods

• progressor$new()

• progressor$completed()

• progressor$completed_found()

• progressor$completed_not_found()

• progressor$prog_start()

• progressor$prog()

• progressor$prog_found()

• progressor$prog_not_found()

• progressor$prog_summary()

• progressor$clone()

Method new()

Create a new progressor object

Usage

progressor$new(items, suppress = FALSE)

Arguments

Returns

A new progressor object

Method completed()

add results to found or not found

Usage

progressor$completed(name, att)

Arguments

Returns

nothing returned; adds to ⁠$found⁠ or ⁠$not_found⁠

Method completed_found()

add to found results

Usage

progressor$completed_found(name)

Arguments

Returns

nothing returned; adds to ⁠$found⁠

Method completed_not_found()

add to not found results

Usage

progressor$completed_not_found(name)

Arguments

Returns

nothing returned; adds to ⁠$not_found⁠

Method prog_start()

print messages of total queries to do, and percent completed

Usage

progressor$prog_start()

Method prog()

prints message of found or not found using packages cli and crayon

Usage

progressor$prog(att)

Arguments

Returns

messages

Method prog_found()

prints found message using packages cli and crayon

Usage

progressor$prog_found()

Returns

messages

Method prog_not_found()

prints not found message using packages cli and crayon

Usage

progressor$prog_not_found()

Returns

messages

Method prog_summary()

prints summary at end of result with total found and not found

Usage

progressor$prog_summary()

Returns

messages

Method clone()

The objects of this class are cloneable with this method.

Usage

progressor$clone(deep = FALSE)

Arguments

Examples

## Not run: 
# nms <- c("Quercus", "Sasdsfasdf")
# x <- progressor$new(items = nms)
# x
# x$prog_start()

# x$completed(nms[1], "found")
# x$prog_found()

# x$completed(nms[2], "not found")
# x$prog_not_found()

# x$prog_summary()

# suppress cli::cat_line
# x <- progressor$new(items = nms, suppress = TRUE)
# x$prog_summary()

## End(Not run)

Lookup-table for IDs of taxonomic ranks

Description

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

Details

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.

Lookup-table for IDs of taxonomic ranks (WoRMS)

Description

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

Description

Aggregate data by given taxonomic rank

Usage

rankagg(data = NULL, datacol = NULL, rank = NULL, fxn = "sum")

Arguments

Examples

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 different data sources

Description

Resolve names from iPlant's name resolver, and the Global Names Resolver (GNR)

Usage

resolve(sci, db = "gnr", query = NULL, ...)

Arguments

Value

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.

Examples

## 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.

Description

Get common names from scientific names.

Usage

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, ...)

Arguments

Value

List of character vectors, named by input taxon name, or taxon ID. character(0) on no match

Authentication

See taxize-authentication for help on authentication

HTTP version for NCBI requests

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')

Author(s)

Scott Chamberlain

See Also

comm2sci()

Examples

## 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)

Find taxon names using Global Names Recognition and Discovery

Description

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 using is extremely buggy.

Usage

scrapenames(
  url = NULL,
  text = NULL,
  format = "csv",
  bytes_offset = FALSE,
  return_content = FALSE,
  unique_names = TRUE,
  ambiguous_names = FALSE,
  no_bayes = FALSE,
  odds_details = FALSE,
  language = "detect",
  words_around = 0,
  verification = TRUE,
  sources = NULL,
  all_matches = FALSE,
  ...,
  file = NULL,
  unique = NULL,
  engine = NULL,
  detect_language = NULL,
  data_source_ids = NULL
)

Arguments

Value

A tibble::tibble() or list representing parsed JSON output depending on the value of the format option.

Author(s)

Scott Chamberlain, Zachary Foster

Examples

## 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(url = 'https://en.wikipedia.org/wiki/Spider', source=c(1, 169))

# Get data from text string
scrapenames(text='A spider named Pardosa moesta Banks, 1892')

# return OCR content
scrapenames(text='A spider named Pardosa moesta Banks, 1892',
            return_content = TRUE, format = 'json')

## End(Not run)

Species names from Species Plantarum

Description

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.

Format

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.

Author(s)

Carl Linnaeus

Source

Hunt Institute for Botanical Documentation

References

Linnaeus, C. 1753. Species Plantarum. 2 vols. Salvius, Stockholm. [Facsimile edition, 1957-1959, Ray Society, London.]

Get HTTP status codes

Description

Get HTTP status codes

Usage

status_codes()

See Also

ping()

Examples

status_codes()

Retrieve synonyms from various sources given input taxonomic names or identifiers

Description

Retrieve synonyms from various sources given input taxonomic names or identifiers

Usage

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)

Arguments

Details

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

Value

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

See Also

get_tsn() get_tpsid() get_nbnid() get_wormsid() get_iucn() get_pow()

Examples

## 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

Description

Aggregate species data to given taxonomic rank

Usage

tax_agg(x, rank, db = "ncbi", messages = FALSE, ...)

## S3 method for class 'tax_agg'
print(x, ...)

Arguments

Details

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.

Value

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.

See Also

tax_name

Examples

## 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

Description

Get taxonomic names for a given rank

Usage

tax_name(
  sci,
  get,
  db = "itis",
  pref = "ncbi",
  messages = TRUE,
  query = NULL,
  ...
)

Arguments

Value

A data.frame with one column for every queried rank, in addition to a column for db and queried term.

Authentication

See taxize-authentication for help on authentication

Note

While tax_rank() returns the actual rank of a taxon, tax_name() searches and returns any specified rank higher in taxonomy.

See Also

classification()

Examples

## 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.

Description

Get rank for a given taxonomic name.

Usage

tax_rank(sci_id, db = NULL, rows = NA, x = NULL, ...)

Arguments

Value

A named list of character vectors with ranks (all lower-cased)

Note

While tax_name() returns the name of a specified rank, tax_rank() returns the actual rank of the taxon.

See Also

classification(),tax_name()

Examples

## 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.

Description

Capitalize the first letter of a character string.

Usage

taxize_capwords(s, strict = FALSE, onlyfirst = FALSE)

Arguments

Examples

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

Description

Get citations and licenses for data sources used in taxize

Usage

taxize_cite(fxn = "itis", what = "citation")

Arguments

Examples

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")

Replacement function for ldply that should be faster in all cases.

Description

Replacement function for ldply that should be faster in all cases.

Usage

taxize_ldfast(x, convertvec = FALSE)

Arguments

taxize options

Description

taxize options

Usage

taxize_options(taxon_state_messages = NULL, ncbi_sleep = NULL, quiet = FALSE)

Arguments

Examples

## 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)

taxize authentication

Description

Help on authentication

What is an API?

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.

What are API keys?

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.

Using API keys

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.

See Also

key_helpers()

Defunct functions in taxize

Description

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

• 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

taxize parameters

Description

Information on standardized parameters across the package

Standardized parameters

• 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())

Keep track of queries in ⁠get_*⁠ functions

Description

Keep track of queries in ⁠get_*⁠ functions

Keep track of queries in ⁠get_*⁠ functions

Details

This object lives inside each ⁠get_*⁠ function call, maintaining results as they are accumulated.

Public fields

Active bindings

Methods

Public methods

• taxon_state$new()

• taxon_state$print()

• taxon_state$add()

• taxon_state$get()

• taxon_state$remove()

• taxon_state$purge()

• taxon_state$taxa_remaining()

• taxon_state$taxa_completed()

• taxon_state$clone()

Method new()

Create a new taxon_state object

Usage

taxon_state$new(class, names)

Arguments

Returns

A new taxon_state object

Method print()

print method for the taxon_state class

Usage

taxon_state$print(x, ...)

Arguments

Method add()

add a record with it's result; duplicates allowed

Usage

taxon_state$add(query, result)

Arguments

Returns

nothing returned; sets only

Method get()

get all records matching 'query'

Usage

taxon_state$get(query = NULL)

Arguments

Returns

a named list, with slots for the taxon id, and other attributes, named by the taxon name

Method remove()

remove's all records matching 'query'

Usage

taxon_state$remove(query)

Arguments

Returns

nothing, removes records matching query

Method purge()

removes all records

Usage

taxon_state$purge()

Returns

nothing returned; sets only

Method taxa_remaining()

get remaining taxa

Usage

taxon_state$taxa_remaining()

Returns

sorted taxon names

Method taxa_completed()

get completed taxa

Usage

taxon_state$taxa_completed()

Returns

sorted taxon names

Method clone()

The objects of this class are cloneable with this method.

Usage

taxon_state$clone(deep = FALSE)

Arguments

Examples

## Not run: 
if (interactive()) {
ts <- taxon_state$new()
taxon_last()
ts
res <- list(
  id = 123456,
  att = "found",
  multiple = FALSE,
  direct = FALSE,
  class = "tsn"
)
ts$add(query = "Quercus robur", result = res)
ts
ts$get(query = "Quercus robur")
ts$count
ts$remove(query = "Quercus robur")
ts
ts$count

res2 <- list(
  id = 3430834535,
  att = "found",
  multiple = FALSE,
  direct = FALSE,
  class = "gbifid"
)
ts$add(query = "Poa annua", result = res2)
res3 <- list(
  id = 1223424,
  att = "found",
  multiple = FALSE,
  direct = FALSE,
  class = "uid"
)
ts$add(query = "Puma concolor", result = res3)
ts
ts$count
ts$get("Puma concolor")
ts$get()

# cleanup
ts$purge()
ts$count
}

## End(Not run)

Last taxon state object from a ⁠get_*⁠ function call

Description

Last taxon state object from a ⁠get_*⁠ function call

Usage

taxon_last()

taxon_clear()

Details

• 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

Value

taxon_last() returns an object of class taxon_state, the last one used, else NULL if none found. taxon_clear() clears the saved state

Examples

## 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)

Lookup-table for family, genus, and species names for ThePlantList

Description

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.

Format

A data frame with 10,000 rows and 3 variables:

• family family name

• genus genus name

• species specific epithet name

Source

http://www.theplantlist.org

Phylotastic Taxonomic Name Resolution Service.

Description

Defunct - service was down far too much to be reliable

Usage

tnrs(...)

Arguments

TNRS sources

Description

Defunct - service was down far too much to be reliable

Usage

tnrs_sources(...)

Arguments

Resolve names using Open Tree of Life (OTL) resolver

Description

Resolve names using Open Tree of Life (OTL) resolver

Usage

tol_resolve(
  names = NULL,
  context_name = NULL,
  do_approximate_matching = TRUE,
  ids = NULL,
  include_suppressed = FALSE,
  ...
)

Arguments

Value

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")).

Author(s)

Francois Michonneau francois.michonneau@gmail.com Scott Chamberlain

References

https://github.com/OpenTreeOfLife/germinator/wiki/TNRS-API-v3#match_names

See Also

gnr_resolve(), tnrs()

Examples

## 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.

Description

Function name changed to tp_accnames.

Usage

tp_acceptednames(...)

Arguments

Return all accepted names for a taxon name with a given id.

Description

Return all accepted names for a taxon name with a given id.

Usage

tp_accnames(id, key = NULL, ...)

Arguments

Value

List or dataframe.

Examples

## Not run: 
tp_accnames(id = 25503923)
tp_accnames(id = 25538750)

# No accepted names found
tp_accnames(id = 25509881)

## End(Not run)

Return all synonyms for a taxon name with a given id.

Description

THIS FUNCTION IS DEFUNCT.

Usage

tp_classification(...)

Return all distribution records for for a taxon name with a given id.

Description

Return all distribution records for for a taxon name with a given id.

Usage

tp_dist(id, key = NULL, ...)

Arguments

Value

List of two data.frame's, one named "location", and one "reference".

References

http://services.tropicos.org/help?method=GetNameDistributionsXml

Examples

## 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 distribution records for for a taxon name with a given id.

Description

Function name changed to tp_dist.

Usage

tp_namedistributions(...)

Arguments

Return all reference records for for a taxon name with a given id.

Description

Function name changed to tp_refs.

Usage

tp_namereferences(...)

Arguments

Return all reference records for for a taxon name with a given id.

Description

Return all reference records for for a taxon name with a given id.

Usage

tp_refs(id, key = NULL, ...)