| Title: | Integrated Taxonomic Information System Client |
| Description: | An interface to the Integrated Taxonomic Information System ('ITIS') (https://www.itis.gov). Includes functions to work with the 'ITIS' REST API methods (https://www.itis.gov/ws_description.html), as well as the 'Solr' web service (https://www.itis.gov/solr_documentation.html). |
| Version: | 1.0.0 |
| License: | MIT + file LICENSE |
| URL: | https://github.com/ropensci/ritis (devel) https://docs.ropensci.org/ritis/ (docs) |
| BugReports: | https://github.com/ropensci/ritis/issues |
| LazyData: | true |
| Encoding: | UTF-8 |
| Language: | en-US |
| Imports: | solrium (≥ 1.1.4), crul (≥ 0.9.0), jsonlite, data.table, tibble |
| Suggests: | testthat, webmockr, vcr (≥ 0.5.4) |
| RoxygenNote: | 7.1.1 |
| X-schema.org-applicationCategory: | Taxonomy |
| X-schema.org-keywords: | taxonomy, biology, nomenclature, JSON, API, web, api-client, identifiers, species, names |
| X-schema.org-isPartOf: | https://ropensci.org |
| NeedsCompilation: | no |
| Packaged: | 2021-02-02 06:21:27 UTC; sckott |
| Author: | Scott Chamberlain 
[aut, cre],
rOpenSci [fnd] (https://ropensci.org/) |
| Maintainer: | Scott Chamberlain <myrmecocystus@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2021-02-02 07:30:02 UTC |
ritis
Description
Interface to Integrated Taxonomic Information (ITIS)
ritis package API
All functions that start with itis_ work with the ITIS Solr
API described at https://www.itis.gov/solr_documentation.html,
which uses the package solrium, and these functions have you
use the solrium function interfaces, so you can pass on parameters
to the solrium functions - so the solrium docs are important
here.
All other functions work with the ITIS REST API described at https://www.itis.gov/ws_description.html. For these methods, they can grab data in either JSON or XML format. JSON is the default. We parse the JSON to R native format, either data.frame, character string, or list. You can get raw JSON as a character string back, or raw XML as a character string, and then parse yourself with jsonlite or xml2
You'll also be interested in the taxize book https://taxize.dev/
Terminology
"mononomial": a taxonomic name with one part, e.g, Poa
"binomial": a taxonomic name with two parts, e.g, Poa annua
"trinomial": a taxonomic name with three parts, e.g, Poa annua annua
Author(s)
Scott Chamberlain myrmecocystus@gmail.com
Get accepted names from tsn
Description
Get accepted names from tsn
Usage
accepted_names(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
Zero row data.frame if the name is accepted, otherwise a data.frame with information on the currently accepted name
Examples
## Not run:
# TSN accepted - good name, empty data.frame returned
accepted_names(tsn = 208527)
# TSN not accepted - input TSN is old name, non-empty data.frame returned
accepted_names(tsn = 504239)
# raw json
accepted_names(tsn = 208527, raw = TRUE)
## End(Not run)
Get any match count.
Description
Get any match count.
Usage
any_match_count(x, wt = "json", raw = FALSE, ...)
Arguments
x |
text or taxonomic serial number (TSN) (character or numeric) |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
An integer containing the number of matches the search will return.
Examples
## Not run:
any_match_count(x = 202385)
any_match_count(x = "dolphin")
any_match_count(x = "dolphin", wt = "xml")
## End(Not run)
Get comment detail from TSN
Description
Get comment detail from TSN
Usage
comment_detail(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
A data.frame with results.
Examples
## Not run:
comment_detail(tsn=180543)
comment_detail(tsn=180543, wt = "xml")
## End(Not run)
Get common names from tsn
Description
Get common names from tsn
Usage
common_names(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
common_names(tsn=183833)
common_names(tsn=183833, wt = "xml")
## End(Not run)
Get core metadata from tsn
Description
Get core metadata from tsn
Usage
core_metadata(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
# coverage and currrency data
core_metadata(tsn=28727)
core_metadata(tsn=28727, wt = "xml")
# no coverage or currrency data
core_metadata(183671)
core_metadata(183671, wt = "xml")
## End(Not run)
Get coverge from tsn
Description
Get coverge from tsn
Usage
coverage(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
# coverage data
coverage(tsn=28727)
# no coverage data
coverage(526852)
coverage(526852, wt = "xml")
## End(Not run)
Get credibility rating from tsn
Description
Get credibility rating from tsn
Usage
credibility_rating(tsn, wt = "json", raw = FALSE, ...)
credibility_ratings(wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Details
methods:
credibility_rating: Get credibility rating for a tsn
credibility_ratings: Get possible credibility ratings
Value
a data.frame
Examples
## Not run:
credibility_rating(tsn = 526852)
credibility_rating(526852, wt = "xml")
credibility_rating(526852, raw = TRUE)
credibility_ratings()
credibility_ratings(wt = "xml")
credibility_ratings(raw = TRUE)
## End(Not run)
Get currency from tsn
Description
Get currency from tsn
Usage
currency(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
# currency data
currency(tsn=28727)
currency(tsn=28727, wt = "xml")
# no currency dat
currency(526852)
currency(526852, raw = TRUE)
## End(Not run)
Get date data from tsn
Description
Get date data from tsn
Usage
date_data(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
date_data(tsn = 180543)
date_data(180543, wt = "xml")
date_data(180543, wt = "json", raw = TRUE)
## End(Not run)
Get description of the ITIS service
Description
Get description of the ITIS service
Usage
description(wt = "json", raw = FALSE, ...)
Arguments
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a string, the ITIS web service description
Examples
## Not run:
description()
description(wt = "xml")
## End(Not run)
Get expert information for the TSN.
Description
Get expert information for the TSN.
Usage
experts(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
experts(tsn = 180544)
experts(180544, wt = "xml")
experts(180544, raw = TRUE)
## End(Not run)
Get full record from TSN or lsid
Description
Get full record from TSN or lsid
Usage
full_record(tsn = NULL, lsid = NULL, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
lsid |
lsid for a taxonomic group (character) |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
# from tsn
full_record(tsn = 50423)
full_record(tsn = 202385)
full_record(tsn = 183833)
full_record(tsn = 183833, wt = "xml")
full_record(tsn = 183833, raw = TRUE)
# from lsid
full_record(lsid = "urn:lsid:itis.gov:itis_tsn:180543")
full_record(lsid = "urn:lsid:itis.gov:itis_tsn:180543")
## End(Not run)
Get geographic divisions from tsn
Description
Get geographic divisions from tsn
Usage
geographic_divisions(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
geographic_divisions(tsn = 180543)
geographic_divisions(tsn = 180543, wt = "xml")
geographic_divisions(tsn = 180543, wt = "json", raw = TRUE)
## End(Not run)
Get all possible geographic values
Description
Get all possible geographic values
Usage
geographic_values(wt = "json", raw = FALSE, ...)
Arguments
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
character vector of geographic names
Examples
## Not run:
geographic_values()
geographic_values(wt = "xml")
geographic_values(wt = "json", raw = TRUE)
## End(Not run)
Get global species completeness from tsn
Description
Get global species completeness from tsn
Usage
global_species_completeness(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
global_species_completeness(tsn = 180541)
global_species_completeness(180541, wt = "xml")
global_species_completeness(180541, wt = "json", raw = TRUE)
## End(Not run)
Get hierarchy down from tsn
Description
Get hierarchy down from tsn
Usage
hierarchy_down(tsn, wt = "json", raw = FALSE, ...)
hierarchy_up(tsn, wt = "json", raw = FALSE, ...)
hierarchy_full(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Details
Hierarchy methods:
hierarchy_down: Get hierarchy down from tsn
hierarchy_up: Get hierarchy up from tsn
hierarchy_full: Get full hierarchy from tsn
Examples
## Not run:
## Full down (class Mammalia)
hierarchy_down(tsn=179913)
## Full up (genus Agoseris)
hierarchy_up(tsn=36485)
## Full hierarchy
### genus Liatris
hierarchy_full(tsn=37906)
### get raw data back
hierarchy_full(tsn=37906, raw = TRUE)
### genus Baetis, get xml back
hierarchy_full(100800, wt = "xml")
## End(Not run)
ITIS Solr facet
Description
ITIS Solr facet
Usage
itis_facet(..., proxy = NULL, callopts = list())
Arguments
... |
Arguments passed on to the |
proxy |
List of arguments for a proxy connection,
including one or more of: url, port, username, password,
and auth. See |
callopts |
Curl options passed on to crul::HttpClient |
Examples
## Not run:
itis_facet(q = "rank:Species", rows = 0, facet.field = "kingdom")$facet_fields
x <- itis_facet(q = "hierarchySoFar:*$Aves$* AND rank:Species AND usage:valid",
facet.pivot = "nameWInd,vernacular", facet.limit = -1, facet.mincount = 1,
rows = 0)
head(x$facet_pivot$`nameWInd,vernacular`)
## End(Not run)
ITIS Solr group search
Description
ITIS Solr group search
Usage
itis_group(..., proxy = NULL, callopts = list())
Arguments
... |
Arguments passed on to the |
proxy |
List of arguments for a proxy connection,
including one or more of: url, port, username, password,
and auth. See |
callopts |
Curl options passed on to crul::HttpClient |
Examples
## Not run:
x <- itis_group(q = "nameWOInd:/[A-Za-z0-9]*[%20]{0,0}*/",
group.field = 'rank', group.limit = 3)
head(x)
## End(Not run)
ITIS Solr highlight
Description
ITIS Solr highlight
Usage
itis_highlight(..., proxy = NULL, callopts = list())
Arguments
... |
Arguments passed on to the |
proxy |
List of arguments for a proxy connection,
including one or more of: url, port, username, password,
and auth. See |
callopts |
Curl options passed on to crul::HttpClient |
Examples
## Not run:
itis_highlight(q = "rank:Species", hl.fl = 'rank', rows=10)
## End(Not run)
ITIS Solr search
Description
ITIS Solr search
Usage
itis_search(..., proxy = NULL, callopts = list())
Arguments
... |
Arguments passed on to the |
proxy |
List of arguments for a proxy connection,
including one or more of: url, port, username, password,
and auth. See |
callopts |
Curl options passed on to crul::HttpClient |
Details
The syntax for this function can be a bit hard to grasp. See https://itis.gov/solr_examples.html for help on generating the syntax ITIS wants for specific searches.
References
https://www.itis.gov/solr_documentation.html
Examples
## Not run:
itis_search(q = "tsn:182662")
# get all orders within class Aves (birds)
z <- itis_search(q = "rank:Class AND nameWOInd:Aves")
hierarchy_down(z$tsn)
# get taxa "downstream" from a target taxon
## taxize and taxizedb packages have downstream() fxns, but
## you can do a similar thing here by iteratively drilling down
## the taxonomic hierarchy
## here, we get families within Aves
library(data.table)
aves <- itis_search(q = "rank:Class AND nameWOInd:Aves")
aves_orders <- hierarchy_down(aves$tsn)
aves_families <- lapply(aves_orders$tsn, hierarchy_down)
rbindlist(aves_families)
# the tila operator
itis_search(q = "nameWOInd:Liquidamber\\ styraciflua~0.4")
# matches only monomials
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/")
# matches only binomials
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*/")
# matches only trinomials
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*/")
# matches binomials or trinomials
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{1,1}[A-Za-z0-9]*[ ]{0,1}[A-Za-z0-9]*/")
itis_search(q = "nameWOInd:Poa\\ annua")
# pagination
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/", rows = 2)
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/", rows = 200)
# select fields to return
itis_search(q = "nameWOInd:/[A-Za-z0-9]*[ ]{0,0}*/",
fl = c('nameWInd', 'tsn'))
## End(Not run)
Get jurisdictional origin from tsn
Description
Get jurisdictional origin from tsn
Usage
jurisdictional_origin(tsn, wt = "json", raw = FALSE, ...)
jurisdiction_origin_values(wt = "json", raw = FALSE, ...)
jurisdiction_values(wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Details
Jurisdiction methods:
jurisdictional_origin: Get jurisdictional origin from tsn
jurisdiction_origin_values: Get jurisdiction origin values
jurisdiction_values: Get all possible jurisdiction values
Value
jurisdictional_origin: data.frame
jurisdiction_origin_values: data.frame
jurisdiction_values: character vector
Examples
## Not run:
jurisdictional_origin(tsn=180543)
jurisdictional_origin(tsn=180543, wt = "xml")
jurisdiction_origin_values()
jurisdiction_values()
## End(Not run)
Get kingdom names from tsn
Description
Get kingdom names from tsn
Usage
kingdom_name(tsn, wt = "json", raw = FALSE, ...)
kingdom_names(wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Details
kingdom_name: Get kingdom name for a TSN
kingdom_names: Get all possible kingdom names
Examples
## Not run:
kingdom_name(202385)
kingdom_name(202385, wt = "xml")
kingdom_names()
## End(Not run)
Provides the date the ITIS database was last updated
Description
Provides the date the ITIS database was last updated
Usage
last_change_date(wt = "json", raw = FALSE, ...)
Arguments
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
character value with a date
Examples
## Not run:
last_change_date()
last_change_date(wt = "xml")
## End(Not run)
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
Description
Gets the TSN corresponding to the LSID, or an empty result if there is no match.
Usage
lsid2tsn(lsid, wt = "json", raw = FALSE, ...)
Arguments
lsid |
(character) lsid for a taxonomic group. Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
lsid2tsn(lsid="urn:lsid:itis.gov:itis_tsn:28726")
lsid2tsn(lsid="urn:lsid:itis.gov:itis_tsn:28726", wt = "xml")
lsid2tsn("urn:lsid:itis.gov:itis_tsn:0")
lsid2tsn("urn:lsid:itis.gov:itis_tsn:0", wt = "xml")
## End(Not run)
Returns a list of the other sources used for the TSN.
Description
Returns a list of the other sources used for the TSN.
Usage
other_sources(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
# results
other_sources(tsn=182662)
# no results
other_sources(tsn=2085272)
# get xml
other_sources(tsn=182662, wt = "xml")
## End(Not run)
Returns the parent TSN for the entered TSN.
Description
Returns the parent TSN for the entered TSN.
Usage
parent_tsn(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
parent_tsn(tsn = 202385)
parent_tsn(tsn = 202385, raw = TRUE)
parent_tsn(tsn = 202385, wt = "xml")
## End(Not run)
Returns a list of the pulications used for the TSN.
Description
Returns a list of the pulications used for the TSN.
Usage
publications(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
publications(tsn = 70340)
publications(tsn = 70340, wt = "xml")
publications(tsn = 70340, verbose = TRUE)
## End(Not run)
Returns the kingdom and rank information for the TSN.
Description
Returns the kingdom and rank information for the TSN.
Usage
rank_name(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame, with rank name and other info
Examples
## Not run:
rank_name(tsn = 202385)
## End(Not run)
Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.
Description
Provides a list of all the unique rank names contained in the database and their kingdom and rank ID values.
Usage
rank_names(wt = "json", raw = FALSE, ...)
Arguments
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame, with columns:
kingdomname
rankid
rankname
Examples
## Not run:
rank_names()
## End(Not run)
Gets a record from an LSID
Description
Gets a record from an LSID
Usage
record(lsid, wt = "json", raw = FALSE, ...)
Arguments
lsid |
lsid for a taxonomic group (character). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Details
Gets the partial ITIS record for the TSN in the LSID, found by comparing the TSN in the search key to the TSN field. Returns an empty result set if there is no match or the TSN is invalid.
Value
a data.frame
Examples
## Not run:
record(lsid = "urn:lsid:itis.gov:itis_tsn:180543")
## End(Not run)
Returns the review year for the TSN.
Description
Returns the review year for the TSN.
Usage
review_year(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
review_year(tsn = 180541)
## End(Not run)
Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.
Description
Returns the scientific name for the TSN. Also returns the component parts (names and indicators) of the scientific name.
Usage
scientific_name(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
scientific_name(tsn = 531894)
## End(Not run)
Search for any matched page
Description
Search for any matched page
Usage
search_any_match_paged(
x,
pagesize = NULL,
pagenum = NULL,
ascend = NULL,
wt = "json",
raw = FALSE,
...
)
Arguments
x |
text or taxonomic serial number (TSN) (character or numeric) |
pagesize |
An integer containing the page size (numeric) |
pagenum |
An integer containing the page number (numeric) |
ascend |
A boolean containing true for ascending sort order or false for descending (logical) |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
a data.frame
See Also
Examples
## Not run:
search_any_match_paged(x=202385, pagesize=100, pagenum=1, ascend=FALSE)
search_any_match_paged(x="Zy", pagesize=100, pagenum=1, ascend=FALSE)
## End(Not run)
Search for any match
Description
Search for any match
Usage
search_anymatch(x, wt = "json", raw = FALSE, ...)
Arguments
x |
text or taxonomic serial number (TSN) (character or numeric) |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
See Also
Examples
## Not run:
search_anymatch(x = 202385)
search_anymatch(x = "dolphin")
# no results
search_anymatch(x = "Pisces")
## End(Not run)
Search for tsn by common name
Description
Search for tsn by common name
Usage
search_common(x, from = "all", wt = "json", raw = FALSE, ...)
Arguments
x |
text or taxonomic serial number (TSN) (character or numeric) |
from |
(character) One of "all", "begin", or "end". See Details. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Details
The from parameter:
all - Search against the
searchByCommonNameAPI route, which searches entire name stringbegin - Search against the
searchByCommonNameBeginsWithAPI route, which searches for a match at the beginning of a name stringend - Search against the
searchByCommonNameEndsWithAPI route, which searches for a match at the end of a name string
Value
a data.frame
See Also
Examples
## Not run:
search_common("american bullfrog")
search_common("ferret-badger")
search_common("polar bear")
# comparison: all, begin, end
search_common("inch")
search_common("inch", from = "begin")
search_common("inch", from = "end")
# end
search_common("snake", from = "end")
## End(Not run)
Search by scientific name
Description
Search by scientific name
Usage
search_scientific(x, wt = "json", raw = FALSE, ...)
Arguments
x |
text or taxonomic serial number (TSN) (character or numeric) |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
See Also
Examples
## Not run:
search_scientific("Tardigrada")
search_scientific("Quercus douglasii")
## End(Not run)
ITIS Solr Methods
Description
ITIS provides access to their data via their Solr service described at https://www.itis.gov/solr_documentation.html. This is a powerful interace to ITIS data as you have access to a very flexible query interface.
Details
See solr_fields and https://www.itis.gov/solr_documentation.html for guidance on available fields.
Functions
-
itis_search()- Search -
itis_group()- Group -
itis_highlight()- Highlight -
itis_facet()- Facet
List of fields that can be used in solr functions
Description
Each element in the list has a list of length tree, with:
Format
A list of length 36
Details
field: the field name, this is the name you can use in your queries
definition: the definition of the field
example: an example value
Source
https://www.itis.gov/solr_documentation.html
Returns a list of the synonyms (if any) for the TSN.
Description
Returns a list of the synonyms (if any) for the TSN.
Usage
synonym_names(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
synonym_names(tsn=183671) # tsn not accepted
synonym_names(tsn=526852) # tsn accepted
## End(Not run)
Returns the author information for the TSN.
Description
Returns the author information for the TSN.
Usage
taxon_authorship(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
taxon_authorship(tsn = 183671)
## 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
terms(query, what = "both", wt = "json", raw = FALSE, ...)
Arguments
query |
One or more common or scientific names, or partial names |
what |
One of both (search common and scientific names), common (search just common names), or scientific (search just scientific names) |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
# Get terms searching both common and scientific names
terms(query='bear')
# Get terms searching just common names
terms(query='tarweed', "common")
# Get terms searching just scientific names
terms(query='Poa annua', "scientific")
# many at once
terms(query=c('Poa annua', 'Pinus contorta'), "scientific")
## End(Not run)
Get tsn by vernacular language
Description
Get tsn by vernacular language
Usage
tsn_by_vernacular_language(language, wt = "json", raw = FALSE, ...)
Arguments
language |
A string containing the language. This is a language string, not the international language code (character) |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a data.frame
Examples
## Not run:
tsn_by_vernacular_language(language = "french")
## End(Not run)
Gets the unique LSID for the TSN, or an empty result if there is no match.
Description
Gets the unique LSID for the TSN, or an empty result if there is no match.
Usage
tsn2lsid(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a character string, an LSID, or NULL if nothing found
Examples
## Not run:
tsn2lsid(tsn = 155166)
tsn2lsid(tsn = 333333333)
tsn2lsid(155166, raw = TRUE)
tsn2lsid(155166, wt = "xml")
## End(Not run)
Returns the unacceptability reason, if any, for the TSN.
Description
Returns the unacceptability reason, if any, for the TSN.
Usage
unacceptability_reason(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
unacceptability_reason(tsn = 183671)
## End(Not run)
Returns the usage information for the TSN.
Description
Returns the usage information for the TSN.
Usage
usage(tsn, wt = "json", raw = FALSE, ...)
Arguments
tsn |
TSN for a taxonomic group (numeric). Required. |
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Examples
## Not run:
usage(tsn = 526852)
usage(tsn = 526852, raw = TRUE)
usage(tsn = 526852, wt = "xml")
## End(Not run)
Provides a list of the unique languages used in the vernacular table.
Description
Provides a list of the unique languages used in the vernacular table.
Usage
vernacular_languages(wt = "json", raw = FALSE, ...)
Arguments
wt |
(character) One of "json" or "xml". Required. |
raw |
(logical) Return raw JSON or XML as character string. Required.
Default: |
... |
curl options passed on to crul::HttpClient |
Value
a character vector of verncular names
Examples
## Not run:
vernacular_languages()
## End(Not run)