Package '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 [email protected]

Description

Get accepted names from tsn

Usage

accepted_names(tsn, wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Get any match count.

Usage

any_match_count(x, wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Get comment detail from TSN

Usage

comment_detail(tsn, wt = "json", raw = FALSE, ...)

Arguments

Value

A data.frame with results.

Examples

## Not run: 
comment_detail(tsn=180543)
comment_detail(tsn=180543, wt = "xml")

## End(Not run)

Description

Get common names from tsn

Usage

common_names(tsn, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame

Examples

## Not run: 
common_names(tsn=183833)
common_names(tsn=183833, wt = "xml")

## End(Not run)

Description

Get core metadata from tsn

Usage

core_metadata(tsn, wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Get coverge from tsn

Usage

coverage(tsn, wt = "json", raw = FALSE, ...)

Arguments

Examples

## Not run: 
# coverage data
coverage(tsn=28727)
# no coverage data
coverage(526852)
coverage(526852, wt = "xml")

## End(Not run)

Description

Get credibility rating from tsn

Usage

credibility_rating(tsn, wt = "json", raw = FALSE, ...)

credibility_ratings(wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Get currency from tsn

Usage

currency(tsn, wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Get date data from tsn

Usage

date_data(tsn, wt = "json", raw = FALSE, ...)

Arguments

Examples

## Not run: 
date_data(tsn = 180543)
date_data(180543, wt = "xml")
date_data(180543, wt = "json", raw = TRUE)

## End(Not run)

Description

Get description of the ITIS service

Usage

description(wt = "json", raw = FALSE, ...)

Arguments

Value

a string, the ITIS web service description

Examples

## Not run: 
description()
description(wt = "xml")

## End(Not run)

Description

Get expert information for the TSN.

Usage

experts(tsn, wt = "json", raw = FALSE, ...)

Arguments

Examples

## Not run: 
experts(tsn = 180544)
experts(180544, wt = "xml")
experts(180544, raw = TRUE)

## End(Not run)

Description

Get full record from TSN or lsid

Usage

full_record(tsn = NULL, lsid = NULL, wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Get geographic divisions from tsn

Usage

geographic_divisions(tsn, wt = "json", raw = FALSE, ...)

Arguments

Examples

## Not run: 
geographic_divisions(tsn = 180543)

geographic_divisions(tsn = 180543, wt = "xml")

geographic_divisions(tsn = 180543, wt = "json", raw = TRUE)

## End(Not run)

Description

Get all possible geographic values

Usage

geographic_values(wt = "json", raw = FALSE, ...)

Arguments

Value

character vector of geographic names

Examples

## Not run: 
geographic_values()
geographic_values(wt = "xml")
geographic_values(wt = "json", raw = TRUE)

## End(Not run)

Description

Get global species completeness from tsn

Usage

global_species_completeness(tsn, wt = "json", raw = FALSE, ...)

Arguments

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)

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

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)

Description

ITIS Solr facet

Usage

itis_facet(..., proxy = NULL, callopts = list())

Arguments

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)

Description

ITIS Solr group search

Usage

itis_group(..., proxy = NULL, callopts = list())

Arguments

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)

Description

ITIS Solr highlight

Usage

itis_highlight(..., proxy = NULL, callopts = list())

Arguments

Examples

## Not run: 
itis_highlight(q = "rank:Species", hl.fl = 'rank', rows=10)

## End(Not run)

Description

ITIS Solr search

Usage

itis_search(..., proxy = NULL, callopts = list())

Arguments

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)

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

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)

Description

Get kingdom names from tsn

Usage

kingdom_name(tsn, wt = "json", raw = FALSE, ...)

kingdom_names(wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Provides the date the ITIS database was last updated

Usage

last_change_date(wt = "json", raw = FALSE, ...)

Arguments

Value

character value with a date

Examples

## Not run: 
last_change_date()
last_change_date(wt = "xml")

## End(Not run)

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

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)

Description

Returns a list of the other sources used for the TSN.

Usage

other_sources(tsn, wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Returns the parent TSN for the entered TSN.

Usage

parent_tsn(tsn, wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Returns a list of the pulications used for the TSN.

Usage

publications(tsn, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame

Examples

## Not run: 
publications(tsn = 70340)
publications(tsn = 70340, wt = "xml")

publications(tsn = 70340, verbose = TRUE)

## End(Not run)

Description

Returns the kingdom and rank information for the TSN.

Usage

rank_name(tsn, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame, with rank name and other info

Examples

## Not run: 
rank_name(tsn = 202385)

## End(Not run)

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

Value

a data.frame, with columns:

• kingdomname

• rankid

• rankname

Examples

## Not run: 
rank_names()

## End(Not run)

Description

Gets a record from an LSID

Usage

record(lsid, wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Returns the review year for the TSN.

Usage

review_year(tsn, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame

Examples

## Not run: 
review_year(tsn = 180541)

## End(Not run)

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

Value

a data.frame

Examples

## Not run: 
scientific_name(tsn = 531894)

## End(Not run)

Description

Search for any matched page

Usage

search_any_match_paged(
  x,
  pagesize = NULL,
  pagenum = NULL,
  ascend = NULL,
  wt = "json",
  raw = FALSE,
  ...
)

Arguments

Value

a data.frame

a data.frame

See Also

search_anymatch

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)

Description

Search for any match

Usage

search_anymatch(x, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame

See Also

search_any_match_paged

Examples

## Not run: 
search_anymatch(x = 202385)
search_anymatch(x = "dolphin")
# no results
search_anymatch(x = "Pisces")

## End(Not run)

Description

Search for tsn by common name

Usage

search_common(x, from = "all", wt = "json", raw = FALSE, ...)

Arguments

Details

The from parameter:

• all - Search against the searchByCommonName API route, which searches entire name string

• begin - Search against the searchByCommonNameBeginsWith API route, which searches for a match at the beginning of a name string

• end - Search against the searchByCommonNameEndsWith API route, which searches for a match at the end of a name string

Value

a data.frame

See Also

search_scientific()

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)

Description

Search by scientific name

Usage

search_scientific(x, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame

See Also

search_common

Examples

## Not run: 
search_scientific("Tardigrada")
search_scientific("Quercus douglasii")

## End(Not run)

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

Description

Returns a list of the synonyms (if any) for the TSN.

Usage

synonym_names(tsn, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame

Examples

## Not run: 
synonym_names(tsn=183671) # tsn not accepted
synonym_names(tsn=526852) # tsn accepted

## End(Not run)

Description

Returns the author information for the TSN.

Usage

taxon_authorship(tsn, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame

Examples

## Not run: 
taxon_authorship(tsn = 183671)

## End(Not run)

Description

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

Usage

terms(query, what = "both", wt = "json", raw = FALSE, ...)

Arguments

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)

Description

Get tsn by vernacular language

Usage

tsn_by_vernacular_language(language, wt = "json", raw = FALSE, ...)

Arguments

Value

a data.frame

Examples

## Not run: 
tsn_by_vernacular_language(language = "french")

## End(Not run)

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

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)

Description

Returns the unacceptability reason, if any, for the TSN.

Usage

unacceptability_reason(tsn, wt = "json", raw = FALSE, ...)

Arguments

Examples

## Not run: 
unacceptability_reason(tsn = 183671)

## End(Not run)

Description

Returns the usage information for the TSN.

Usage

usage(tsn, wt = "json", raw = FALSE, ...)

Arguments

Examples

## Not run: 
usage(tsn = 526852)
usage(tsn = 526852, raw = TRUE)
usage(tsn = 526852, wt = "xml")

## End(Not run)

Description

Provides a list of the unique languages used in the vernacular table.

Usage

vernacular_languages(wt = "json", raw = FALSE, ...)

Arguments

Value

a character vector of verncular names

Examples

## Not run: 
vernacular_languages()

## End(Not run)