itis_search: ITIS Solr search

In ritis: Integrated Taxonomic Information System Client

Description

ITIS Solr search

Usage

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

Arguments

...	Arguments passed on to the params parameter of the solrium::solr_search() function. See solr_fields for possible parameters, and examples below
proxy	List of arguments for a proxy connection, including one or more of: url, port, username, password, and auth. See crul::proxy() for help, which is used to construct the proxy connection.
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)

ritis documentation built on Feb. 2, 2021, 9:06 a.m.