Get list of taxa and their occurrence counts

Source: R/specieslist.R

Retrieve a list of taxa matching a search query, within a spatial search area, or both.

species_list(taxon, wkt, fq)

Arguments

taxon

string: (optional) query of the form field:value (e.g. "genus:Leuctra") or a free text search (e.g. "macropodidae"). For reliable results it is recommended to use a specific field where possible (see sbdi_fields("occurrence_indexed") for valid fields). It is also good practice to quote the taxon name if it contains multiple words, for example taxon="taxon_name:Vulpes vulpes" (noting, however, that multi-word names are unlikely in the context of a specieslist search, where one would typically be searching for all species within, say, a genus or family)
wkt

string: WKT (well-known text) defining a polygon within which to limit taxon search, e.g. "POLYGON((-3 56,-4 56,-4 57,-3 57,-3 56))"
fq

string: character string or vector of strings, specifying filters to be applied to the original query. These are of the form "INDEXEDFIELD:VALUE" e.g. "kingdom:Fungi". See sbdi_fields("occurrence_indexed",as_is=TRUE) for all the fields that are queryable. NOTE that fq matches are case-sensitive, but sometimes the entries in the fields are not consistent in terms of case (e.g. kingdom names "Fungi" and "Plantae" but "ANIMALIA"). fq matches are ANDed by default (e.g. c("field1:abc","field2:def") will match records that have field1 value "abc" and field2 value "def"). To obtain OR behaviour, use the form c("field1:abc OR field2:def")

Value

data frame of results, where each row is a taxon, its classification information, and its occurrence count

References

Associated SBDI web service: https://api.biodiversitydata.se/#ws78

http://www.geoapi.org/3.0/javadoc/org/opengis/referencing/doc-files/WKT.html

See also

sbdi_fields for occurrence fields that are queryable via the fq parameter

Examples

if (FALSE) {
wkt <- "MULTIPOLYGON(((18.3284 58.9611, 17.3284 58.9611, 17.3284 59.9611, 
                       18.3284 59.9611, 18.3284 58.9611)))"
x <- species_list(taxon="genus:Leuctra", 
                 wkt=wkt)

x <- species_list(wkt=wkt, fq="rank:species")

x <- species_list(wkt=wkt, fq="genus:Leuctra")

x <- species_list(wkt=wkt, fq="kingdom:Plantae")
## NOTE that this response might include records with empty or NA kingdom, 
## phylum, or class values, as per the note above.
}