specieslist: Get list of taxa and their occurrence counts

In fozy81/NBN4R: National Biodiversity Network Atlas (UK and Ireland) Data and Resources in R

Description

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

Usage

specieslist(taxon, wkt, fq)

Arguments

taxon	string: (optional) query of the form field:value (e.g. "genus:Macropus") or a free text search (e.g. "macropodidae"). For reliable results it is recommended to use a specific field where possible (see nbn_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 nbn_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 NBN web service: https://api.nbnatlas.org/#ws78

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

See Also

nbn_fields for occurrence fields that are queryable via the fq parameter

Examples

## Not run: 
x <- specieslist(taxon="genus:Leuctra",wkt="POLYGON((-3 56,-4 56,-4 57,-3 57,-3 56))")

x <- specieslist(wkt="POLYGON((-3 56,-4 56,-4 57,-3 57,-3 56))",fq="rank:species")

x <- specieslist(wkt="POLYGON((-3 56,-4 56,-4 57,-3 57,-3 56))",fq="genus:Macropus")

x <- specieslist(wkt="POLYGONPOLYGON((-3 56,-4 56,-4 57,-3 57,-3 56))",
fq="kingdom:Plantae")
## NOTE that this response might include records with empty or NA kingdom, phylum, or
##  class values, as per the note above.

## End(Not run)

fozy81/NBN4R documentation built on May 19, 2019, 8:22 a.m.