rvertnet (version 0.3.0)

searchbyterm: Search for records using keywords/terms to control how your query is interpreted.

Description

Returns only those records in which the targeted input is found in association with the specified search terms.

Usage

searchbyterm(specificepithet = NULL, genus = NULL, family = NULL,
  order = NULL, class = NULL, limit = 1000, compact = TRUE,
  year = NULL, date = NULL, mappable = NULL, error = NULL,
  continent = NULL, cntry = NULL, stateprovince = NULL, county = NULL,
  island = NULL, igroup = NULL, inst = NULL, id = NULL,
  catalognumber = NULL, collector = NULL, type = NULL,
  hastypestatus = NULL, media = NULL, rank = NULL, tissue = NULL,
  resource = NULL, verbose = TRUE, ...)

Arguments

specificepithet

Taxonomic specific epithet, e.g. (sapiens in Homo sapiens) (character)

genus

Taxonomic genus (character)

family

Taxonomic family (character)

order

Taxonomic order (character)

class

Taxonomic class (character)

limit

(numeric) Limit on the number of records returned. Up to 1000. We'll incorporate paging later for higher limits. See bigsearch to get larger result sets in a text file via email.

compact

Return a compact data frame (logical)

year

Year (numeric) or range of years designated by comparison operators "<", "="">", "<=" or="" "="">=". You can pass in more than one of these queries, in a vector. See example below. (character)

date

Event date associated with this occurrence record; yyyy-mm-dd or the range yyyy-mm-dd/yyyy-mm-dd (character)

mappable

Record includes valid coordinates in decimal latitude and decimal longitude (logical)

error

Coordinate uncertainty in meters (numeric) or range of uncertainty values designated by comparison operators "<", "="">", "<=" or="" "="">=" (character)

continent

Continent to search for occurrence (character)

cntry

Country to search for occurrence (character)

stateprovince

State or province to search for occurrence (character)

county

County to search for occurrence (character)

island

Island to search for occurrence (character)

igroup

Island group to search for occurrence (character)

inst

Code name for the provider/institution of record (character)

id

Provider's unique identifier for this occurrence record (character)

catalognumber

Provider's catalog number or other ID for this record (character)

collector

Collector name (character)

type

Type of record; "specimen" or "observation" (character)

hastypestatus

Specimen associated with this record is identified as a holotype, paratype, neotype, etc. (character)

media

Record also references associated media, such as a film or video (logical)

rank

TBD (numeric)

tissue

Record is likely to reference tissues (logical)

resource

Identifier for the resource/dataset from which the record was indexed (character)

verbose

Print progress and information messages. Default: TRUE

...

Curl arguments passed on to GET

Value

• A data frame of search results

Details

searchbyterm builds a query from input parameters based on Darwin Core (dwc) terms (for the full list of terms, see https://code.google.com/p/darwincore/wiki/DarwinCoreTerms). The query string is appended to the base URL for VertNet search requests. View the query string for specification of dwc terms used in the search.

References

https://github.com/VertNet/webapp/wiki/The-API-search-function

Examples

# Limit the number of records returned to <1000; use bigsearch() for >1000 records
(out <- searchbyterm(class = "aves", st = "california", lim = 10))

# Find multiple species
(out <- searchbyterm(gen = "ochotona", specificepithet = "(princeps OR collaris)", limit=10))

# Specifying a single year (no quotes) or range of years (use quotes)
(out <- searchbyterm(class = "aves", st = "california", y = 1976, limit=10))
(out <- searchbyterm(class = "aves", st = "california", y = ">=1976", limit=10))

# Specifying a range (in meters) for uncertainty in spatial location (use quotes)
out <- searchbyterm(class = "aves", st = "nevada", error = "<25")
out <- searchbyterm(class = "aves", st = "california", y = 1976, error = "<=1000")

# Specifying records by event date (use quotes)
out <- searchbyterm(class = "aves", st = "california", date = "2009-03-25")
# ...but specifying a date range may not work
out <- searchbyterm(specificepithet = "nigripes", date = "1935-09-01/1935-09-30")

# Pass in curl options for curl debugging
library("httr")
out <- searchbyterm(class = "aves", limit = 10, config=verbose())
# out <- searchbyterm(class = "aves", limit = 500, config=timeout(1))

# Request more than 1000 records
out <- searchbyterm(genus = "Ochotona", limit = 1500)
out$meta
out$data
NROW(out$data)

# Use more than one year query
searchbyterm(class = "aves", year = c(">=1976", "<=1986"))