occurrence: Find occurrence records

In robis: Ocean Biodiversity Information System (OBIS) Client

Find occurrence records

Description

Download occurrence records from OBIS. A set of filters can be used to delimit which data will be downloaded. Note that scientificname can be a species name or any other taxon name (e.g. a family name).

Usage

occurrence(scientificname = NULL, taxonid = NULL, datasetid = NULL,
  nodeid = NULL, instituteid = NULL, areaid = NULL, startdate = NULL, enddate = NULL,
  startdepth = NULL, enddepth = NULL, geometry = NULL,
  measurementtype = NULL, measurementtypeid = NULL, measurementvalue = NULL,
  measurementvalueid = NULL, measurementunit = NULL, measurementunitid = NULL,
  redlist = NULL, hab = NULL, wrims = NULL, extensions = NULL, hasextensions = NULL,
  mof = NULL, dna = NULL, absence = NULL, event = NULL, dropped = NULL,
  flags = NULL, exclude = NULL, fields = NULL, qcfields = NULL, q=NULL, verbose = FALSE)

Arguments

scientificname	the scientific name.
taxonid	the taxon identifier (WoRMS AphiaID).
datasetid	the dataset identifier.
nodeid	the OBIS node identifier.
instituteid	the OBIS institute identifier.
areaid	the OBIS area identifier.
startdate	the earliest date on which occurrence took place.
enddate	the latest date on which the occurrence took place.
startdepth	the minimum depth below the sea surface.
enddepth	the maximum depth below the sea surface.
geometry	a WKT geometry string.
measurementtype	the measurement type to be included in the measurements data.
measurementtypeid	the measurement type ID to be included in the measurements data.
measurementvalue	the measurement value to be included in the measurements data.
measurementvalueid	the measurement value ID to be included in the measurements data.
measurementunit	the measurement unit to be included in the measurements data.
measurementunitid	the measurement unit ID to be included in the measurements data.
redlist	include only IUCN Red List species.
hab	include only IOC-UNESCO HAB species.
wrims	include only WRiMS species.
extensions	which extensions to include (e.g. MeasurementOrFact, DNADerivedData, default = NULL).
hasextensions	which extensions need to be present (e.g. MeasurementOrFact, DNADerivedData, default = NULL).
mof	include measurements data (default = NULL).
dna	include DNA data (default = NULL).
absence	only include absence records (TRUE), exclude absence records (NULL) or include absence records (include).
event	only include pure event records (TRUE), exclude pure event records (NULL) or include event records (include).
dropped	only include dropped records (TRUE), exclude dropped records (NULL) or include dropped records (include).
flags	quality flags which need to be set.
exclude	quality flags to be excluded from the results.
fields	fields to be included in the results.
qcfields	include lists of missing and invalid fields (default = NULL).
q	text search query.
verbose	logical. Optional parameter to enable verbose logging (default = FALSE).

Value

The occurrence records in a tibble format. The number of columns will vary according to the number of information associated with the records. For more information about the type of data available with OBIS occurrences, see the OBIS manual.

Note

When using a geometry, the function will fail if the geometry is too complex. One alternative is to use a bounding box or a simplified version of the geometry.

Examples

records <- occurrence(scientificname = "Abra sibogai")
records <- occurrence(taxonid = 141438, startdate = as.Date("2007-10-10"))

robis documentation built on July 25, 2026, 1:07 a.m.