occurrencelist: Occurrencelist searches for taxon concept records matching a range of filters.

Description

This function is deprecated.

Usage

occurrencelist(scientificname = NULL,
    taxonconceptkey = NULL, dataproviderkey = NULL,
    dataresourcekey = NULL, institutioncode = NULL,
    collectioncode = NULL, catalognumber = NULL,
    resourcenetworkkey = NULL, basisofrecordcode = NULL,
    minlatitude = NULL, maxlatitude = NULL,
    minlongitude = NULL, maxlongitude = NULL,
    minaltitude = NULL, maxaltitude = NULL,
    mindepth = NULL, maxdepth = NULL, cellid = NULL,
    centicellid = NULL, typesonly = NULL,
    coordinatestatus = NULL, coordinateissues = NULL,
    hostisocountrycode = NULL, originisocountrycode = NULL,
    originregioncode = NULL, startdate = NULL,
    enddate = NULL, startyear = NULL, endyear = NULL,
    year = NULL, month = NULL, day = NULL,
    modifiedsince = NULL, startindex = NULL,
    maxresults = 10, format = "brief", icon = NULL,
    mode = NULL, stylesheet = NULL, removeZeros = FALSE,
    writecsv = NULL, curl = getCurlHandle(),
    fixnames = "none")

Arguments

scientificname

scientitic name of taxon. See details. (character)

taxonconceptkey

unique key for taxon. See details (numeric)

dataproviderkey

Filter records to those provided by the supplied numeric key for a data provider. See providers. (character)

dataresourcekey

Filter records to those provided by the supplied numeric key for a data resource See resources. (character)

institutioncode

Return only records from a given institution code.

collectioncode

Return only records from a given collection code.

catalognumber

Return only records from a given catalog number.

resourcenetworkkey

count only records which have been made available by resources identified as belonging to the network identified by the supplied numeric key.

basisofrecordcode

return only records with the specified basis of record. Supported values are: "specimen, observation, living, germplasm, fossil, unknown". (character)

minlatitude

return only records from locations with latitudes greater than the supplied value (southern hemisphere with negative latitudes). (numeric)

maxlatitude

return only records from locations with latitudes lower than the supplied value (southern hemisphere with negative latitudes). (numeric)

minlongitude

return only records from locations with longitudes greater than the supplied value (western hemisphere with negative longitudes). (numeric)

maxlongitude

return only records from locations with longitudes lower than the supplied value (western hemisphere with negative longitudes). (numeric)

minaltitude

return only records from altitudes greater than or equal to the supplied value. (integer)

maxaltitude

return only records from altitudes less than or equals to the supplied value. (integer)

mindepth

return only records from depth greater than or equal to the supplied value. (numeric 2 decimal places)

maxdepth

return only records from depth less than or equals to the supplied value. (numeric 2 decimal places)

cellid

identifier for a one degree cell (O - 64,799)

centicellid

identifier for a 0.1 degree cell within a one degree cell

typesonly

if set to "true", return only records with a type status specified.

coordinatestatus

if set to "true", return only records with coordinates. If set to "false", return only records without coordinates.

coordinateissues

if set to "true", return only records for which the portal has detected possible issues in georeferencing. If set to "false", return only records for which the portal has not detected any such issues.

hostisocountrycode

return only records served by providers from the country identified by the supplied 2-letter ISO code.

originisocountrycode

return only records of occurrences which occurred within the country identified by the supplied 2-letter ISO code.

originregioncode

return only records of occurrences which occurred within the region identified by the supplied 3-letter code.

startdate

return only records occurring on or after the supplied date (format YYYY-MM-DD, e.g. 2006-11-28).

enddate

return only records occurring on or before the supplied date (format YYYY-MM-DD, e.g. 2006-11-28).

startyear

return only records from during or after the supplied year.

endyear

return only records from during or before the supplied year.

year

return only records from during the supplied year.

month

return only records from during the supplied month (expressed as an integer in the range 1 to 12).

day

return only records from during the supplied day of month (expressed as an integer in the range 1 to 31).

modifiedsince

return only records which have been indexed or modified in the GBIF data portal index on or after the supplied date (format YYYY-MM-DD, e.g. 2006-11-28).

startindex

return the subset of the matching records that starts at the supplied (zero-based index).

maxresults

max number of results (integer) (1-10000); defaults to 10

format

specifies the format in which the records are to be returned,

icon

(only when format is set to kml) specified the URL for an icon to be used for the KML Placemarks.

mode

One of processed or raw. Specifies whether the response data should (as far as possible) be the raw values originally retrieved from the data resource or processed (normalised) values used within the data portal (character)

stylesheet

Sets the URL of the stylesheet to be associated with the

removeZeros

remove records with both Lat Long zero values (logical)

writecsv

If path to a file is given, a text file is written out and a success message is returned to the console (logical)

curl

If using in a loop, call getCurlHandle() first and pass the returned value in here (avoids unnecessary footprint)

fixnames

One of "match","change","none", just keep those records that match original search term, change all names to the original search term (beware using this option), or do nothing, respectively. Default is "none".

Details

Including many possible values for a particular parameter: The following parameters may have many values passed to them (e.g., like parameter=c('a','b')): scientificname, taxonconceptkey, dataproviderkey, dataresourcekey, resourcenetworkkey, basisofrecordcode, cellid, centicellid, hostisocountrycode, originisocountrycode, originregioncode, year, month, and day.

More on scientificname: Returns only records where the scientific name matches that supplied - this is based on the scientific name found in the original record from the data provider and does not make use of extra knowledge of possible synonyms or of child taxa. For these functions, use taxonconceptkey. Including an asterisk '*' in the search string causes the service to return records for any name starting with the string preceding the asterisk. There must be at least three characters preceding the asterisk. The scientificname parameter may be repeated within a single request - the results will include records matching any of the supplied scientific names.

More on taxonconceptkey: Returns only records which are for the taxon identified by the supplied numeric key, including any records provided under synonyms of the taxon concerned, and any records for child taxa (e.g. all genera and species within a family). Values for taxonconceptkey can be found through the taxon web service (see http://data.gbif.org/ws/rest/taxon). Note that the service will always search using the corresponding concept in the synthetic generated "PORTAL" taxonomy (even if the taxonconceptkey is for a concept from a specific resource. Use dataresourcekey to limit the search to a single data resource. The most efficient and thorough way to search will be to limit searches to taxa belonging to the following ranks: kingdom, phylum, class, order, family, genus, species, any infraspecific rank. Each record returned from this action (and from the get action) also includes a taxonKey attribute which can be used in the taxonconceptkey parameter on subsequent invocations of the list and count actions. The taxonconceptkey parameter may be repeated within a single request - the results will include records for any of the specified taxa.

See the GBIF API docs for more details on each parameter: http://data.gbif.org/ws/rest/occurrence

Examples

Run this code

# Query for a single species
occurrencelist(scientificname = 'Puma concolor', coordinatestatus = TRUE)
occurrencelist(scientificname = 'Puma concolor', coordinatestatus = TRUE,
   maxresults = 40)
occurrencelist(scientificname = 'Accipiter erythronemius', coordinatestatus = TRUE,
   maxresults = 5)

# Query for many species, in this case using parallel fuctionality with plyr::llply
# Also, see \code{\link{occurrencelist_many}} as an alternative way to search for
# many species, which is better for going straight to a map with the output data.
library(doMC); library(plyr)
registerDoMC(cores=4)
splist <- c('Accipiter erythronemius', 'Junco hyemalis', 'Aix sponsa')
out <- llply(splist, function(x) occurrencelist(x, coordinatestatus = TRUE,
             maxresults = 100), .parallel=T)
lapply(out, function(x) head(gbifdata(x)))

# Write the output to csv file
occurrencelist(scientificname = 'Erebia gorge*',
   coordinatestatus = TRUE, maxresults = 200, writecsv="~/adsdf.csv")

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Description

Usage

Arguments

Details

See Also

Examples