gbif
Data from GBIF
This function downloads species occurence records from the Global Biodiversity Information Facility (GBIF) data portal. You can download either a single species (if you append a '*' to the species name) or a subspecies of comparable level. You can download the data for an entire genus by using species='*'
. Before using this function, please first check the GBIF data use agreement.
- Keywords
- spatial
Usage
gbif(genus, species="", ext=NULL, args=NULL, geo=TRUE, sp=FALSE,
removeZeros=FALSE, download=TRUE, ntries=5, nrecs=300, start=1, end=Inf)
Arguments
- genus
character. genus name
- species
character. species name. Use '*' to download the entire genus. Append '*' to the species name to get all naming variants (e.g. with and witout species author name) and sub-taxa
- ext
Extent object to limit the geographic extent of the records. An extent can be created using functions like
drawExtent
andextent
- args
character. Additional arguments to refine the query. See query parameters in https://www.gbif.org/developer/occurrence for more details
- geo
logical. If
TRUE
, only records that have a georeference (longitude and latitude values) will be downloaded- sp
logical. If
TRUE
,geo
will be set toTRUE
and a SpatialPointsDataFrame will be returned- removeZeros
logical. If
TRUE
, all records that have a latitude OR longitude of zero will be removed ifgeo==TRUE
, or set toNA
ifgeo==FALSE
. IfFALSE
, only records that have a latitude AND longitude that are zero will be removed or set toNA
- download
logical. If
TRUE
, records will be downloaded, else only the number of records will be shown- ntries
integer. How many times should the function attempt to download the data, if an invalid response is returned (perhaps because the GBIF server is very busy)
- nrecs
integer. How many records to download in a single request (max is 300)?
- start
integer. Record number from which to start requesting data
- end
integer. Last record to request
Value
data frame
References
Examples
# NOT RUN {
gbif('solanum', download=FALSE)
gbif('solanum', 'acaule', download=FALSE)
gbif('Batrachoseps', '' , down=FALSE)
gbif('Batrachoseps', 'luciae', down=FALSE)
g <- gbif('Batrachoseps', 'luciae', geo=TRUE)
plot(g$lon, g$lat)
gs <- gbif('Batrachoseps', 'luciae', sp=TRUE)
plot(gs)
# }