sp_occurrence | R Documentation |
Download data from the Global Biodiversity Information Facility (GBIF) data portal.
sp_genus
returns a data.frame with all the species names associated with a genus.
sp_occurrence
downloads species occurrence records. You can download data for a single species or for an entire genus by using species=""
. Note that the maximum number of records that can be downloaded for a single search is 100,000.
You can check the number of records returned by using the option download=FALSE
.
To avoid getting more than 100,000 records, you can do separate queries for different geographic areas. This has been automated in sp_occurrence_split
. This function recursively splits the area of interest into smaller areas until the number of records in an area is less than 50,000. It then downloads these records and saves them in a folder called "gbif". After all areas have been evaluated, the data are combined into a single file and returned as a data.frame). If the function is interrupted, it can be run again, and it will resume where it left off.
If you want to download data for an entire genus, first run sp_genus
and then download data for the returned species names one by one.
Before using this function, please first check the GBIF data use agreement and see the note below about how to cite these data.
sp_genus(genus, simple=TRUE, ...)
sp_occurrence(genus, species="", ext=NULL, args=NULL, geo=TRUE,
removeZeros=FALSE, download=TRUE, ntries=5, nrecs=300,
start=1, end=Inf, fixnames=TRUE, ...)
sp_occurrence_split(genus, species="", path=".", ext=c(-180,180,-90,90),
args=NULL, geo=TRUE, removeZeros=FALSE, ntries=5, nrecs=300,
fixnames=TRUE, prefix=NULL, ...)
genus |
character. genus name |
species |
character. species name. Can be left blank to get the entire genus |
ext |
SpatExtent object to limit the geographic extent of the records. A SpatExtent can be created using functions like |
args |
character. Additional arguments to refine the query. See query parameters in http://www.gbif.org/developer/occurrence for more details |
geo |
logical. If |
removeZeros |
logical. If |
download |
logical. If |
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 |
fixnames |
If |
path |
character. Where should the data be downloaded to (they will be put in a subdirectory "gbif")? |
prefix |
character. prefix of the downloaded filenames (best left NULL, the function will then use "genus_species" |
simple |
logical. If |
... |
additional arguments passed to |
data.frame
Under the terms of the GBIF data user agreement, users who download data agree to cite a DOI. Citation rewards data-publishing institutions and individuals and provides support for sharing open data [1][2]. You can get a DOI for the data you downloaded by creating a "derived" dataset. For this to work, you need to keep the "datasetKey" variable in your dataset.
https://www.gbif.org/occurrence https://www.gbif.org/derived-dataset/about
sp_occurrence("solanum", download=FALSE)
sp_occurrence("solanum", "acaule", download=FALSE)
sp_occurrence("Batrachoseps", "" , down=FALSE)
sp_occurrence("Batrachoseps", "luciae", down=FALSE)
g <- sp_occurrence("Batrachoseps", "luciae", geo=TRUE, end=25)
#plot(g[, c("lon", "lat")])
## args
a1 <- sp_occurrence("Elgaria", "multicarinata",
args="recordNumber=Robert J. Hijmans RH-2")
a2 <- sp_occurrence("Batrachoseps", "luciae",
args=c("year=2023", "identifiedBy=Anthony Ye"))
## year supports "range queries"
a3 <- sp_occurrence("Batrachoseps", "luciae",
args=c("year=2020,2023", "identifiedBy=Kuoni W"))
#table(a3[,c("year")])
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