Takes rectified list of specimens from
studyTaxonList
and returns point data from
rgbif
with metadata.
occQuery(
x = NULL,
datasources = c("gbif", "bien"),
GBIFLogin = NULL,
GBIFDownloadDirectory = NULL,
loadLocalGBIFDownload = F,
checkPreviousGBIFDownload = T,
options = NULL
)
An object of class occCiteData
(the results of
a studyTaxonList
search) OR a vector with a list of species
names. Note: If the latter, taxonomic rectification uses NCBI
taxonomies. If you want more control than this, use
studyTaxonList
to create a occCiteData
object
first.
A vector of occurrence data sources to search. This is currently limited to GBIF and BIEN, but may expand in the future.
An object of class GBIFLogin
to log in to
GBIF to begin the download.
An optional argument that specifies the local directory where GBIF downloads will be saved. If this is not specified, the downloads will be saved to your current working directory.
If loadLocalGBIFDownload = T
, then
occCite will load occurrences for the specified species that have been
downloaded by the user and stored in the directory specified by
GBIFDownloadDirectory
.
If loadLocalGBIFDownload = T
,
occCite will check for previously-prepared GBIF downloads on the user's
GBIF account. Setting this option to `TRUE` can significantly speed up
query time if the user has previously queried GBIF for the same taxa.
A vector of options to pass to occ_download
.
The object of class occCiteData
supplied by the user
as an argument, with occurrence data search results, as well as metadata
on the occurrence sources queried.
If you are querying GBIF, note that `occQuery()` only returns records from GBIF that have coordinates, aren't flagged as having geospatial issues, and have an occurrence status flagged as "PRESENT".
if (FALSE) {
## If you have already created a occCite object, and have not previously
## downloaded GBIF data.
occQuery(
x = myOccCiteObject,
datasources = c("gbif", "bien"),
GBIFLogin = myLogin,
GBIFDownloadDirectory = "./Desktop",
loadLocalGBIFDownload = F
)
## If you don't have an occCite object yet
occQuery(
x = c("Buteo buteo", "Protea cynaroides"),
datasources = c("gbif", "bien"),
GBIFLogin = myLogin,
GBIFDownloadDirectory = "./Desktop",
loadLocalGBIFDownload = F
)
## If you have previously downloaded occurrence data from GBIF
## and saved it in a folder called "GBIFDownloads".
occQuery(
x = c("Buteo buteo", "Protea cynaroides"),
datasources = c("gbif", "bien"),
GBIFLogin = myLogin,
GBIFDownloadDirectory = "./Desktop/GBIFDownloads",
loadLocalGBIFDownload = T
)
}