occCite (version 0.6.0)

occQuery: Query from Taxon List

Description

Takes rectified list of specimens from studyTaxonList and returns point data from rgbif with metadata.

Usage

occQuery(
  x = NULL,
  datasources = c("gbif", "bien"),
  GBIFLogin = NULL,
  GBIFDownloadDirectory = NULL,
  loadLocalGBIFDownload = F,
  checkPreviousGBIFDownload = T,
  options = NULL
)

Value

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.

Arguments

x

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.

datasources

A vector of occurrence data sources to search. This is currently limited to GBIF and BIEN, but may expand in the future.

GBIFLogin

An object of class GBIFLogin to log in to GBIF to begin the download.

GBIFDownloadDirectory

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.

loadLocalGBIFDownload

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.

checkPreviousGBIFDownload

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.

options

A vector of options to pass to occ_download.

Details

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".

Examples

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
)
}