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Combine results from occ calls to a single data.frame

Source: R/occ2df.R
occ2df.Rd

Combine results from occ calls to a single data.frame

Usage

occ2df(obj, what = "data")

Arguments

obj

Input from occ, an object of class occdat, or an object of class occdatind, the individual objects from each source within the occdat class.

what

(character) One of data (default) or all (with metadata)

Details

This function combines a subset of data from each data provider to a single data.frame, or metadata plus data if you request what="all". The single data.frame contains the following columns:

  • name - scientific (or common) name

  • longitude - decimal degree longitude

  • latitude - decimal degree latitude

  • prov - data provider

  • date - occurrence record date

  • key - occurrence record key

Examples

if (FALSE) {
# combine results from output of an occ() call
spnames <- c('Accipiter striatus', 'Setophaga caerulescens',
  'Spinus tristis')
out <- occ(query=spnames, from='gbif', gbifopts=list(hasCoordinate=TRUE),
  limit=10)
occ2df(out)
occ2df(out$gbif)

out <- occ(
  query='Accipiter striatus',
  from=c('gbif','ebird','inat'),
  gbifopts=list(hasCoordinate=TRUE), limit=2)
occ2df(out)
occ2df(out$gbif)

# or combine many results from a single data source
spnames <- c('Accipiter striatus', 'Spinus tristis')
out <- occ(query=spnames, from='gbif', limit=2)
occ2df(out$gbif)
}