Return occurrence records

The most common form of data stored by living atlases are observations of individual life forms, known as 'occurrences'. This function allows the user to search for occurrence records that match their specific criteria, and return them as a data.frame for analysis. Optionally, the user can also request a DOI for a given download to facilitate citation and re-use of specific data resources.

Usage

atlas_occurrences(
  request = NULL,
  identify = NULL,
  filter = NULL,
  geolocate = NULL,
  data_profile = NULL,
  select = NULL,
  mint_doi = FALSE,
  doi = NULL,
  refresh_cache = FALSE
)

Arguments

request

optional data_request object: generated by a call to galah_call().

identify

data.frame: generated by a call to galah_identify().

filter

data.frame: generated by a call to galah_filter()

geolocate

string: generated by a call to galah_geolocate()

data_profile

string: generated by a call to galah_apply_profile()

select

data.frame: generated by a call to galah_select()

mint_doi

logical: by default no DOI will be generated. Set to TRUE if you intend to use the data in a publication or similar

doi

Use collect_occurrences instead.

string: this argument enables retrieval of occurrence records previously downloaded from the ALA, using the DOI generated by the data.

refresh_cache

logical: if set to TRUE and galah_config(caching = TRUE) then files cached from a previous query will be replaced by the current query

Value

An object of class tbl_df and data.frame (aka a tibble) of occurrences, containing columns as specified by galah_select(). The data.frame object has the following attributes:

• a listing of the user-supplied arguments of the data_request (i.e., identify, filter, geolocate, select)

• a doi of the data download

• the search_url of the query to ALA API

Details

Note that unless care is taken, some queries can be particularly large. While most cases this will simply take a long time to process, if the number of requested records is >50 million the call will not return any data. Users can test whether this threshold will be reached by first calling atlas_counts() using the same arguments that they intend to pass to atlas_occurrences(). It may also be beneficial when requesting a large number of records to show a progress bar by setting verbose = TRUE in galah_config().

Examples

if (FALSE) {
# Download occurrence records for a specific taxon
galah_config(email = "your_email_here")
galah_call() |>
  galah_identify("Reptilia") |>
  atlas_occurrences()

# Download occurrence records in a year range
galah_call() |>
  galah_identify("Litoria") |>
  galah_filter(year >= 2010 & year <= 2020) |>
  atlas_occurrences()

# Download occurrences records in a WKT-specified area
polygon <- "POLYGON((146.24960 -34.05930,
                     146.37045 -34.05930,
                     146.37045 -34.152549,
                     146.24960 -34.15254,
                     146.24960 -34.05930))"
galah_call() |> 
  galah_identify("Reptilia") |>
  galah_filter(year >= 2010, year <= 2020) |>
  galah_geolocate(polygon) |>
  atlas_occurrences()
}