get_GBIF: Get an occurrence record set from GBIF

In Acanthiza/envImport: Combine Disparate Data Sources

Get an occurrence record set from GBIF

Description

Get new occurrence record set from GBIF and save as .rds. GBIF is the Global Biodiversity Information Facility.

Usage

get_gbif(
  aoi = NULL,
  save_dir = NULL,
  get_new = FALSE,
  data_map = NULL,
  predicates = NULL,
  request_wait = 20,
  name = "gbif",
  filter_inconsistent = TRUE,
  filter_NA_date = TRUE,
  occ_char = TRUE,
  adj_spa_rel = TRUE,
  previous_key = NULL,
  ...
)

Arguments

aoi	sf defining area of interest.
save_dir	Character. File path into which to save outputs. If null results will be saved to fs::path("out", "ds", "gbif") as file gbif.rds.
get_new	Logical. If FALSE will attempt to load data from previously saved results.
data_map	Dataframe or NULL. Mapping of fields to retrieve. See example envImport::data_map
predicates	List. Any number of gbif predicates
request_wait	Integer. Time in seconds to wait between rgbif::occ_download_meta() requests. Used by rgbif::occ_download_wait() status_ping argument.
name	Character or NULL. data_name value in envImport::data_map (or other data_map). Required if data_map is not NULL
filter_inconsistent	Logical. If TRUE inconsistencies between the occurrenceStatus column and either organismQuantity or individualCount are removed. e.g. a record with occurrenceStatus == "ABSENT" but individualCount == 1 would be filtered.
filter_NA_date	Logical. Filter if is.na(eventDate).
occ_char	Logical. If true, occ_derivation will be coerced to character (to match other data sources).
adj_spa_rel	Logical. If true, an attempt will be made to check coordinateUncertaintyInMeters against: information in informationWithheld. If informationWithheld contains "Coordinate uncertainty increased to", readr::parse_number() is used to retrieve that number, which is then used to replace any value in coordinateUncertaintyInMeters; and if the column issue contains COORDINATE_UNCERTAINTY_METERS_INVALID, coordinateUncertaintyInMeters is limited to 10000 or greater.
previous_key	Character. e.g. 0092123-240506114902167. If provided, an attempt will be made to load (or download) a previous query of occurrence data.
...	Passed to envImport::file_prep()

Details

Uses various rgbif functions to return a dataframe of occurence records. Requires gbif credentials.

Any arguments to rgbif::occ_download() can be passed via extra_prediates. For convenience, aoi can also be passed directly and internally it is converted to a bounding box in appropriate lat/long and passed to rgbif::pred_within() in WKT format.

Value

Dataframe of occurrences, full download (as key.zip) in save_dir and file saved to save_dir as gbif.parquet.

Examples

  # setup -------
  library("envImport")

  # no aoi ------
  out_dir <- file.path(system.file(package = "envImport"), "examples", "get_gbif_ex")

  gbif_data <- get_gbif(save_dir = out_dir
                        , get_new = FALSE
                        #, data_map = envImport::data_map
                        , predicates = rgbif::pred_and(rgbif::pred("taxonKey", 2474903)
                                                       , rgbif::pred("year", 2000)
                                                       )
                        , previous_key = "0057516-240626123714530"
                        )

  # 667 records 2024-08-09
  nrow(gbif_data)
  head(gbif_data)

  # with aoi
  out_dir <- file.path(system.file(package = "envImport"), "examples", "get_gbif_aoi_ex")

  gbif_data <- get_gbif(save_dir = out_dir
                        , aoi = envClean::aoi
                        , data_map = envImport::data_map
                        , get_new = FALSE
                        , predicates = rgbif::pred("year", 2000)
                        )

  # 107 records 2024-08-09
  nrow(gbif_data)

  # .bib created
  readr::read_lines(fs::path(out_dir, "gbif", "gbif.bib"))

Acanthiza/envImport documentation built on Aug. 14, 2024, 8:18 a.m.