get_obis: Get data using 'robis::occurrence()'

In Acanthiza/envImport: Combine Disparate Data Sources

Get data using robis::occurrence()

Description

Requires an aoi. i.e. aoi is not optional for this implementation of get_obis

Usage

get_obis(
  aoi = NULL,
  save_dir = NULL,
  get_new = FALSE,
  name = "obis",
  data_map = NULL,
  filter_inconsistent = TRUE,
  removes = list(basisOfRecord = c("LIVING_SPECIMEN", "FOSSIL_SPECIMEN",
    "MATERIAL_CITATION")),
  ...
)

Arguments

aoi	Optional simple feature (sf). Used to limit the occurrences returned via obis::occurence()
save_dir	Character. Path to directory into which to save outputs. If NULL results will be saved to here::here("out", "ds", "obis"). File will be named obis.parquet
get_new	Logical. If FALSE, will attempt to load from existing save_dir.
name	Character. data_name value in envImport::data_map (or other data_map)
data_map	Dataframe or NULL. Mapping of fields to retrieve. See example envImport::data_map
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.
removes	Named list. Names need to match column names in the result of a call to robis::occurrence() (i.e. generally Darwin core column names). Levels within each name are matched and, if present, removed. Note that this filtering occurs after download so it does not save on download time and can also be done after a call to get_obis(). It does enable filtering on columns that are not passed through to the return value as they are not in the data_map.
...	Passed to envImport::file_prep()

Value

Dataframe of occurrences and file saved to save_dir.

Examples

aoi <- sf::st_read(file.path(system.file(package = "envImport"), "aoi.shp"))

obis_data <- get_obis(aoi
                      , save_dir = tempdir()
                      , data_map = envImport::data_map
                      , get_new = TRUE
                      )

obis_data |>
  dplyr::count()

# Removing certain methods
obis_data <- get_obis(aoi
                      , save_dir = tempdir()
                      , data_map = envImport::data_map
                      , removes = list(basisOfRecord = c("PreservedSpecimen"))
                      , get_new = TRUE
                      )

obis_data |>
  dplyr::count()

Acanthiza/envImport documentation built on April 14, 2025, 6:17 a.m.