Get or set configuration options that control sbdi4r2 behavior

List valid download reasons

Usage

sbdi_config(atlas = "SBDI", ...)

sbdi_reasons()

Arguments

atlas

string: Living Atlas to point to, SBDI by default. Can be an organisation name, acronym, or region (see [show_all_atlases()] for admissible values).

...

Options can be defined using the form `name = "value"`. Valid arguments are:

* `api-key` string: A registered API key (currently unused).

* `directory` string: the directory to use for the cache. By default this is a temporary directory, which means that results will only be cached within an R session and cleared automatically when the user exits R. The user may wish to set this to a non-temporary directory for caching across sessions. The directory must exist on the file system.

* `download_reason_id` numeric or string: the "download reason" required by some ALA services, either as a numeric ID (currently 0--13) or a string (see `show_all(reasons)` for a list of valid ID codes and names). By default this is NA. Some ALA services require a valid download_reason_id code, either specified here or directly to the associated R function.

* `email` string: An email address that has been registered with the chosen atlas. For the SBDI, you can register at [this address](https://auth.biodiversitydata.se/userdetails/registration/createAccount).

* `password` string: A registered password (GBIF only)

* `run_checks` logical: should `sbdi4r2` run checks for filters and columns. If making lots of requests sequentially, checks can slow down the process and lead to HTTP 500 errors, so should be turned off. Defaults to TRUE.

* `send_email` logical: should you receive an email for each query to [atlas_occurrences()]? Defaults to `FALSE`; but can be useful in some instances, for example for tracking DOIs assigned to specific downloads for later citation.

* `username` string: A registered username (GBIF only)

* `verbose` logical: should `sbdi4r2` give verbose such as progress bars? Defaults to FALSE.

Value

For `sbdi_config()`, a `list` of all options. When `sbdi_config(...)` is called with arguments, nothing is returned but the configuration is set.

References

https://api.biodiversitydata.se/

https://spatial.biodiversitydata.se/layers/ this will eventually move to the api link

#' The `sbdi4r2` package (via the `galah` package) supports large data downloads, and also interfaces with the SBDI which requires that users of some services provide a registered email address and reason for downloading data. The `sbdi_config` function provides a way to manage these issues as simply as possible.

Invoking sbdi_config() with no arguments returns a list with the current values of the options.

sbdi_reasons() returns a data frame with information describing the valid options for download_reason_id

Examples

if (FALSE) {
# To download occurrence records, enter your email in `sbdi_config()`.
# This email should be registered with the atlas in question.
sbdi_config(email = "your-email@email.com")

# Some ALA services require that you add a reason for downloading data.
# Add your selected reason using the option `download_reason_id`
sbdi_config(download_reason_id = 0)

# To look up all valid reasons to enter, use `show_all(reasons)`
# show_all(reasons) or simply `show_reasons()`

# Make debugging in your session easier by setting `verbose = TRUE`
sbdi_config(verbose = TRUE)
}