galah_select: Specify fields for occurrence download

Description

The living atlases store content on hundreds of different fields, and users often require thousands or millions of records at a time. To reduce time taken to download data, and limit complexity of the resulting data.frame, it is sensible to restrict the fields returned by atlas_occurrences(). This function allows easy selection of fields, or commonly-requested groups of columns, following syntax shared with dplyr::select().

Usage

galah_select(..., group = c("basic", "event", "assertions"))

Arguments

...

zero or more individual column names to include

group

string: (optional) name of one or more column groups to include. Valid options are "basic", "event" and "assertion"

Value

An object of class data.frame and galah_select specifying the name and type of each column to include in the call to atlas_counts() or atlas_occurrences().

Examples

Download occurrence records of Perameles taken in 2001, only returning scientific name and event date

galah_config(email = "your-email@email.com")
galah_call() |>
  galah_identify("perameles")|>
  galah_filter(year == 2001) |>
  galah_select(scientificName, eventDate) |>
  atlas_occurrences()

Download occurrence record of Perameles taken in 2001, returning the "basic" group of columns plus the Basis of Record

galah_call() |>
  galah_identify("perameles") |>
  galah_filter(year == 2001) |>
  galah_select(group = "basic", basisOfRecord) |>
  atlas_occurrences()

Details

Calling the argument group = "basic" returns the following columns:

decimalLatitude
decimalLongitude
eventDate
scientificName
taxonConceptID
recordID
dataResourceName

Using group = "event" returns the following columns:

eventRemarks
eventTime
eventID
eventDate
samplingEffort
samplingProtocol

Using group = "assertions" returns all quality assertion-related columns. The list of assertions is shown by search_fields(type = "assertions").