Downloading data using the galah package

Introduction

This manual provides a step-by-step guide on how to download data for the species for example Sepia apama (Giant Cuttlefish) using the galah package in R. The galah package is an interface to the Atlas of Living Australia (ALA) APIs, which allows you to query and download biodiversity data.

Prerequisites

Ensure you have R and RStudio installed on your computer. You’ll also need an internet connection to download the data.

Installation

First, you need to install the galah package if you haven’t already. You can do this by running the following command in your R console:

install.packages("galah")

Loading the galah Package

After installing the package, load it into your R session:

library(galah)

Configuration

Before you can download data, you need to configure the galah package with your email. This email will be used to identify your requests to the ALA servers.

galah_config(email = "youremail@email.com")

Replace "youremail@email.com" with your own email address.

Downloading Sepia apama Data

You can now download data for Sepia apama by using a series of galah functions. Here’s the complete code to do so:

sepia <- galah_call() |>
  galah_identify("Sepia apama") |>
  galah_select(basisOfRecord, recordedBy, recordedByID, eventType, group = c("basic", "event")) |>
  atlas_occurrences()

Explanation of the Code

galah_call(): Initializes the call to the ALA API.
galah_identify("Sepia apama"): Specifies the species of interest.
galah_select(...): Selects specific fields to download. In this case, we are selecting basisOfRecord, recordedBy, recordedByID, eventType, along with groups basic and event.
atlas_occurrences(): Executes the query and retrieves the occurrence data.

Saving the Data

Once you have downloaded the data, you might want to save it for future use. You can do this using the save function:

save(sepia, file = "data-raw/sepia.RDA")

This will save the data to a file named sepia.RDA in the data-raw directory. You can load this data in future sessions using:

load("data-raw/sepia.RDA")

Conclusion

By following this manual, you should be able to download and save occurrence data for Sepia apama using the galah package. This process can be adapted to download data for other species by changing the species name in the galah_identify function.

References

For more information on the galah package, visit the galah GitHub page.

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Javad Vahdat

2024-07-31