library(arrow)
library(dplyr)
library(readr)
library(here)Data in this book
This book uses data DOIs to preserve reproducible data downloads, as most data is downloaded from the Atlas of Living Australia (ALA) using the galah package, the ALA’s R interface to downloading biodiversity data. At the beginning of each chapter, in the Prerequisites section, we have provided options for you to either download the identical dataset using these DOIs or reproduce the query using our code.
Using original download queries
If you download data using a galah query (rather than a DOI), the results you return when running the examples might not exactly match results in this book. This difference arises because data in the ALA is constantly being ingested (including from previous years) and galah downloads data directly from the ALA. This means that using the same query after the date this book was last rendered—even a query for a specific time-period (e.g., 2010–2015)—might return different data today.
In general, that is a good thing; updates improve data quantity and/or quality. But they can affect reproducibility, too. Getting the latest data shouldn’t affect whether the example works correctly, but it may affect whether the results you return in your console match the results returned in this book. The main advantage to using Prerequisites sections is that data downloads are transparent and up-to-date.
There are a few datasets used in this book that were not retrieved from the ALA. To ensure reproducibility, we have provided download links to those datasets in this chapter.
Prerequisites
Data
bees
This is a subset of a larger dataset—Curated Plant and Invertebrate Dataset for Bushfire Modelling.
Click on the download button below to download as a parquet file. Save the parquet in your working directory and load it using the code below.
bees <- read_parquet(here("path", "to", "bees.parquet"))inverts
This is a subset of a larger dataset—Curated Plant and Invertebrate Dataset for Bushfire Modelling.
Click on the download button below to download as a parquet file. Save the parquet in your working directory and load it using the code below.
inverts <- read_parquet(here("path", "to", "inverts.parquet"))gbif_species_list
A species list of Eucalyptus downloaded from GBIF.
Click on the download button below to download as a parquet file. Save the parquet in your working directory and load it using the code below.
gbif_species_list <- read_parquet(here("path", "to", "gbif_species_list.parquet"))marine_sp
A subset of World Register of Marine Species (WoRMS) data.
Click on the download button to download as a .csv file. Save the csv in your working directory and load it using the code below.
marine_sp <- read_csv(here("path","to", "worms.csv"))