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infinitylists

R-CMD-check DOI lifecycle

This shiny-based application allows users to extract species occurrence data from the Atlas of Living Australia (ALA) and generate a species list for any defined area. All records associated with either a physical voucher (stored in Australian herbaria or museums), or a photographic voucher or audio file uploaded to iNaturalist are extracted. For each species within the defined area, the application will return voucher type, number of vouchers, date of the most recent voucher, spatial coordinates, voucher location, and the voucher collector. Records are displayed both in a table and on a map, and are downloadable as a CSV. The app is currently using data downloaded from the ALA on 22 October 2024.

Which records are returned?

The map and table outputs will only display the most recent record per species per voucher type. Each species will therefore be represented on the map and in the table by a maximum of 3 records (for species with a physical voucher, photographic voucher and audio voucher in the target area). The text statement indicates the total number of records, and the downloadable CSV file contains all records from the target area, not just the most recent records.

Use the app

The app can be accessed here: https://unsw.shinyapps.io/infinitylists/

Local installation

You can install and run a local version of infinitylists from GitHub. This allows more flexibility for loading taxa that are not automatically loaded in the web app. The code to do this is:

# install.packages("remotes")

remotes::install_github("traitecoevo/infinitylists", build_vignettes = TRUE)

library(infinitylists)

infinitylistApp()

Adding new taxa

infinitylists comes with 5 taxa loaded to start with: plants, butterflies, cicadas, marsupials, and dragonflies + damselflies. If you want to add another taxon, you’ll need to download the data first via the galah interface to the ALA. The function download_ala_obs will download the data and put it into a directory where infinitylists can find it. The value for taxon needs to be a valid taxonomic group as recognized by the ALA. The download step is fast for taxa with small number of observations in ALA and slower for taxa with millions of observations.

# install.packages("galah")

# register with ALA
galah::galah_config(email = "YOUR EMAIL HERE")

# download the data, this needs to be a valid taxa name
download_ala_obs(taxon = "Orthoptera")

infinitylistApp()

Adapt infinitylists for other countries

We have developed functions to assist users to create their own infinitylist for their chosen taxa and country. Check out the vignette which shows you how to do so!

vignette("diy")

All our documentation is also neatly rendered at this pkgdown website: https://traitecoevo.github.io/infinitylists/

Why did I get disconnected from the server?

If infinitylists is left open but idle in your browser for too long, you will be disconnected from the server.

Applying the Use my location filter without first having given your browser access to your current location will also disconnect you from the server. If this occurs, please amend your settings and try again.