infinitylists: A Shiny application and R package for rapid generation of place-based species checklists

This is a Preprint and has not been peer reviewed. This is version 2 of this Preprint.

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Authors

Thomas Mesaglio , Fonti Kar, Hervé Sauquet, Will Cornwell

Abstract

Premise: Online biodiversity databases like GBIF hold billions of occurrence records, including vouchered specimens and citizen science records. Integrating these two data streams facilitates more robust species checklists. However, processing huge biodiversity datasets can be time-consuming, and most databases are species-focused, rather than place-based, visualisation tools. Methods and Results: infinitylists is a Shiny application and R package that allows users to generate regional species checklists. Our implementation of ‘lazy loading’ using Apache parquet for data storage allows rapid loading of records. After selecting an area, records are retrieved from the Atlas of Living Australia or GBIF. Queries return a text summary, map, table and CSV file. Conclusions: infinitylists is an easy-to-use tool with applications including supplementing survey data, planning collecting expeditions, and informing gap-filling exercises. infinitylists is a complementary tool to existing databases to allow users to rapidly answer the question ‘which species of taxon X have been documented in (or near) spatial polygon Y?’.

DOI

https://doi.org/10.32942/X27S60

Subjects

Life Sciences

Keywords

Atlas of Living Australia, biodiversity data, iNaturalist, R package, Shiny, species checklist, voucher

Dates

Published: 2024-10-25 04:57

Last Updated: 2024-10-25 11:57

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License

CC-BY Attribution-NonCommercial 4.0 International

Additional Metadata

Language:
English

Data and Code Availability Statement:
The online version of infinitylists is available at https://unsw.shinyapps.io/infinitylists/. The R package version of infinitylists can be run natively on a user's computer and is downloadable from GitHub at https://github.com/traitecoevo/infinitylists, with all data and code for release 2.0.1 available at Zenodo (https://doi.org/10.5281/zenodo.13967588).