Supporting open science and data through an R package ecosystem

Biodiversity research relies on the easy accessibility of large amounts of data for hypothesis testing, modelling efforts and informing policy. Access to these data, as well as documenting these workflows and supporting code are key in biodiversity research and open science in general.

In this context, we present a comprehensive ecosystem of R packages designed to provide researchers with a transparent, end-to-end framework for reproducible and open scientific practices. These tools span the entire research pipeline from knowledge acquisition through documentation and course material over automating data acquisition, analysis/modelling and reporting for a variety of ecological applications (https://github.com/bluegreen-labs).

Here, we highlight a subset of our 11 packages listed on the The Comprehensive R Archive Network (CRAN) that enable access, modelling and processing of environmental variables at both point and grid scales, which can be used in “rapid prototyping” hypothesis testing and model development. For example, the {ecmwfr} package streamlines access to data within the European Center for Medium-Range Weather Forecasts Climate Data Store (CDS), including the widely used ERA5 re-analysis dataset. Similarly, the {appeears} package provides access to a diverse range of remote sensing products, such as Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation indices, in support of ecological research.

We believe that our open-source R software and workflows offer significant value to biodiversity research and hope to solicit feedback from the community on our R package ecosystem.