finsyncR, an R package to synchronize 27 years of fish and invertebrate data across the United States

Abstract

The United States government collects some of the most comprehensive data on freshwater systems in existence, but barriers exist for new users to apply these data without institutional guidance. ‘finsyncR’ (fish andinvertebratesynchronizer inR) is an R package that streamlines the process of acquiring, processing, and integrating fish and macroinvertebrate datasets collected in streams and rivers, increasing access to cleaned data and ensuring straightforward application of the data. The data sources are the US Environmental Protection Agency’s National River and Streams Assessment and US Geological Survey’s BioData. The resulting datasets span 27 years (1993 to 2019) and include 8,115 sites, 15,169 sampling events, 963 macroinvertebrate genera, and 687 fish species. We document common challenges to working with these data including understanding sampling designs, harmonizing taxonomy, calculating densities and standardized abundances, accounting for differences in sampling effort, and considering improvements in taxonomic identifications. We anticipate this package will spur research exploring changes in fish and macroinvertebrate communities across space and time and the causes and consequences of those changes.