ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database

Abstract

The US EPA ECOTOX database provides key ecotoxicological data that are crucial in environmental risk assessment. It can be used for computational predictions of toxicity or indications of hazard in a wide range of situations. There is no standardised or formalised method for extracting and subsetting data from the database for these purposes. Consequently, results in such meta-analyses are difficult to reproduce. The present study introduces the software package ECOTOXr, which provides the means to formalise data retrieval from the ECOTOX database in the R scripting language. Three cases are presented to evaluate the performance of the package in relation to earlier data extractions and searches on the website. These cases demonstrate that the package can reproduce data sets relatively well. Furthermore, they illustrate how future studies can further improve traceability and reproducibility by applying the package and adhering to some simple guidelines. This contributes to the FAIR principles, credibility and acceptance of research that uses data from the ECOTOX database.