ECOTOXr

ECOTOXr can be used to explore and analyse data from the US EPA ECOTOX database. More specifically you can:

• Build a local SQLite copy of the US EPA ECOTOX database
• Search and extract data from the local database
• Sanitise raw data from the local database
• Use experimental features to search the online dashboards: ECOTOX and CompTox

Why use ECOTOXr?

The ECOTOXr package allows you to search and extract data from the ECOTOXicological Knowledgebase and import it directly into R. This will allow you to formalize and document the search- and extract-procedures in R code. This makes it easier to share and reproduce such procedures and its results. As illustrated in the graphical abstract below. Moreover, you can directly apply any statistical analysis offered in R.

Installation

Get CRAN version

install.packages("ECOTOXr")

Get development version from r-universe

install.packages("ECOTOXr", repos = c("https://pepijn-devries.r-universe.dev", "https://cloud.r-project.org"))

Usage

Preparing the database

Although ECOTOXr has experimental features to search the online database. The package will reach its full potential when you build a copy of the database on your local machine.

Download and build a local copy of the latest ASCII export of the US EPA ECOTOX database

download_ecotox_data()

Searching the local database for species and substances

Once built, you can search the local database for species and substances using different strategies. You can use the build-in search function of this package, or you can write custom queries using either the simple query language (SQL) or dplyr verbs. More details in the following vignettes: vignette("searching-ecotox") and vignette("ecotox-schema").

Disclaimers

It is the end-users own responsibility to check the quality of collected data, using the original referenced source in order to evaluate its fitness for use, see also: https://cfpub.epa.gov/ecotox/help.cfm#info-limitations.

Note that the package maintainer is not affiliated with the US EPA, this package is therefore not official US EPA software.

Resources

• De Vries, P. (2024) ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA’s ECOTOX database. Chemosphere 364 143078 https://doi.org/10.1016/j.chemosphere.2024.143078
• Manual of the CRAN release
• EPA ECOTOX help https://cfpub.epa.gov/ecotox/help.cfm
• Olker, Jennifer H.; Elonen, Colleen M.; Pilli, Anne; Anderson, Arne; Kinziger, Brian; Erickson, Stephen; Skopinski, Michael; Pomplun, Anita; LaLone, Carlie A.; Russom, Christine L.; Hoff, Dale. (2022): The ECOTOXicology Knowledgebase: A Curated Database of Ecologically Relevant Toxicity Tests to Support Environmental Research and Risk Assessment. Environmental Toxicology and Chemistry 41(6) 1520-1539 https://doi.org/10.1002/etc.5324