ECOTOXr
Download and Extract Data from US EPA's ECOTOX Database
The US EPA ECOTOX database is a freely available database
with a treasure of aquatic and terrestrial ecotoxicological data.
As the online search interface doesn't come with an API, this
package provides the means to easily access and search the database
in R. To this end, all raw tables are downloaded from the EPA website
and stored in a local SQLite database
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.
From
De Vries et
al. (2024);
Creative
commons
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.
Code of Conduct
Please note that the ECOTOXr project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
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