ECOTOXr

Provides access in R to ECOTOX, a comprehensive knowledgebase providing single chemical environmental toxicity data on aquatic and terrestrial species.
https://github.com/pepijn-devries/ecotoxr

Category: Biosphere
Sub Category: Ecological and Environmental Modeling

Keywords

data database

Last synced: about 6 hours ago
JSON representation

Repository metadata

R package that creates a local SQLite build of (and allows querying of) the US EPA ECOTOX database.

• Host: GitHub
• URL: https://github.com/pepijn-devries/ecotoxr
• Owner: pepijn-devries
• License: gpl-3.0
• Created: 2021-10-03T13:46:03.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2025-04-16T15:17:15.000Z (11 days ago)
• Last Synced: 2025-04-17T23:50:53.101Z (10 days ago)
• Topics: data, database
• Language: R
• Homepage: https://pepijn-devries.github.io/ECOTOXr/
• Size: 5.88 MB
• Stars: 10
• Watchers: 1
• Forks: 2
• Open Issues: 4
• Releases: 7
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • License: LICENSE.md
  • Code of conduct: CODE_OF_CONDUCT.md

README.Rmd

          ---
output: github_document
---

```{r, echo = FALSE, message = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
library(ECOTOXr)
```

# `ECOTOXr`


[![R build status](https://github.com/pepijn-devries/ECOTOXr/workflows/R-CMD-check/badge.svg)](https://github.com/pepijn-devries/ECOTOXr/actions)
![cranlogs](https://cranlogs.r-pkg.org/badges/ECOTOXr)
[![CRAN version](https://www.r-pkg.org/badges/version/ECOTOXr)](https://CRAN.R-project.org/package=ECOTOXr)
[![cran checks](https://badges.cranchecks.info/worst/ECOTOXr.svg)](https://cran.r-project.org/web/checks/check_results_ECOTOXr.html)
[![R-universe version](https://pepijn-devries.r-universe.dev/ECOTOXr/badges/version)](https://pepijn-devries.r-universe.dev/ECOTOXr)
[![Codecov test coverage](https://codecov.io/gh/pepijn-devries/ECOTOXr/branch/main/graph/badge.svg)](https://app.codecov.io/gh/pepijn-devries/ECOTOXr?branch=main)



`ECOTOXr` can be used to explore and analyse data from the [US EPA ECOTOX database](https://cfpub.epa.gov/ecotox/).
More specifically you can:

 * Build a local SQLite copy of the [US EPA ECOTOX database](https://cfpub.epa.gov/ecotox/)
 * Search and extract data from the local database
 * Sanitise raw data from the local database
 * Use experimental features to search the online dashboards: [ECOTOX](https://cfpub.epa.gov/ecotox/search.cfm) and
   [CompTox](https://comptox.epa.gov/dashboard/batch-search)

## Why use `ECOTOXr`?

The `ECOTOXr` package allows you to search and extract data from the [ECOTOXicological Knowledgebase](https://cfpub.epa.gov/ecotox/)
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](man/figures/graphical-abstract.png)

## Installation 

> Get CRAN version
```{r eval=FALSE}
install.packages("ECOTOXr")
```

> Get development version from r-universe
```{r eval=FALSE}
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

```{r eval=FALSE}
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: .

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](https://pepijn-devries.github.io/ECOTOXr/CODE_OF_CONDUCT.html). 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 
 * [Manual of the CRAN release](https://CRAN.R-project.org/package=ECOTOXr)
 * EPA ECOTOX help 
 * 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 

        

---

Owner metadata

• Name:
• Login: pepijn-devries
• Email:
• Kind: user
• Description:
• Website:
• Location:
• Twitter: pepijn_devries
• Company:
• Icon url: https://avatars.githubusercontent.com/u/13707449?u=f66d5b7fe8ed105c9bbe946f944af08f789a2133&v=4
• Repositories: 3
• Last ynced at: 2023-03-11T09:35:28.620Z
• Profile URL: https://github.com/pepijn-devries

---

GitHub Events

Total

• Issues event: 9
• Watch event: 1
• Delete event: 9
• Issue comment event: 38
• Push event: 77
• Pull request event: 36
• Create event: 2

Last Year

• Issues event: 9
• Watch event: 1
• Delete event: 9
• Issue comment event: 38
• Push event: 77
• Pull request event: 36
• Create event: 2

---

Committers metadata

Last synced: 8 days ago

Name	Email	Commits
pepijn-devries	p****2@g****m	67
Vries	p****s@w****l	27

Committer domains:

• wur.nl: 1

---

Issue and Pull Request metadata

Last synced: 1 day ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/pepijn-devries/ecotoxr

---

---

---

Package metadata

• Total packages: 1
• Total downloads:
  • cran: 704 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 10
• Total maintainers: 1

---

Dependencies

Score: 9.890402312987472