ecotoxr

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

https://github.com/pepijn-devries/ecotoxr

Science Score: 39.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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DOI references
Found 6 DOI reference(s) in README
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Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary

Keywords

data database

Last synced: 6 months ago · JSON representation

Repository

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

Basic Info

Host: GitHub
Owner: pepijn-devries
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://pepijn-devries.github.io/ECOTOXr/
Size: 5.94 MB

Statistics

Stars: 12
Watchers: 1
Forks: 2
Open Issues: 5
Releases: 7

Topics

data database

Created over 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Code of conduct

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

Login: pepijn-devries
Kind: user

Twitter: pepijn_devries
Repositories: 3
Profile: https://github.com/pepijn-devries

GitHub Events

Total

Issues event: 11
Watch event: 3
Delete event: 9
Issue comment event: 41
Push event: 83
Pull request event: 40
Create event: 2

Last Year

Issues event: 11
Watch event: 3
Delete event: 9
Issue comment event: 41
Push event: 83
Pull request event: 40
Create event: 2

Committers

Last synced: 6 months ago

All Time

Total Commits: 95
Total Committers: 2
Avg Commits per committer: 47.5
Development Distribution Score (DDS): 0.284

Past Year

Commits: 57
Committers: 2
Avg Commits per committer: 28.5
Development Distribution Score (DDS): 0.07

Top Committers

Name	Email	Commits
pepijn-devries	p**2@g**m	68
Vries	p**s@w**l	27

Committer Domains (Top 20 + Academic)

wur.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 16
Total pull requests: 80
Average time to close issues: 3 months
Average time to close pull requests: about 1 hour
Total issue authors: 8
Total pull request authors: 1
Average comments per issue: 1.69
Average comments per pull request: 0.39
Merged pull requests: 74
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 8
Pull requests: 40
Average time to close issues: 5 days
Average time to close pull requests: about 3 hours
Issue authors: 5
Pull request authors: 1
Average comments per issue: 0.88
Average comments per pull request: 0.73
Merged pull requests: 36
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

pepijn-devries (8)
CassandraStr (2)
flor14 (1)
pabloamadorc (1)
marcelomachado (1)
seanthimons (1)
mattreusswig (1)
irmoodie (1)

Pull Request Authors

pepijn-devries (80)

Top Labels

Issue Labels

enhancement (2)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 493 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 11
Total maintainers: 1

cran.r-project.org: ECOTOXr

Download and Extract Data from US EPA's ECOTOX Database

Homepage: https://github.com/pepijn-devries/ECOTOXr
Documentation: http://cran.r-project.org/web/packages/ECOTOXr/ECOTOXr.pdf
License: GPL (≥ 3)
Latest release: 1.2.2
published 6 months ago

Versions: 11
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 493 Last month

Rankings

Forks count: 17.8%

Stargazers count: 22.5%

Average: 26.7%

Downloads: 28.0%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Maintainers (1)

pepijn.devries@outlook.com

Last synced: 6 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions

actions/checkout v3 composite
r-lib/actions/setup-r f57f1301a053485946083d7a45022b278929a78a composite

DESCRIPTION cran

R >= 3.5.0 depends
RSQLite * depends
crayon * imports
dbplyr * imports
dplyr * imports
httr * imports
jsonlite * imports
lifecycle * imports
purrr * imports
rappdirs * imports
readr * imports
readxl * imports
rlang * imports
rvest * imports
stringr * imports
tibble * imports
tidyr * imports
tidyselect * imports
utils * imports
DBI * suggests
standartox * suggests
testthat >= 3.0.0 suggests
webchem * suggests

ecosyste.ms

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Open Source Science

ecotoxr

Science Score: 39.0%

Keywords

Repository

Basic Info

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Topics

Metadata Files

README.Rmd

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cran.r-project.org: ECOTOXr

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