{"id":13724620,"url":"https://github.com/pepijn-devries/ECOTOXr","last_synced_at":"2025-05-07T18:33:13.169Z","repository":{"id":46601132,"uuid":"413090034","full_name":"pepijn-devries/ECOTOXr","owner":"pepijn-devries","description":"R package that creates a local SQLite build of (and allows querying of) the US EPA ECOTOX 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and Environmental Modeling"],"readme":"---\noutput: github_document\n---\n\n```{r, echo = FALSE, message = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\"\n)\nlibrary(ECOTOXr)\n```\n\n# `ECOTOXr`\n\n\u003c!-- badges: start --\u003e\n[![R build status](https://github.com/pepijn-devries/ECOTOXr/workflows/R-CMD-check/badge.svg)](https://github.com/pepijn-devries/ECOTOXr/actions)\n![cranlogs](https://cranlogs.r-pkg.org/badges/ECOTOXr)\n[![CRAN version](https://www.r-pkg.org/badges/version/ECOTOXr)](https://CRAN.R-project.org/package=ECOTOXr)\n[![cran checks](https://badges.cranchecks.info/worst/ECOTOXr.svg)](https://cran.r-project.org/web/checks/check_results_ECOTOXr.html)\n[![R-universe version](https://pepijn-devries.r-universe.dev/ECOTOXr/badges/version)](https://pepijn-devries.r-universe.dev/ECOTOXr)\n[![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)\n\u003c!-- badges: end --\u003e\n\n\u003ca href=\"https://github.com/pepijn-devries/ECOTOXr/\"\u003e\u003cimg src=\"man/figures/logo.png\" alt=\"ECOTOXr logo\" align=\"right\" class=\"pkgdown-hide\" /\u003e\u003c/a\u003e\n`ECOTOXr` can be used to explore and analyse data from the [US EPA ECOTOX database](https://cfpub.epa.gov/ecotox/).\nMore specifically you can:\n\n * Build a local SQLite copy of the [US EPA ECOTOX database](https://cfpub.epa.gov/ecotox/)\n * Search and extract data from the local database\n * Sanitise raw data from the local database\n * Use experimental features to search the online dashboards: [ECOTOX](https://cfpub.epa.gov/ecotox/search.cfm) and\n   [CompTox](https://comptox.epa.gov/dashboard/batch-search)\n\n## Why use `ECOTOXr`?\n\nThe `ECOTOXr` package allows you to search and extract data from the [ECOTOXicological Knowledgebase](https://cfpub.epa.gov/ecotox/)\nand import it directly into `R`. This will allow you to formalize and document the search- and extract-procedures in `R` code.\nThis makes it easier to share and reproduce such procedures and its results. As illustrated\nin the graphical abstract below. Moreover, you can directly apply any statistical\nanalysis offered in `R`.\n\n![From \u003ca href=\"https://doi.org/10.1016/j.chemosphere.2024.143078\"\u003eDe Vries et al. (2024)\u003c/a\u003e; \u003ca href=\"https://creativecommons.org/licenses/by/4.0/\"\u003eCreative commons\u003c/a\u003e](man/figures/graphical-abstract.png)\n\n## Installation \n\n\u003e Get CRAN version\n```{r eval=FALSE}\ninstall.packages(\"ECOTOXr\")\n```\n\n\u003e Get development version from r-universe\n```{r eval=FALSE}\ninstall.packages(\"ECOTOXr\", repos = c(\"https://pepijn-devries.r-universe.dev\", \"https://cloud.r-project.org\"))\n```\n\n## Usage\n\n### Preparing the database\n\nAlthough `ECOTOXr` has experimental features to search the online database. The package will\nreach its full potential when you build a copy of the database on your local machine.\n\n\u003e Download and build a local copy of the latest ASCII export of the US EPA ECOTOX database\n\n```{r eval=FALSE}\ndownload_ecotox_data()\n```\n\n### Searching the local database for species and substances\n\nOnce built, you can search the local database for species and substances using different strategies.\nYou can use the build-in search function of this package, or you can write custom queries using\neither the simple query language (SQL) or `dplyr` verbs. More details in the following vignettes:\n`vignette(\"searching-ecotox\")` and `vignette(\"ecotox-schema\")`.\n\n## Disclaimers\n\nIt is the end-users own responsibility to check the quality of collected data, using the original referenced source in order to evaluate its\nfitness for use, see also: \u003chttps://cfpub.epa.gov/ecotox/help.cfm#info-limitations\u003e.\n\nNote that the package maintainer is not affiliated with the US EPA, this package is therefore **not** official US EPA software.\n\n## Code of Conduct\n\nPlease 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.\n\n## Resources\n\n * De Vries, P. (2024) ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database. _Chemosphere_ 364 143078 \u003chttps://doi.org/10.1016/j.chemosphere.2024.143078\u003e\n * [Manual of the CRAN release](https://CRAN.R-project.org/package=ECOTOXr)\n * EPA ECOTOX help \u003chttps://cfpub.epa.gov/ecotox/help.cfm\u003e\n * Olker, Jennifer H.; Elonen, Colleen M.; Pilli, Anne; Anderson, Arne; Kinziger, Brian; Erickson, Stephen; Skopinski, Michael;\n   Pomplun, Anita; LaLone, Carlie A.; Russom, Christine L.; Hoff, Dale. (2022): The ECOTOXicology Knowledgebase: A Curated Database of\n   Ecologically Relevant Toxicity Tests to Support Environmental Research and Risk Assessment. _Environmental Toxicology and Chemistry_\n   41(6) 1520-1539 \u003chttps://doi.org/10.1002/etc.5324\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpepijn-devries%2FECOTOXr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpepijn-devries%2FECOTOXr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpepijn-devries%2FECOTOXr/lists"}