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3.0.0","direct":true,"kind":"suggests","optional":false}]}],"score":10.625805110395852,"created_at":"2025-06-20T00:23:40.585Z","updated_at":"2026-06-13T11:30:23.246Z","avatar_url":"https://github.com/NIEHS.png","language":"R","category":"Natural Resources","sub_category":"Ecotoxicology","monthly_downloads":571,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# GeoTox \u003ca href=\"https://github.com/NIEHS/GeoTox\"\u003e\u003cimg src=\"man/figures/logo.svg\" align=\"right\" height=\"139\" alt=\"GeoTox website\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![R-CMD-check](https://github.com/NIEHS/GeoTox/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/R-CMD-check.yaml)\n[![pkgdown](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml)\n[![cov](https://NIEHS.github.io/GeoTox/badges/coverage.svg)](https://github.com/NIEHS/GeoTox/actions)\n[![CRAN status](https://www.r-pkg.org/badges/version/GeoTox)](https://CRAN.R-project.org/package=GeoTox)\n\n\u003c!-- badges: end --\u003e\n\n`GeoTox` is an open-source R software package for characterizing the risk of perturbing molecular targets involved in adverse human health outcomes based on exposure to spatially-referenced stressor mixtures via the GeoTox framework - otherwise known as source-to-outcome-continuum modeling. The package, methods, and case-studies are described in [Messier, Reif, and Marvel, 2025, Human Genomics](https://doi.org/10.1186/s40246-024-00711-8).\n\nThe GeoTox framework was first described in\n[Eccles et al. A geospatial modeling approach to quantifying the risk of exposure to environmental chemical mixtures via a common molecular target. Sci Total Environ. 2023 Jan 10;855:158905.](https://pubmed.ncbi.nlm.nih.gov/36152849/)\n\n## Installation\n\nThe current stable version of the package can be installed from CRAN.\n\n```{r, eval=FALSE}\ninstall.packages(\"GeoTox\")\n```\n\nThe previous implementation of the package, which uses in-memory storage instead of DuckDB, can be installed by specifying the version.\n\n```{r, eval=FALSE}\n#install.packages(\"pak\")\npak::pak(\"GeoTox@0.3.0\")\n```\n\n## Development Version\n\nThe development version can be installed from GitHub.\n\n```{r, eval=FALSE}\n#install.packages(\"pak\")\npak::pak(\"NIEHS/GeoTox@dev\")\n```\n\n## Overview\n\nFigure 1 below shows the steps in the source-to-outcome-continuum or GeoTox modeling framework that is capable in the `GeoTox` package. The `GeoTox` package uses R S3 object-oriented programming to create the **GeoTox** object. The **GeoTox** object contains all of the information required to run the analysis including tracking exposure, assays, dose-response, and geospatial referencing. Each component of the object and pipeline are stored in a relational DuckDB​​ database.\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"man/figures/GeoTox.png\" alt=\"GeoTox\"\u003e\n  \u003cbr\u003e\n  \u003cem\u003eFigure 1: Overview of the steps in the GeoTox framework\u003c/em\u003e\n\u003c/p\u003e\n\n## Getting Started\n\nPlease refer to the [package website](https://niehs.github.io/GeoTox/) for a detailed description of how to use `GeoTox`. The development version can be accessed [here](https://niehs.github.io/GeoTox/dev/).\n\n## Citation \n\nFor citation information, please refer to our [CITATION file](inst/CITATION).\n\n## Issues and Contributions\n\nTo add or edit functionality, open a pull request into the main branch with a detailed description of the proposed changes. Pull requests must pass all status checks, and then will be approved or rejected by the GeoTox maintainers.\n\nUtilize [GitHub issues](https://github.com/NIEHS/GeoTox/issues) to notify the authors of bugs, questions, or recommendations. Identify each issue with the appropriate label to help ensure a timely response.\n\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1186/s40246-024-00711-8"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/319013","html_url":"https://ost.ecosyste.ms/projects/319013"}