GeoTox

Characterizing the risk of perturbing molecular targets involved in adverse human health outcomes based on exposure to spatially-referenced stressor mixtures.
https://github.com/niehs/geotox

Category: Natural Resources
Sub Category: Ecotoxicology

Last synced: about 16 hours ago
JSON representation

Repository metadata

Open-source software for connecting spatiotemporal exposure to individual and population-level risk

• Host: GitHub
• URL: https://github.com/niehs/geotox
• Owner: NIEHS
• License: other
• Created: 2023-08-31T02:14:25.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2026-05-19T22:50:49.000Z (15 days ago)
• Last Synced: 2026-05-23T01:03:19.708Z (12 days ago)
• Language: R
• Homepage: https://niehs.github.io/GeoTox/
• Size: 50.4 MB
• Stars: 7
• Watchers: 3
• Forks: 3
• Open Issues: 1
• Releases: 4
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

README.Rmd

          ---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# GeoTox 



[![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)
[![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)
[![pkgdown](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/NIEHS/GeoTox/actions/workflows/pkgdown.yaml)
[![cov](https://NIEHS.github.io/GeoTox/badges/coverage.svg)](https://github.com/NIEHS/GeoTox/actions)
[![CRAN status](https://www.r-pkg.org/badges/version/GeoTox)](https://CRAN.R-project.org/package=GeoTox)



`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).

The GeoTox framework was first described in
[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/)

## Installation

The current stable version of the package can be installed from CRAN.

```{r, eval=FALSE}
install.packages("GeoTox")
```

The previous implementation of the package, which uses in-memory storage instead of DuckDB, can be installed by specifying the version.

```{r, eval=FALSE}
#install.packages("pak")
pak::pak("GeoTox@0.3.0")
```

## Development Version

The development version can be installed from GitHub.

```{r, eval=FALSE}
#install.packages("pak")
pak::pak("NIEHS/GeoTox@dev")
```

## Overview

Figure 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.


  
  

  Figure 1: Overview of the steps in the GeoTox framework


## Getting Started

Please 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/).

## Citation 

For citation information, please refer to our [CITATION file](inst/CITATION).

## Issues and Contributions

To 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.

Utilize [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.


        

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Owner metadata

• Name: National Institute of Environmental Health Science
• Login: NIEHS
• Email:
• Kind: organization
• Description: The mission of the National Institute of Environmental Health Sciences is to discover how the environment affects people in order to promote healthier lives.
• Website: https://www.niehs.nih.gov/
• Location: Durham, NC
• Twitter:
• Company:
• Icon url: https://avatars.githubusercontent.com/u/22938605?v=4
• Repositories: 55
• Last ynced at: 2023-08-13T07:43:51.753Z
• Profile URL: https://github.com/NIEHS

---

GitHub Events

Total

• Release event: 1
• Delete event: 21
• Pull request event: 21
• Fork event: 1
• Issues event: 8
• Watch event: 4
• Issue comment event: 7
• Push event: 89
• Pull request review event: 2
• Create event: 14

Last Year

• Delete event: 4
• Pull request event: 2
• Issues event: 1
• Watch event: 1
• Push event: 17
• Pull request review event: 1
• Create event: 2

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Committers metadata

Last synced: 4 days ago

Name	Email	Commits
SkylarMarvel	s****l@g****m	79
kyle-messier	k****r@n****v	41
{SET}group	1****y	40
Spatiotemporal-Exposures-and-Toxicology	m****p@a****v	6
Spatiotemporal-Exposures-and-Toxicology	m****p@a****l	6
Spatiotemporal-Exposures-and-Toxicology	m****p@a****n	4
Spatiotemporal-Exposures-and-Toxicology	m****p@a****v	4
David Reif	4****f	2
Reif	r****m@a****v	2

Committer domains:

• almbp02012943.local.niehs.nih.gov: 1
• almbp02184136.localdomain.niehs.nih.gov: 1
• almbp02184136.localdomain: 1
• almbp02184136.niehs.nih.gov: 1
• nih.gov: 1

---

Issue and Pull Request metadata

Last synced: 4 days ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/niehs/geotox

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Package metadata

• Total packages: 1
• Total downloads:
  • cran: 551 last-month
• Total dependent packages: 0
• Total dependent repositories: 0
• Total versions: 3
• Total maintainers: 1

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Dependencies

Score: 10.590214165293151