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geotox

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

https://github.com/niehs/geotox

Science Score: 67.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    4 of 9 committers (44.4%) from academic institutions
  • ✓
    Institutional organization owner
    Organization niehs has institutional domain (www.niehs.nih.gov)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (19.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 6
  • Watchers: 4
  • Forks: 3
  • Open Issues: 1
  • Releases: 2
Created over 2 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.Rmd 

---
output: github_document
---



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

# GeoTox GeoTox website



[![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` 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

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

## Development Version

The development version can be installed from GitHub.

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

## Overview

Figure 1 below shows the steps in the source-to-outcome-continuum or GeoTox modeling framework that is capable in the `GeoTox` package. blue text nodes represent an object and green text, rounded nodes represent a methodology or function required to go from one to the next. The `GeoTox` package uses R S3 object-oriented programming to create the **GeoTox** object. The **GeoTox** object is a list that contains all of the information required to run the analysis including tracking exposure, assays, dose-response, and geospatial referencing. 



  GeoTox
  

  Figure 1: Overview of the steps in the GeoTox framework



## Getting Started

Please refer to the [introduction vignette](https://niehs.github.io/GeoTox/articles/introduction.html) for a detailed description of how to use `GeoTox`.

## 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.

Owner

  • Name: National Institute of Environmental Health Science
  • Login: NIEHS
  • Kind: organization
  • Location: Durham, NC

The mission of the National Institute of Environmental Health Sciences is to discover how the environment affects people in order to promote healthier lives.

GitHub Events

Total
  • Create event: 12
  • Release event: 1
  • Issues event: 7
  • Watch event: 4
  • Delete event: 17
  • Issue comment event: 7
  • Push event: 72
  • Pull request review event: 1
  • Pull request event: 19
  • Fork event: 1
Last Year
  • Create event: 12
  • Release event: 1
  • Issues event: 7
  • Watch event: 4
  • Delete event: 17
  • Issue comment event: 7
  • Push event: 72
  • Pull request review event: 1
  • Pull request event: 19
  • Fork event: 1

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 161
  • Total Committers: 9
  • Avg Commits per committer: 17.889
  • Development Distribution Score (DDS): 0.652
Past Year
  • Commits: 44
  • Committers: 2
  • Avg Commits per committer: 22.0
  • Development Distribution Score (DDS): 0.409
Top Committers
Name Email Commits
SkylarMarvel 5****l 56
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 (Top 20 + Academic)
almbp02012943.local.niehs.nih.gov: 1 almbp02184136.localdomain.niehs.nih.gov: 1 almbp02184136.localdomain: 1 almbp02184136.niehs.nih.gov: 1 nih.gov: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 20
  • Total pull requests: 57
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 11 hours
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 1.2
  • Average comments per pull request: 0.21
  • Merged pull requests: 53
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 25
  • Average time to close issues: 21 days
  • Average time to close pull requests: about 6 hours
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.04
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kyle-messier (16)
  • SkylarMarvel (1)
Pull Request Authors
  • kyle-messier (43)
  • SkylarMarvel (41)
Top Labels
Issue Labels
enhancement (4) documentation (4) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 335 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: GeoTox

Spatiotemporal Mixture Risk Assessment

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 335 Last month
Rankings
Dependent packages count: 27.8%
Dependent repos count: 34.2%
Average: 49.6%
Downloads: 87.0%
Maintainers (1)
kyle.messier@nih.gov
Last synced: 6 months ago

Dependencies

.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • truncnorm * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests